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    [{"authors":["cheyenne-jarman"],"categories":null,"content":"","date":1771372800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1771372800,"objectID":"921ca9152cf638b0ac48cbc5a85bb5f8","permalink":"https://novaklabosu.github.io/authors/cheyenne-jarman/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/cheyenne-jarman/","section":"authors","summary":"","tags":null,"title":"Cheyenne Jarman","type":"authors"},{"authors":null,"categories":null,"content":"","date":1771372800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1771372800,"objectID":"6ef2eeba3c6bec8e5712643b9e1468df","permalink":"https://novaklabosu.github.io/authors/mark-novak/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/mark-novak/","section":"authors","summary":"","tags":null,"title":"Mark Novak","type":"authors"},{"authors":["andres-pinos-sanchez"],"categories":null,"content":"Co-advised by Will White\n","date":1768953600,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1768953600,"objectID":"499cd0195d10b5b533581901274f996b","permalink":"https://novaklabosu.github.io/authors/andres-pinos-sanchez/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/andres-pinos-sanchez/","section":"authors","summary":"Co-advised by Will White","tags":null,"title":"Andrés Pinos-Sánchez","type":"authors"},{"authors":["arina-martin"],"categories":null,"content":"","date":1768953600,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1768953600,"objectID":"bf2352386fa02e986a38fc752709fa02","permalink":"https://novaklabosu.github.io/authors/arina-martin/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/arina-martin/","section":"authors","summary":"","tags":null,"title":"Arina Martin","type":"authors"},{"authors":["chris-wolf"],"categories":null,"content":"","date":1768953600,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1768953600,"objectID":"b9a0c822485c1a8caa6d5c5e4baaf94c","permalink":"https://novaklabosu.github.io/authors/chris-wolf/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/chris-wolf/","section":"authors","summary":"","tags":null,"title":"Chris Wolf","type":"authors"},{"authors":["dan-preston"],"categories":null,"content":"","date":1768953600,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1768953600,"objectID":"90a2f258c941a1f14f24c53fd8882410","permalink":"https://novaklabosu.github.io/authors/dan-preston/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/dan-preston/","section":"authors","summary":"","tags":null,"title":"Dan Preston","type":"authors"},{"authors":["daniel gradison"],"categories":null,"content":"","date":1768953600,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1768953600,"objectID":"2f812bfc94ced6103b95fe59261ff600","permalink":"https://novaklabosu.github.io/authors/daniel-gradison/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/daniel-gradison/","section":"authors","summary":"","tags":null,"title":"Daniel Gradison","type":"authors"},{"authors":["jeremy-henderson"],"categories":null,"content":"","date":1768953600,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1768953600,"objectID":"c4b526372950339acadb77f7d66ac909","permalink":"https://novaklabosu.github.io/authors/jeremy-henderson/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/jeremy-henderson/","section":"authors","summary":"","tags":null,"title":"Jeremy Henderson","type":"authors"},{"authors":["kurt-ingeman"],"categories":null,"content":"","date":1768953600,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1768953600,"objectID":"d38a4fbe4bcaf8e4cc704f611637e6b7","permalink":"https://novaklabosu.github.io/authors/kurt-ingeman/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/kurt-ingeman/","section":"authors","summary":"","tags":null,"title":"Kurt Ingeman","type":"authors"},{"authors":["kyle-coblentz"],"categories":null,"content":"","date":1768953600,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1768953600,"objectID":"3911ff475b343a1c7c810ee895cd234c","permalink":"https://novaklabosu.github.io/authors/kyle-coblentz/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/kyle-coblentz/","section":"authors","summary":"","tags":null,"title":"Kyle Coblentz","type":"authors"},{"authors":["landon-falke"],"categories":null,"content":"","date":1768953600,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1768953600,"objectID":"2fb068fa10654cc9157503c2e48dab2e","permalink":"https://novaklabosu.github.io/authors/landon-falke/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/landon-falke/","section":"authors","summary":"","tags":null,"title":"Landon Falke","type":"authors"},{"authors":["leah-segui"],"categories":null,"content":"","date":1768953600,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1768953600,"objectID":"436ecf76da9923c3ce793b4b8c122147","permalink":"https://novaklabosu.github.io/authors/leah-segui/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/leah-segui/","section":"authors","summary":"","tags":null,"title":"Leah Segui","type":"authors"},{"authors":["paige-foust"],"categories":null,"content":"","date":1768953600,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1768953600,"objectID":"535dd4e257bd23deb7d716ab24784140","permalink":"https://novaklabosu.github.io/authors/paige-foust/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/paige-foust/","section":"authors","summary":"","tags":null,"title":"Paige Foust","type":"authors"},{"authors":["rodrigo-alves"],"categories":null,"content":"Co-advised by Bruce Menge\n","date":1768953600,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1768953600,"objectID":"8adab3f3b28b114877530468663f7b7f","permalink":"https://novaklabosu.github.io/authors/rodrigo-alves/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/rodrigo-alves/","section":"authors","summary":"Co-advised by Bruce Menge","tags":null,"title":"Rodrigo Alves","type":"authors"},{"authors":["shannon-hennessey"],"categories":null,"content":"","date":1768953600,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1768953600,"objectID":"1ec8fc11ef7948fba701204c831c111a","permalink":"https://novaklabosu.github.io/authors/shannon-hennessey/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/shannon-hennessey/","section":"authors","summary":"","tags":null,"title":"Shannon Hennessey","type":"authors"},{"authors":["tamara-layden"],"categories":null,"content":"","date":1768953600,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1768953600,"objectID":"328f7ba41233643b3d7971227023525e","permalink":"https://novaklabosu.github.io/authors/tamara-layden/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/tamara-layden/","section":"authors","summary":"","tags":null,"title":"Tamara Layden","type":"authors"},{"authors":["timeyin-pajiah"],"categories":null,"content":"","date":1768953600,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1768953600,"objectID":"093f5839574e874662279d39507909a2","permalink":"https://novaklabosu.github.io/authors/timeyin-pajiah/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/timeyin-pajiah/","section":"authors","summary":"","tags":null,"title":"Timeyin Pajiah","type":"authors"},{"authors":["zachary-randell"],"categories":null,"content":"   Watch Zach’s defense seminar on IB’s YouTube channel: (https://youtu.be/PpVOXf6_830?t=420)  ","date":1768953600,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1768953600,"objectID":"8eb76bd32d2b95914ee2e3831e241da0","permalink":"https://novaklabosu.github.io/authors/zachary-randell/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/zachary-randell/","section":"authors","summary":"   Watch Zach’s defense seminar on IB’s YouTube channel: (https://youtu.be/PpVOXf6_830?t=420)  ","tags":null,"title":"Zachary Randell","type":"authors"},{"authors":["david-rocow"],"categories":null,"content":"","date":1622505600,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1622647292,"objectID":"c521d69e155074f9f36db34cd8ae9d4e","permalink":"https://novaklabosu.github.io/authors/david-rockow/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/david-rockow/","section":"authors","summary":"","tags":null,"title":"David Rockow","type":"authors"},{"authors":["stephanie-merhoff"],"categories":null,"content":"","date":1609459200,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1617371667,"objectID":"921f256cf032f3e07de767ddee8b316e","permalink":"https://novaklabosu.github.io/authors/stephanie-merhoff/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/stephanie-merhoff/","section":"authors","summary":"","tags":null,"title":"Stephanie Merhoff","type":"authors"},{"authors":["alison-iles"],"categories":null,"content":"","date":1546300800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1617371666,"objectID":"da7934b05fb062a1a66ba4a828095a08","permalink":"https://novaklabosu.github.io/authors/alison-iles/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/alison-iles/","section":"authors","summary":"","tags":null,"title":"Alison Iles","type":"authors"},{"authors":["isaac-shepard"],"categories":null,"content":"","date":1483228800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1617376892,"objectID":"5d59ed18a170e45989a3acda42a84000","permalink":"https://novaklabosu.github.io/authors/isaac-shepard/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/isaac-shepard/","section":"authors","summary":"","tags":null,"title":"Isaac Shepard","type":"authors"},{"authors":["julia-bingham"],"categories":null,"content":"","date":1451606400,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1617376892,"objectID":"748ee92947ce5667f5d5b7df0d9f7f31","permalink":"https://novaklabosu.github.io/authors/julia-bingham/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/julia-bingham/","section":"authors","summary":"","tags":null,"title":"Julia Bingham","type":"authors"},{"authors":["wendy-saepharn"],"categories":null,"content":"","date":1451606400,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1617376892,"objectID":"69ffea4912c33f7df6be7bc37343fc45","permalink":"https://novaklabosu.github.io/authors/wendy-saepharn/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/wendy-saepharn/","section":"authors","summary":"","tags":null,"title":"Wendy Saepharn","type":"authors"},{"authors":["hamza-moulvi"],"categories":null,"content":"","date":1388534400,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1617376892,"objectID":"d0b5650d929e9388887d6fd2dcea9a09","permalink":"https://novaklabosu.github.io/authors/hamza-moulvi/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/hamza-moulvi/","section":"authors","summary":"","tags":null,"title":"Hamza Moulvi","type":"authors"},{"authors":["alicen-billings"],"categories":null,"content":"","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"841d1a99e17ae2279f2eba78b109fb2c","permalink":"https://novaklabosu.github.io/authors/alicen-billings/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/alicen-billings/","section":"authors","summary":"","tags":null,"title":"Alicen Billings","type":"authors"},{"authors":["beatriz werber"],"categories":null,"content":"","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"216b8ec0b2e14f302143695df7cf9e4c","permalink":"https://novaklabosu.github.io/authors/beatriz-werber/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/beatriz-werber/","section":"authors","summary":"","tags":null,"title":"Beatriz Werber","type":"authors"},{"authors":["jonny-schwartz"],"categories":null,"content":"","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"62f67693864e9fd352cd6389d0504747","permalink":"https://novaklabosu.github.io/authors/samantha-sturman/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/samantha-sturman/","section":"authors","summary":"","tags":null,"title":"Jonny Schwartz","type":"authors"},{"authors":null,"categories":null,"content":"  Our lab studies how the interactions between species affect the structure and dynamics of ecological communities. We are particularly interested in aquatic systems, both marine and freshwater, and use a combination of observational and experimental approaches to inform and test mathematical models of multispecies interactions. We thereby aim to contribute theory that integrates our understanding of the behaviour of individuals (e.g., predator foraging) with the ecosystem-level consequences of the interacting populations and species they constitute.\n Our lab values diversity. We are immigrants and the descendants of immigrants. We are atheists, agnostics, and people of faith. We don’t all look the same, love the same, or share the same heroes. We are scientists.\n -- Join us *\n* Unless you are an adult who plays Pokémon.† \n† Pokémon Go is still okay though.\n-- ","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"2525497d367e79493fd32b198b28f040","permalink":"https://novaklabosu.github.io/authors/admin/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/admin/","section":"authors","summary":"Our lab studies how the interactions between species affect the structure and dynamics of ecological communities. We are particularly interested in aquatic systems, both marine and freshwater, and use a combination of observational and experimental approaches to inform and test mathematical models of multispecies interactions.","tags":null,"title":"NovakLab","type":"authors"},{"authors":["samantha-sturman"],"categories":null,"content":"","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"482222d6731bb381ed99e2f6d9c3ba93","permalink":"https://novaklabosu.github.io/authors/jonny-schwartz/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/jonny-schwartz/","section":"authors","summary":"","tags":null,"title":"Sam Sturman","type":"authors"},{"authors":["simone-vachon"],"categories":null,"content":"","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"86911528771cbcffaf980ea6b325af15","permalink":"https://novaklabosu.github.io/authors/simone-vachon/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/simone-vachon/","section":"authors","summary":"","tags":null,"title":"Simone Vachon","type":"authors"},{"authors":["trevor-bark"],"categories":null,"content":"","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"5d59f32a3f7a2940564770151042c70f","permalink":"https://novaklabosu.github.io/authors/trevor-bark/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/trevor-bark/","section":"authors","summary":"","tags":null,"title":"Trevor Bark","type":"authors"},{"authors":["Cheyenne Jarman","Taal Levi","Mark Novak"],"categories":[],"content":"","date":1771372800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1771372800,"objectID":"8b454581d353734d07d2a3617c0cf27c","permalink":"https://novaklabosu.github.io/publication/jarman-2026-aa/","publishdate":"2026-02-18T00:00:00Z","relpermalink":"/publication/jarman-2026-aa/","section":"publication","summary":" Applications of machine learning in ecology are rapidly expanding. Symbolic regression is gaining particular attention for its success in reverse-engineering human-readable explanatory population models, including the logistic growth and Lotka-Volterra equations, from simulated and laboratory-based population time series. However, field-based populations often lack the characteristics of the idealized time series used in prior assessments. We evaluated the utility of symbolic regression for such time series by quantifying its success for synthetic data varying in sampling density, population cycle asymmetry, process noise, and the erroneous consideration of spurious variables. We further compared two data preprocessing options for estimating population growth rates, and four evaluation workflows for selecting equations. Results indicate that a trade-off between sampling density and process noise primarily drives equation and variable recovery. Symbolic regression failed to recover the underlying equation at sampling densities below 10 points per cycle; however, at higher sampling densities, process noise did increase equation recovery rates. Importantly, although the true model was frequently recovered at sampling densities of 25 or more points per cycle, it was not consistently selected by the evaluation workflows. This discrepancy highlights a need for more robust post-algorithm selection criteria to identify the focal equation among competing candidates. ","tags":["Dynamics","Time-series"],"title":"Symbolic regression for empirically realistic population dynamic time series","type":"publication"},{"authors":["Mark Novak","Paige Foust","Shannon Hennessey","Brian Tanis","Kyle Coblentz","Chris Wolf","Leah Segui","Jeremy Henderson","Kurt Ingeman","Landon Falke","Tamara Layden","Daniel Gradison","Zachary Randell","Colin Harris","Serena Lester","Kira Naito","Thanachot Nakata","Grayden Nichols","Benjamin Postma","Rodrigo Alves","Cheyenne Jarman","Augustin Kalytiak-Davis","Arina Martin","Timeyin Pajiah","Andrés Pinos-Sánchez","Dan Preston"],"categories":[],"content":"","date":1768953600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1768953600,"objectID":"8e60f3f459cbdc56c3414be65b39a518","permalink":"https://novaklabosu.github.io/publication/novak-2026-ad/","publishdate":"2026-01-21T00:00:00Z","relpermalink":"/publication/novak-2026-ad/","section":"publication","summary":" The proportion of individuals that are found to have empty stomachs during a survey of a predator population’s diet has been used as an indicator of the average individual’s state of energy balance and of the degree to which its feeding rate (i.e., its functional response) is saturated with respect to prey availability. As such, the proportion of empty stomachs provides insights into the effects of prey on predators and vice versa, although it is typically unreported in deference to descriptions of the contents of the non-empty stomachs. The FracFeed database is an ongoing compilation of the proportions of empty and non-empty stomachs (for gut content surveys) and of feeding and not feeding individuals (for direct observation surveys) reported in publications of predator diet surveys. FracFeed contains data from 4920 diet surveys on 1507 taxa ( 4.3 million individuals) spanning cnidarians, ctenophores, chaetognaths, birds, annelids, amphibians, arthropods, mammals, molluscs, reptiles, echinoderms, and fishes that were surveyed in terrestrial, marine, and freshwater ecosystems across the globe over more than 135 years (1887-2023). For most surveys, covariate data includes information on the spatial and temporal extent of the diet survey, its central geographical coordinates, the method by which the survey was performed (lethal gut contents, lavage, or direct observation), as well as each predator’s standardized taxonomic name and identifier in the Open Tree of Life, its body mass (compiled mostly from independent compilations and additional publications), and its apparent diet’s taxonomic richness and resolution. We appeal to more researchers who perform diet surveys to report on the number of empty stomachs they find and encourage additional contributions to the database — particularly from underrepresented geographic regions (e.g., North and Central Asia, North and Central Africa) — to help grow its scope and utility. The database is provided under a CC-BY-NC-S4 4.0 license. Users are requested to cite this data paper when using the data. ","tags":["Interaction strength"],"title":"FracFeed: Global database of the fraction of feeding predators","type":"publication"},{"authors":["Zachary Randell","Casey Sheridan","Jessica Frey","Mark Carr","Mark Novak"],"categories":[],"content":"","date":1762819200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1762819200,"objectID":"48ca2c464535147a5c4a23a073cdf28d","permalink":"https://novaklabosu.github.io/publication/randell-2025-aa/","publishdate":"2025-11-11T00:00:00Z","relpermalink":"/publication/randell-2025-aa/","section":"publication","summary":" Rocky reef kelp forests can exhibit abrupt shifts between forested and barren states where unchecked sea urchin grazing inhibits kelp recovery. Forefront to urchin barren formation is a behavioral switch where sedentary urchins become active and graze upon attached kelp. This is hypothesized to occur when the availability of drift (i.e., detached kelp on the surface of the reef), which urchins are believed to prefer over intact and attached kelp, declines. Although observed repeatedly, the density-dependent nature of this apparent resource preference has not been characterized quantitatively. We used a series of subtidal functional response experiments in central California, USA, to quantify how consumption rates by *Strongylocentrotus purpuratus* (purple urchins) on *Macrocystis pyrifera* (giant kelp) and drift varied with their relative availability and over time as urchins became satiated. Our experiments indicate that the preference for drift over kelp is strong when drift and kelp are at equal abundance, that the abundance of drift has a strong effect on kelp consumption but not vice versa, and that the preferences for drift is indeed density dependent with the qualitative switch to a greater preference for kelp occurring when the availability of drift declines below approximately 1 g of drift for every 82 g of kelp. Our analyses suggest further that maintaining a minimum of approximately 1 g of drift for every 1 g of kelp is sufficient to all but preclude urchins from grazing on live kelp. We recommend these thresholds be used by managers to inform the use of drift subsidies to preserve and restore kelp forests. ","tags":["Interaction strength","Functional response","Dynamics"],"title":"Sea urchin consumption of kelp controlled by the density of drift algae","type":"publication"},{"authors":["Mark Novak"],"categories":[],"content":"","date":1751328000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1751328000,"objectID":"c31c4e22716bea38a70f248230e1d758","permalink":"https://novaklabosu.github.io/publication/novak-2025-ac/","publishdate":"2025-07-01T00:00:00Z","relpermalink":"/publication/novak-2025-ac/","section":"publication","summary":" ","tags":null,"title":"Upper’s (1974) unsuccessful self-treatment of a case of “writer’s block”: Renewed attempt using chat-based large language models","type":"publication"},{"authors":["Mark Novak","Kyle Coblentz","John DeLong"],"categories":[],"content":"","date":1749859200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1749859200,"objectID":"de35935b7f9389de90fb0de1d0f8f0ab","permalink":"https://novaklabosu.github.io/publication/novak-2025-ab/","publishdate":"2025-06-14T00:00:00Z","relpermalink":"/publication/novak-2025-ab/","section":"publication","summary":" Ecologists differ in the degree to which they consider the linear Type I functional response to be an unrealistic versus sufficient representation of predator feeding rates. Empiricists tend to consider it unsuitably non-mechanistic and theoreticians tend to consider it necessarily simple. Holling’s original rectilinear model is dismissed by satisfying neither desire, with most compromising on the smoothly saturating Type II response for which searching and handling are assumed to be mutually exclusive activities. We derive a “multiple-prey-at-a-time” functional response and a generalization that includes the Type III to reflect predators that can continue to search when handling an arbitrary number of already-captured prey. The multi-prey model clarifies the empirical relevance of Holling’s linear and rectilinear models and the conditions under which linearity can be a mechanistically-reasoned description of predator feeding rates, even when handling times are long. We find support for the presence of linearity in 35% of 2,591 compiled empirical datasets, and find evidence that larger predator-prey body-mass ratios permit predators to search while handling greater numbers of prey. Incorporating the multi-prey response into the Rosenzweig-MacArthur population-dynamics model reveals that a non-exclusivity of searching and handling can lead to coexistence states and dynamics that are not anticipated by theory built on Holling’s traditional models. In particular, it can lead to bistable fixed-point and limit-cycle dynamics with long-term crawl-by transients between them under conditions where abundance ratios reflect top-heavy food webs and the functional response is linear. We conclude that functional response linearity should not be considered empirically unrealistic but also that that more bounded conclusions should be drawn in theory presuming the Type I to be appropriate. ","tags":["Interaction strength","Functional response","Dynamics","Ecosystem stability"],"title":"In defense of Type I functional responses: The frequency and population-dynamic effects of feeding on multiple prey at a time","type":"publication"},{"authors":["Kyle Coblentz","Mark Novak","John DeLong"],"categories":[],"content":"","date":1745971200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1745971200,"objectID":"99441e0b54f75d0cb4fa00e3f648d589","permalink":"https://novaklabosu.github.io/publication/coblentz-2025/","publishdate":"2025-04-30T00:00:00Z","relpermalink":"/publication/coblentz-2025/","section":"publication","summary":"Many critical drivers of ecological systems exhibit regular scaling relationships, yet, often, the underlying mechanisms explaining these relationships are unknown. Trophic interactions strengths, which underpin ecosystem stability and dynamics, are no exception, exhibiting statistical and scaling relationships with predator and prey traits that lack a causal evolutionary explanation. Here we propose two universal rules that explain the scaling of trophic interaction strengths through predator functional responses - the relationship between predator feeding rates and prey densities. First, functional responses must allow predators to meet their energetic demands when prey are rare. Second, functional responses should approach their maxima near the highest prey densities that predators experience. We show that parameterized mathematical equations derived from these two rules predict functional response parameters across over 2,100 functional response experiments. They also provide additional predictions including consistent patterns of feeding rate saturation with prey densities among predators, a slow-fast continuum in functional response parameters, and the allometric scaling of those parameters. The two rules thereby offer an ultimate explanation for the determinants of trophic interaction strengths and their scaling, revealing the importance of ecologically realized constraints to the complex, adaptive nature of functional response evolution.","tags":["Interaction strength","Functional response"],"title":"Simple, universal rules predict trophic interaction strengths","type":"publication"},{"authors":["Xiaoxiao Li","Wei Yang","Mark Novak","Lei Zhao","Peter de Ruiter","Zhifeng Yang","Christian Guill"],"categories":[],"content":"","date":1738368000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1738368000,"objectID":"d89979fe15858be5e2685362210b1554","permalink":"https://novaklabosu.github.io/publication/li-2025-aa/","publishdate":"2025-02-01T00:00:00Z","relpermalink":"/publication/li-2025-aa/","section":"publication","summary":" Identifying species with disproportionate effects on other species under press perturbations is essential, yet how species traits drive their keystone-ness and how this depends on community context remain unclear. We quantified species' keystone-ness as the linearly approximated per capita net effect from normalized inverse community matrix and the nonlinear per capita community biomass change from simulated perturbations in food webs with varying biomass structure, the relationship between species' body mass and their biomass within the web towards negative (bottom-heavy) or positive (top-heavy). We found top-heavy biomass structure weakened or even reversed the relationships between species' energetic traits and keystone-ness observed in bottom-heavy webs. In bottom-heavy webs, larger species at higher trophic levels tend to be keystone species, whereas the opposite is true in top-heavy webs. Linear approximations aligned well with nonlinear responses in bottom-heavy webs but showed decreased consistency in top-heavy webs. These findings highlight the importance of community context in shaping species' keystone-ness and informing effective conservation actions. ","tags":["Interaction strength","Dynamics","Food webs","Community matrix","Networks","Press perturbations"],"title":"Body mass–biomass scaling modulates species keystone-ness to press perturbations","type":"publication"},{"authors":["Dan Preston","Landon Falke","Mark Novak"],"categories":[],"content":"","date":1736380800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1736380800,"objectID":"afadba1186457e0aeaa8a3f181ed4aa6","permalink":"https://novaklabosu.github.io/publication/preston-2025-aa/","publishdate":"2025-01-09T00:00:00Z","relpermalink":"/publication/preston-2025-aa/","section":"publication","summary":"The relationship between infection prevalence and host age is informative because it can reveal processes underlying disease dynamics. Most prior work has assumed that age-prevalence curves are shaped by infection rates, host immunity and/or infection-induced mortality. Interactions between parasites within a host have largely been overlooked as a source of variation in age-prevalence curves. We used field survey data and models to examine the role of interspecific interactions between parasites in shaping age-prevalence curves. The empirical dataset included quantification of parasite infection prevalence for eight co-occurring trematodes in over 15,000 snail hosts. We characterized age-prevalence curves for each taxon, examined how they changed over space in relation to co-occurring trematodes and tested whether the shape of the curves aligned with expectations for the frequencies of coinfections by two taxa in the same host. The models explored scenarios that included negative interspecific interactions between parasites, variation in the force-of-infection (FOI) and infection-induced mortality that varied with host age, which were mechanisms hypothesized to be important in the empirical dataset. In the empirical dataset, four trematode parasites had monotonic increasing age-prevalence curves and four had unimodal age-prevalence curves. Some of the curves remained consistent in shape in relation to the prevalence of other potentially interacting trematodes, while some shifted from unimodal to monotonic increasing, suggesting release from negative interspecific interactions. The most common taxa with monotonic increasing curves had lower co-infection frequencies than expected, suggesting they were competitively dominant. Taxa with unimodal curves had coinfection frequencies that were closer to those expected by chance. The model showed that negative interspecific interactions between parasites can cause a unimodal age-prevalence curve in the subordinate taxon. Increases in the FOI and/or infection-induced mortality of the dominant taxon cause shifts in the peak prevalence of the subordinate taxon to a younger host age. Infection-induced mortality that increased with host age was the only scenario that caused a unimodal curve in the dominant taxon. Results indicated that negative interspecific interactions between parasites contributed to variation in the shape of age-prevalence curves across parasite taxa and support the growing importance of incorporating interactions between parasites in explaining population-level patterns of host infection over space and time.","tags":["Interaction strength","Streams","Parasites"],"title":"Age-prevalence curves in a multi-species parasite community","type":"publication"},{"authors":["Mark Novak","Daniel Stouffer"],"categories":[],"content":"","date":1710288000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1710288000,"objectID":"851a775d3ae1cb0681d148873880757f","permalink":"https://novaklabosu.github.io/publication/novak-2024-aa/","publishdate":"2024-03-13T00:00:00Z","relpermalink":"/publication/novak-2024-aa/","section":"publication","summary":" Due to an error in our formulation of the citardauq solution to quadratic equations, our reformulation of the Steady State Saturation (SSS) model of Jeschke et al. (2002) to a more traditional Holling-type form was incorrect. ","tags":["Interaction strength","Functional response"],"title":"Corrigendum: Geometric complexity and the information-theoretic comparison of functional-response models","type":"publication"},{"authors":["Mark Novak"],"categories":[],"content":"","date":1677628800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1678233600,"objectID":"6d5e6bbafa4082f839f7731be1b680f7","permalink":"https://novaklabosu.github.io/publication/novak-2023-aa/","publishdate":"2023-02-19T00:00:00Z","relpermalink":"/publication/novak-2023-aa/","section":"publication","summary":" Historical resurveys of ecological communities are important for placing the structure of modern ecosystems in context. Rarely, however, are surveys alone sufficient for providing direct insight into the rates of ecological processes that underlie how communities function, either now or in the past. In this study, I used a statistically-reasoned observational approach to estimate the feeding rates of a New Zealand intertidal predator, *Haustrum haustorium*, using diet surveys performed at several sites by Robert Paine in 1968--9 and by me in 2004. Comparisons between time periods reveal a remarkable consistency in *Haustrum haustorium*'s prey-specific feeding rates, which contrasts with the changes I observed in prey abundances, *Haustrum haustorium*'s body size distribution, and the proportional contributions of *Haustrum haustorium*'s prey to its apparent diet. Although these results imply accompanying and perhaps adaptive changes in\t*Haustrum haustorium*'s prey preferences, they are nonetheless anticipated by *Haustrum haustorium*'s high range of variation in prey-specific handling times that dictate not only its maximum possible feeding rates but also the probabilities with which feeding events may be detected during diet surveys. Similarly high variation in detection times (i.e. handling and digestion times) is evident in predator species throughout the animal kingdom. The potential disconnect between a predator's apparent diet and its actual feeding rates suggests that much of the temporal and biogeographic variation that is perceived in predator diets and food-web structures may be of less functional consequence than currently assumed. ","tags":["Interaction strength","Functional response","Observational approach"],"title":"High variation in handling times confers 35-year stability to predator feeding rates despite community change","type":"publication"},{"authors":["Kyle Coblentz","Mark Novak","John DeLong"],"categories":[],"content":"","date":1675123200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1675123200,"objectID":"0837f5d6e9e4f5d45b2f4e6dea559a48","permalink":"https://novaklabosu.github.io/publication/coblentz-2023/","publishdate":"2023-01-31T00:00:00Z","relpermalink":"/publication/coblentz-2023/","section":"publication","summary":"Predator feeding rates (described by their functional response) must saturate at high prey densities. Although thousands of manipulative functional response experiments show feeding rate saturation at high densities under controlled conditions, it is unclear how saturated feeding rates are at natural prey densities. The general degree of feeding rate saturation has important implications for the processes determining feeding rates and how they respond to changes in prey density. To address this, we linked two databases – one of functional response parameters and one on mass-abundance scaling – through prey mass to calculate a feeding rate saturation index. We find that: 1) feeding rates may commonly be unsaturated and 2) the degree of saturation varies with predator and prey taxonomic identities and body sizes, habitat, interaction dimension, and temperature. These results reshape our conceptualization of predator-prey interactions in nature and suggest new research on the ecological and evolutionary implications of unsaturated feeding rates.","tags":["Interaction strength","Functional response"],"title":"Predator feeding rates may often be unsaturated under typical prey densities","type":"publication"},{"authors":["Kurt Ingeman","Mark Novak"],"categories":[],"content":"","date":1646956800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1646956800,"objectID":"ebf906b688fb1c05bf9dfcfe2acafeff","permalink":"https://novaklabosu.github.io/publication/ingeman-2022-aa/","publishdate":"2022-03-11T00:00:00Z","relpermalink":"/publication/ingeman-2022-aa/","section":"publication","summary":" Understanding coexistence within community modules such as intraguild predation (IGP), where an omnivore both preys on and competes with an intermediate consumer for a shared resource, has provided insight into the mechanisms that promote persistence of complex food webs. Adaptive, predator-specific defense has been shown theoretically to enhance coexistence of IGP communities when employed by shared prey. Yet to date, all such theory has assumed that prey have accurate perception of predation risk and appropriate antipredator responses, assumptions that may not be justified when considering a novel predator. We therefore consider the effects of an introduced predator on IGP coexistence, describing two invasion scenarios: suboptimal defense, whereby a similar invader elicits an ineffective antipredator response; and naïveté toward an unfamiliar invader, for which prey fail to accurately estimate predation risk. We examine predictions for native predator persistence across gradients of enrichment and defense costs using invasibility analysis methods. The model predicts that predator novelty can weaken the effect of adaptive defense, causing exclusion of native predators that would persist in the absence of novelty. Coexistence is predicted to be more sensitive to the effects of suboptimal defense compared to naïveté and differentially leads to exclusion of native predators in highly productive environments and when defense costs are low. Moderate novelty of the omnivore can increase resource density via a trophic cascade, while consumer novelty can either lead to omnivore exclusion or facilitate three-species coexistence by providing a subsidy to the otherwise excluded native omnivore. Our results suggest that models of adaptive defense are sensitive to assumptions regarding predator-prey eco-evolutionary experience and that predator novelty has significant implications for food web dynamics. ","tags":["Dynamics","Intraguild predation and trophic omnivory","Ecosystem stability","Theory","Food webs"],"title":"Effects of predator novelty on intraguild predation communities with adaptive prey defense","type":"publication"},{"authors":["Zachary Randell","Michael Kenner","Josheph Tomoleoni","Julie Yee","Mark Novak"],"categories":[],"content":"","date":1645142400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1645197693,"objectID":"554d3ff5c58d14eb4649ac9574712408","permalink":"https://novaklabosu.github.io/publication/randell-2022-ab/","publishdate":"2022-02-18T00:00:00Z","relpermalink":"/publication/randell-2022-ab/","section":"publication","summary":" The factors that determine why ecosystems exhibit abrupt shifts in state are of paramount importance for management, conservation, and restoration efforts. Kelp forests are emblematic of such abruptly shifting ecosystems, transitioning from kelp-dominated to urchin-dominated states around the world with increasing frequency, yet the underlying processes and mechanisms that control their dynamics remain unclear. Here, we analyze four decades of data from biannual monitoring around San Nicolas Island, CA, USA, to show that substrate complexity controls both the number of possible (alternative) states and the velocity with which shifts between states occur. The superposition of community dynamics with reconstructions of system stability landscapes reveals that shifts between alternative states at low-complexity sites reflect abrupt, high-velocity events initiated by pulse perturbations that rapidly propel species across dynamically unstable state-space. In contrast, high-complexity sites exhibit a single state of resilient kelp-urchin coexistence. Our analyses suggest that substrate complexity influences both top-down and bottom-up regulatory processes in kelp forests, highlight its influence on kelp-forest stability at both large (island-wide) and small (","tags":["Subtidal","Dynamics","Time-series","Ecosystem stability"],"title":"Kelp-forest dynamics controlled by substrate complexity","type":"publication"},{"authors":["David Koslicki","Dana Gibbon","Mark Novak"],"categories":[],"content":"","date":1644624000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1644674065,"objectID":"7cc0388daf220fc2a94e0ded64f07999","permalink":"https://novaklabosu.github.io/publication/koslicki-2022-un/","publishdate":"2022-02-11T13:54:25.278468Z","relpermalink":"/publication/koslicki-2022-un/","section":"publication","summary":" While the use of networks to understand how complex systems respond to perturbations is pervasive across scientific disciplines, the uncertainty associated with estimates of pairwise interaction strengths (edge weights) remains rarely considered. Mischaracterizations of interaction strength can lead to qualitatively incorrect predictions regarding system responses as perturbations propagate through often counteracting direct and indirect effects.\nHere, we introduce PressPurt, a computational package for identifying the interactions whose strengths must be estimated most accurately in order to produce robust predictions of a network's response to press perturbations. The package provides methods for calculating and visualizing these edge-specific sensitivities (tolerances) when uncertainty is associated to one or more edges according to a variety of different error distributions. The software requires the network to be represented as a numerical (quantitative or qualitative) Jacobian matrix evaluated at stable equilibrium. ","tags":["Theory","Dynamics","Community matrix","Press perturbations","Networks"],"title":"PressPurt - Network sensitivity to press perturbations under interaction uncertainty","type":"publication"},{"authors":["Zachary Randell"],"categories":[],"content":"","date":1632182400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1630596093,"objectID":"e9401ed42609a12e254ab70b7ef10a21","permalink":"https://novaklabosu.github.io/publication/randell-2021-aa/","publishdate":"2021-09-21T15:21:32.998191Z","relpermalink":"/publication/randell-2021-aa/","section":"publication","summary":"\nHow the direct and indirect effects of species interactions cascade to affect community struc- ture, functioning, and stability is a fundamental question in ecology. In temperate kelp forests, species interactions, in conjunction with environmental processes, produce rich spatiotemporal dy- namics. Arguably the most dramatic of these are abrupt shifts in community state, where forested locations are grazed by herbivorous urchins to establish what is known as an “urchin barren”. The increasing frequency and intensity of perturbation events associated with climate change have in- creased the frequency of shifts towards the barren-state. Understanding not only the mechanisms precipitating state shifts but also those that stabilize both the forested and barren states is essential to guide effective kelp-forest conservation and management strategies. Central to urchin barren establishment is a switch in behavior, where urchins leave cracks and crevices to move across the seafloor and graze upon kelp. While it is known that urchin predators can control urchin density and behavior, it is less clear how resource availability affects urchin behavior, or how the switch in behavior affects kelp-forest dynamics at large. This dissertation evaluated urchin behavior, the “bottom-up” processes controlling it, and the subsequent effects upon kelp-forest dynamics and stability from three distinct directions.\nIn Chapter 2, I analyzed 38 years of kelp-forest community data and found distinct spatiotem- poral patterns: certain sites exhibited abrupt shifts in state, others exhibited resilient kelp-forest persistence. I suggest that substrate complexity (the rugosity of the benthic substrate) modified both “top-down” and “bottom-up” processes regulating urchin density and behavior. In particular, I suggest that substrate complexity altered the retention of drift algae (also known as kelp detritus, and henceforth, drift)—the senescent form of kelp that has detached from the seafloor. Urchins are believed to prefer drift, such that when drift is abundant urchin remain inactive, consume the drift, and do not graze live kelp. Variation in the retention of drift may thus in-part be responsible for the urchin behavioral switch that leads to the establishment and stabilization of the barren state.\nIn Chapter 3, I used a one-consumer (urchins) two-resource (kelp and drift) model to test if and how a switch in urchin grazing can precipitate kelp-forest dynamics such as alternative stable states and the emergence of kelp population cycles. Under the assumption that urchins prefer drift over live kelp, results demonstrated that all shifts in state are associated with urchins switching between resources.\nIn Chapter 4, I experimentally tested the core assumption from Chapter 3, i.e., that urchins “prefer” drift. Specifically, I used a subtidal caging experiment to evaluate the density-dependent effects of drift and kelp upon urchin consumption rates. Results demonstrated a strong preference in urchins to consume drift, that kelp consumption is controlled by the availability of drift (not by kelp itself), and that urchins exhibit a rank switch—a switch in the proportion of resources consumed as total biomass increases—from kelp to drift.\nAltogether, this dissertation used long-term monitoring, dynamical modeling, and subtidal experimentation to evaluate the influence of grazer-resource behavior, interactions, and feedbacks upon kelp-forest dynamics and stability. While urchin predators are predominantly thought to control the switch in urchin behavior, I demonstrate how resource availability can also control this behavioral switch. This may help explain shifts to the urchin barren state at locations where urchin predator abundances remain unchanged. Furthermore, my inferences involving substrate complexity and drift as a preferred urchin resource point towards potential strategies with which to conserve or restore kelp-forest ecosystems. ","tags":["Interaction strength","Subtidal","Functional response","Dynamics","Time-series","Ecosystem stability"],"title":"Grazer-resource behavior, interactions, and feedbacks control kelp-forest dynamics and stability","type":"publication"},{"authors":["Ben Dalziel","Mark Novak","James Watson","Stephen Ellner"],"categories":[],"content":"","date":1628726400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1628726400,"objectID":"4aea2ddd184a8ce0bf823b62dc5621e8","permalink":"https://novaklabosu.github.io/publication/dalziel-2021/","publishdate":"2021-08-12T00:00:00Z","relpermalink":"/publication/dalziel-2021/","section":"publication","summary":"Collective behaviour is common in bacteria, plants, and animals, and thus across ecosystems, from biofilms to cities. With collective behaviour, social interactions among individuals propagate to affect the behaviour of groups, while group-level responses in turn affect individual behaviour. These cross-scale feedbacks between individuals, populations and their environments can provide fitness benefits, such as efficient exploitation of uncertain resources as well as costs, such as increased resource competition. While the social mechanics of collective behaviour are increasingly well-studied, its ecological significance remains poorly understood. Here we introduce collective movement into a model of consumer-resource dynamics to demonstrate that collective behaviour can attenuate consumer-resource cycles and promote species coexistence. We focus on collective movement as a particularly well-understood example of collective behaviour. Adding collective movement to canonical unstable ecological scenarios causes emergent social-ecological feedback which mitigates conditions that would otherwise result in extinction. Collective behaviour could play a key role in the maintenance of biodiversity.","tags":["functional response","intraspecific variation","theory"],"title":"Collective behaviour can stabilize ecosystems","type":"publication"},{"authors":["Mark Novak","Daniel Stouffer"],"categories":[],"content":"","date":1624147200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1624406400,"objectID":"7f69ed148707822dd9bf439c6f064222","permalink":"https://novaklabosu.github.io/publication/novak-2021-ab/","publishdate":"2021-07-06T00:00:00Z","relpermalink":"/publication/novak-2021-ab/","section":"publication","summary":" The assessment of relative model performance using information criteria like AIC and BIC has become routine among functional-response studies, reflecting trends in the broader ecological literature. Such information criteria allow comparison across diverse models because they penalize each model’s fit by its parametric complexity — in terms of their number of free parameters — which allows simpler models to outperform similarly fitting models of higher parametric complexity. However, criteria like AIC and BIC do not consider an additional form of model complexity, referred to as geometric complexity, which relates specifically to the mathematical form of the model. Models of equivalent parametric complexity can differ in their geometric complexity and thereby in their ability to flexibly fit data. Here we use the Fisher Information Approximation criterion to compare, explain, and contextualize how geometric complexity varies across a large compilation of single-prey functional-response models — including prey-, ratio-, and predator-dependent formulations — reflecting varying levels of phenomenological generality and varying apparent degrees and forms of non-linearity. Because a model’s geometric complexity varies with the data’s underlying experimental design, we also sought to determine which designs are best at leveling the playing field among functional-response models. Our analyses illustrate (1) the large differences in geometric complexity that exist among functional-response models, (2) there is no experimental design that can minimize these differences across all models, and (3) even the qualitative nature by which some models are more or less flexible than others is reversed by changes in experimental design. Failure to appreciate geometric complexity in the empirical evaluation of functional-response models may therefore lead to biased inferences for predator-prey ecology, particularly at low experimental sample sizes where the relative effects of geometric complexity are strongest. We conclude by discussing the statistical and epistemological challenges that geometric complexity poses for the study of functional responses as it relates to the attainment of biological truth and predictive ability. ","tags":["Interaction strength","Functional response"],"title":"Geometric complexity and the information-theoretic comparison of functional-response models","type":"publication"},{"authors":["David Taylor","Elia DeJesus","Mark Novak","Rebecca Terry"],"categories":[],"content":"","date":1624147200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1624406400,"objectID":"15d5356f31ab35990d27ebc4bee1d97a","permalink":"https://novaklabosu.github.io/publication/taylor-2021-aa/","publishdate":"2021-06-20T00:00:00Z","relpermalink":"/publication/taylor-2021-aa/","section":"publication","summary":" Stable isotopes are increasingly being used to unlock the wealth of information contained in specimens preserved in museum collections. However, preservation methods that employ formalin may confound ecological interpretations. To quantify the effects of formalin fixation and subsequent fluid storage in ethanol on the isotopic signatures of small mammal hair, we analyzed δ13C and δ15N values from specimens of seven rodent species that were sampled repeatedly both before and after varying lengths of formalin fixation (1 – 11 days) and ethanol storage (1 – 6 years). We supplemented these data with a two-week fixation experiment using deer mice (Peromyscus maniculatus) in which no ethanol storage was employed. As expected, preservation in formalin and ethanol had no discernable effect on δ15N values.  In contrast, specimen δ13C values decreased in a saturating fashion during formalin fixation and over subsequent years of fluid storage in ethanol.  On the basis of models that we fit to these time series, we estimate the long-term effect of fixation and storage on δ13C values to be -0.92‰ after 4 years. This biologically relevant shift in δ13C values should be accounted for when inferring the diets of species from fluid-stored museum collections and when comparing across specimens with different preservation histories. ","tags":["Interaction strength","Stable isotopes"],"title":"The effects of formalin fixation and fluid storage on stable isotopes in rodent hair","type":"publication"},{"authors":["David Rockow"],"categories":[],"content":"","date":1622505600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1622647292,"objectID":"7ba3ad4fdb5b8279d5fb78950d235e97","permalink":"https://novaklabosu.github.io/publication/rockow-2021/","publishdate":"2021-06-02T15:21:28.098015Z","relpermalink":"/publication/rockow-2021/","section":"publication","summary":" Food webs are extraordinarily complex, containing myriad direct interactions and indirect effects. Determining how this network of interactions and effects influences a food web’s qualitative dynamics is a challenging task, especially because data on food web structure and individual interaction strengths is unknown in virtually all real-world ecosystems. The goal of this project was to determine how extinctions and invasions impacted the probability of correctly predicting species dynamics in computationally generated food webs, when these webs were subjected to press perturbations under progressively higher levels of interaction strength uncertainty. It was expected that extinctions, by reducing the number of direct interactions and indirect effects, would generally make responses easier to predict. Since introductions would have the opposite impact, it was predicted adding species would generally make responses harder to predict. Overall, removing species had varied results, but generally made responses easier to predict. There was a strongly supported negative relationship between the number of direct interactions had by a species, and the median percent of mispredicted press perturbation responses of remaining species interactions, after that species was removed. Adding species generally made responses easier to predict. It is possible that network instability caused this pattern to occur. ","tags":["Interaction strength","Press perturbations","Theory","Networks","Community matrix"],"title":"The predictability of qualitative food web dynamics in response to extinction and invasion","type":"publication"},{"authors":null,"categories":null,"content":"A key challenge for ecology is the development of Theory to guide our responses to ongoing environmental change. To more effectively inform conservation and resource-use policy we need to understand the processes by which species – and the interactions among them – affect the dynamics of their communities and the functioning of their ecosystems. While we have made tremendous advances in our understanding, there still exist large gaps between mathematical theory and our empirical knowledge of nature’s complex ecological systems. How and when do species’ direct and indirect interactions affect the structure, dynamics, and functioning of their communities? How well can we predict the response of ecological systems to acute and chronic perturbations, including when these amount to only subtle changes in the environment?\nTo date, our contributions to answering questions like these largely fall into two categories:\n Applying community matrix methods to learn how the reticulate nature of species interacton networks (i.e. the counteracting feedbacks of direct and indirect species effects) and uncertainties in the pairwise strength of species interactions (be it due to estimation error or natural variation) influence our ability to understand and predict how species respond to chronic press perturbations; and Using time-series data, field experiments, and simple models of population dynamics to characterize species- and community dynamics, test ecological theory on how species interactions affect population sizes, and better understand the processes that underlie these effects.  ","date":1617235200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617235200,"objectID":"da500da62ee07af8e04f74064ea6a884","permalink":"https://novaklabosu.github.io/project/dynamics/","publishdate":"2021-04-01T00:00:00Z","relpermalink":"/project/dynamics/","section":"project","summary":"Understanding population, community and network dynamics","tags":null,"title":"Dynamics","type":"project"},{"authors":null,"categories":null,"content":"For us, Homo sapiens, it is clear that what we eat and how we prefer to eat some things over others affects not only our own bodies but collectively has important ramifications for the ways we, as individuals, affect the world around us. Not surprisingly, other animals who are “generalist” predators as a population exhibit diet specialization at the individual level as well, but the scope, patterns, and community-level consequences of this form of intraspecific variation remain poorly resolved. The goal is to go beyond appropriately documenting and describing the variation that exists among individuals, to understanding when (and when not) its consideration is necessary. This is particularly challenging given the reticulate and potentially nonlinear nature of species interactions in species-rich systems.\n","date":1617235200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617235200,"objectID":"312385a2e01512961c2434b91edf9cdc","permalink":"https://novaklabosu.github.io/project/intrasppvar/","publishdate":"2021-04-01T00:00:00Z","relpermalink":"/project/intrasppvar/","section":"project","summary":"Quantifying patterns and effects of intraspecific (diet) variation","tags":null,"title":"Individual variation","type":"project"},{"authors":null,"categories":null,"content":"Efforts to characterize and estimate the functional forms and strengths of species interactions in species-rich communities are hampered by the multitude of direct and indirect interactions such systems exhibit. Empirical insights have also been constrained by an assumption that the feeding behaviors of specialist predators are representative of the behaviors exhibited by generalist predators, which are far more common in nature. This is largely because logistical and statistical constraints have limited almost all studies to species-poor systems of single predator species interacting with only one primary prey species. Even inherently generalist predators have thereby been reduced to effective specialists, whether in manipulative experiments or in time-series analyses. New ways to quantify species interaction strengths are needed to identify keystone species, inform the development of mathematical models, and further our understanding of the processes that regulate community structure and dynamics.\nMuch of our work to date has sought to develop an observational approach with which to overcome many of the aforementioned limitations. The approach relies on (1) predator feeding surveys for estimating the proportions of predator indivdiuals who are caught in the act of feeding on different prey categories (i.e. species), and (2) estimates of prey detection times, typically derived from laboratory experiments, that determine the probability of observing a feeding event when conducting a feeding survey. These data allow us to estimate a predator population’s (or predator indivdiual’s) prey-specific feeding rates which, in conjuction with (3) estimates of prey and predator abundances, allow us characterize the functional forms of their interactions. We have applied the approach in both stream and intertidal communities.\n","date":1617235200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617235200,"objectID":"f631f28f049d9db5e20809ddb9d9ed8b","permalink":"https://novaklabosu.github.io/project/intxnstrngth/","publishdate":"2021-04-01T00:00:00Z","relpermalink":"/project/intxnstrngth/","section":"project","summary":"Characterizing the forms and strengths of species interactions","tags":null,"title":"Interaction strengths","type":"project"},{"authors":null,"categories":null,"content":"","date":1617235200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617235200,"objectID":"c976e50db4b4ab3d2639fa17d0269ddb","permalink":"https://novaklabosu.github.io/project/intertidal/","publishdate":"2021-04-01T00:00:00Z","relpermalink":"/project/intertidal/","section":"project","summary":"Intertidal ecology","tags":null,"title":"Intertidal","type":"project"},{"authors":null,"categories":null,"content":"I welcome applications from students and postdocs interested in developing projects at the interface of empirical and theoretical ecology. While the empirical side of my own research is primarily focused on aquatic systems (intertidal, subtidal and streams), I’m happy to advise students working on whatever system is best-suited for answering their research questions.\nGraduate students If you’re interested in joining the lab, please send me an email to tell me about your general research interests, what you’d like to get out of grad-school, and why you’d like to join my lab in particular. (Chances are that your specific interests will change several times during your first years of grad-school, so don’t worry if you don’t have a project all figured-out. Please just help me get a good sense of the type of topics you’d like to work on, what motivates you to work on them, and what you’d like to come away with at the end in terms of your “tool kit”.) Please also attach a CV/resume and contact information for three references. The application deadline for our department is December 1st. Our department guarantees 5 years of support to all its PhD students in the form of TAships. Nevertheless, I strongly encourage you to have applied for the various pre-doctoral fellowships, most of which have earlier deadlines. More information on the department’s grad program and application process can be found on our Integrative Biology department’s website.\nUndergraduate students Undergraduates become involved in our research through a variety of ways, ranging from volunteer opportunities, paid assistantships, as well as independent research experiences. We are actively fostering diversity within the lab, so I encourage all interested students to contact me (or the lab’s graduate students and postdocs). Volunteer and paid assistantship opportunities often involve working with myself or a graduate student supporting the research projects of the lab. Volunteers have often ended up becoming paid research assistants or have pursued their own independent research projects (particularly when they’ve joined the lab early in their undergraduate careers). Independent research experiences typically involve student-led projects for transcript credit (incl. transcript-visible “distinction in research”), fulfilling Honors requirements, or academic- and/or summer quarter research supported by scholarships or fellowships (e.g., URISC, SURE, etc.). Note that you don’t need to have a project in mind before joining the lab, but please do articulate why you’re interested in our lab when you contact us.\n   2024    2017    2014  ","date":1617235200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617235200,"objectID":"eac7998147c3739bfc80f5175edcd13e","permalink":"https://novaklabosu.github.io/authors/admin/","publishdate":"2021-04-01T00:00:00Z","relpermalink":"/authors/admin/","section":"authors","summary":"How to contact us to express interest in joining the lab.","tags":null,"title":"Join us","type":"page"},{"authors":null,"categories":null,"content":"If you’re interested in reading more, please see this 2019 lay summary of our stream ecology research.\n","date":1617235200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617235200,"objectID":"ed1de08011bb9f3ec3601155339f20ca","permalink":"https://novaklabosu.github.io/project/streams/","publishdate":"2021-04-01T00:00:00Z","relpermalink":"/project/streams/","section":"project","summary":"Stream ecology","tags":null,"title":"Streams","type":"project"},{"authors":null,"categories":null,"content":"","date":1617235200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617235200,"objectID":"b81927c0652c638dd44e21e042ed08fe","permalink":"https://novaklabosu.github.io/project/subtidal/","publishdate":"2021-04-01T00:00:00Z","relpermalink":"/project/subtidal/","section":"project","summary":"Subtidal ecology","tags":null,"title":"Subtidal","type":"project"},{"authors":null,"categories":null,"content":"","date":1617235200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617235200,"objectID":"021790bbe65e3f00292a81f11e58a8bf","permalink":"https://novaklabosu.github.io/project/theory/","publishdate":"2021-04-01T00:00:00Z","relpermalink":"/project/theory/","section":"project","summary":"Theoretical ecology","tags":null,"title":"Theory","type":"project"},{"authors":["Daniel Stouffer","Mark Novak"],"categories":null,"content":"","date":1609459200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371667,"objectID":"a7c7c05f959f66543d77ff7ea1b34a03","permalink":"https://novaklabosu.github.io/publication/stouffer-2021-aa/","publishdate":"2021-04-02T13:54:27.830215Z","relpermalink":"/publication/stouffer-2021-aa/","section":"publication","summary":" Functional responses relate a consumer's feeding rates to variation in its abiotic and biotic environment, providing insight into consumer behaviour and fitness, and underpinning population and food‐web dynamics. Despite their broad relevance and long‐standing history, we show here that the types of density dependence found in classic resource‐ and consumer‐dependent functional‐response models equate to strong and often untenable assumptions about the independence of processes underlying feeding rates. We first demonstrate mathematically how to quantify non‐independence between feeding and consumer interference and between feeding on multiple resources. We then analyse two large collections of functional‐response data sets to show that non‐independence is pervasive and borne out in previously hidden forms of density dependence. Our results provide a new lens through which to view variation in consumer feeding rates and disentangle the biological underpinnings of species interactions in multi‐species contexts. ","tags":["Interaction strength","Functional response","Higher-order effects"],"title":"Hidden layers of density dependence in consumer feeding rates","type":"publication"},{"authors":["Kyle Coblentz","Stephanie Merhoff","Mark Novak"],"categories":[],"content":"","date":1609459200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371667,"objectID":"9c5231c4f005cdd511eb4752e786e8b3","permalink":"https://novaklabosu.github.io/publication/coblentz-2021/","publishdate":"2021-04-02T13:54:27.830215Z","relpermalink":"/publication/coblentz-2021/","section":"publication","summary":"Theory suggests that intraspecific trait variation will alter species interaction strengths through nonlinear averaging when interaction strengths are nonlinear functions of individuals' traits. This effect is expected to be widespread, yet what factors mediate its magnitude in nature and hence its potential effects on ecosystems and communities are unclear.\nWe sought to quantify how nonlinear predator functional responses, variation in prey densities and counteracting variation in attack rates and handling times among predator individuals of similar body size alter their population-level feeding rates through nonlinear averaging in a natural system, and to determine the processes influencing the net magnitude of this effect.\nWe used a field caging experiment in the rocky intertidal of Oregon, USA to quantify attack-rate variation and feeding rates of the whelk Nucella ostrina on its barnacle and mussel prey. We also used empirically parameterized simulations to examine the effects of handling-time variation among individuals on population-level feeding rates.\nWithin cages, individual attack-rate variation reduced population-level whelk feeding rates. However, the magnitude of this reduction differed among prey species and cages depending on cage-specific magnitudes of attack-rate variation and functional-response nonlinearity. The inferred effects of handling-time variation among individuals were of smaller magnitude than those of attack-rate variation, yet counteracted them to cause a net weakening of the effect of individual attack-rate variation on population-level feeding rates. Across cages, attack-rate and prey-density variation had non-additive effects that produced greater feeding-rate reductions at the experiment scale relative to the cage scale.\nOur results indicate that the effects of trait variation via nonlinear averaging depend critically on the features of systems that determine the magnitudes of nonlinearities and trait variation. Because of counteracting trait variation, nonlinear-averaging effects may be quite complex, involving both the variances and covariances of all traits and environmental variables influencing the ecological process of interest. ","tags":["Intraspecific variation","Intertidal","Interaction strength","Observational approach"],"title":"Quantifying the effects of intraspecific variation on predator feeding rates through nonlinear averaging","type":"publication"},{"authors":["Mark Novak","Daniel Stouffer"],"categories":[],"content":"","date":1609459200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371666,"objectID":"0da1faa2594bf15f67f6a380cfe209a8","permalink":"https://novaklabosu.github.io/publication/novak-2021-aa/","publishdate":"2021-04-02T13:54:26.225358Z","relpermalink":"/publication/novak-2021-aa/","section":"publication","summary":"Functional responses are a cornerstone to our understanding of consumer-resource interactions, so how to best describe them using models has been actively debated. Here we focus on the consumer dependence of functional responses to evidence systematic bias in the statistical comparison of functional-response models and the estimation of their parameters. Both forms of bias are universal to nonlinear models (irrespective of consumer dependence) and are rooted in a lack of sufficient replication. Using a large compilation of published datasets, we show that ? due to the prevalence of low sample size studies ? neither the overall frequency by which alternative models achieve top rank nor the frequency distribution of parameter point estimates should be treated as providing insight into the general form or central tendency of consumer interference. We call for renewed clarity in the varied purposes that motivate the study of functional responses, purposes that can compete with each other in dictating the design, analysis and interpretation of functional-response experiments.","tags":["Interaction strength","Functional response"],"title":"Systematic bias in studies of consumer functional responses","type":"publication"},{"authors":["Dan Preston","Tamara Layden","Leah Segui","Landon Falke","Sara Brant","Mark Novak"],"categories":[],"content":"","date":1609459200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371667,"objectID":"f5425e5bdd434311cc2198e005d07adb","permalink":"https://novaklabosu.github.io/publication/preston-2021-aa/","publishdate":"2021-04-02T13:54:27.242693Z","relpermalink":"/publication/preston-2021-aa/","section":"publication","summary":"Although parasites are increasingly recognized for their ecosystem roles, it is often assumed that free-living organisms dominate animal biomass in most ecosystems and therefore provide the primary pathways for energy transfer. To examine the contributions of parasites to ecosystem energetics in freshwater streams, we quantified the standing biomass of trematodes and free-living organisms at nine sites in three streams in western Oregon, USA. We then compared the rates of biomass flow from snails Juga plicifera into trematode parasites relative to aquatic vertebrate predators (sculpin, cutthroat trout and Pacific giant salamanders). The trematode parasite community had the fifth highest dry biomass density among stream organisms (0.40 g/m2) and exceeded the combined biomass of aquatic insects. Only host snails (3.88 g/m2), sculpin (1.11 g/m2), trout (0.73 g/m2) and crayfish (0.43 g/m2) had a greater biomass. The parasite ?extended phenotype?, consisting of trematode plus castrated host biomass, exceeded the individual biomass of every taxonomic group other than snails. The substantial parasite biomass stemmed from the high snail density and infection prevalence, and the large proportional mass of infected hosts that consisted of trematode tissue (M = 31% per snail). Estimates of yearly biomass transfer from snails into trematodes were slightly higher than the combined estimate of snail biomass transfer into the three vertebrate predators. Pacific giant salamanders accounted for 90% of the snail biomass consumed by predators. These results demonstrate that trematode parasites play underappreciated roles in the ecosystem energetics of some freshwater streams.","tags":["Interaction strength","Food webs","Streams","Parasites"],"title":"Trematode parasites exceed aquatic insect biomass in Oregon stream food webs","type":"publication"},{"authors":["Landon Falke","Jeremy Henderson","Mark Novak","Dan Preston"],"categories":[],"content":"","date":1577836800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371662,"objectID":"d7e81b76ebaae0a70d852a6c676da369","permalink":"https://novaklabosu.github.io/publication/falke-2020-aa/","publishdate":"2021-04-02T13:54:21.952572Z","relpermalink":"/publication/falke-2020-aa/","section":"publication","summary":"Intraspecific variation is increasingly recognized as an important factor  in ecological interactions that can exceed the role of interspecific variation. Few studies, however, have examined how variation in intra- and interspecific resource use affect trophic interactions over time within a seasonally-dynamic food web.  We compared diets with respect to predator body size and predator species identity  over 3 seasons by collecting stomach contents from 2028 Reticulate Sculpin (Cottus perplexus), 479 Coastal Cutthroat Trout (Oncorhynchus clarkii clarkii), and 107 Pacific Giant Salamanders (Dicamptodon tenebrosus) in western Oregon streams. In each season, predator body size was strongly associated with dietary composition and positively related to taxonomic breadth and the size of individual prey. Intra- and interspecific diet variation changed substantially across seasons, with much greater interspecific variation in spring than in summer and autumn. Interspecific differences in foraging mode (e.g., benthic vs drift feeding) were associated with predator-specific responses to a seasonal pulse in the availability of terrestrial thrip larvae (Thysanoptera) and contributed to temporal variation in trophic niche differentiation. These findings show that the relative magnitudes of intra- and interspecific diet differentiation can change over time in systems that receive seasonal resource pulses. Our results highlight the dynamic nature of food webs and the need to incorporate sampling over relevant temporal scales to understand species interactions. ","tags":["Intraspecific variation","Streams"],"title":"Temporal shifts in intraspecific and interspecific diet variation among 3 stream predators","type":"publication"},{"authors":["Shannon Hennessey"],"categories":[],"content":"","date":1577836800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617376892,"objectID":"462034a5580757d386e9abf06e1320d7","permalink":"https://novaklabosu.github.io/publication/hennessey-2019-aa/","publishdate":"2021-04-02T15:21:32.607426Z","relpermalink":"/publication/hennessey-2019-aa/","section":"publication","summary":" Fluctuations and spatial heterogeneity of habitat and resources is thought to underlie niche variation in animal populations, with intraspecific differences serving to produce or maintain population-, community-, or ecosystem-level patterns. Individual diet variation, defined as individual variation in food resource use within a population that is consistent over time, is gaining recognition as an important factor influencing larger-scale processes. Spatial and temporal predictability of prey resources, individual movement behaviors, and diet choice may all serve to maintain individual diet specialization. However, the relationships between these factors in establishing and maintaining individual-level variation at ecological scales remains poorly understood. This dissertation provides insight into the dependence of individual diet specialization on the predictability, productivity, and spatial structure of prey by integrating feedbacks between individual behaviors, populations, and communities at local and regional scales.\n\nForaging theory seeks to understand the relationships between the energetic demands of a predator, prey selection, patchiness of prey, and individual movement. To maximize energetic intake, a foraging predator must balance energy expended by foraging movements with energy gained via prey consumption, with foraging success greatly impacted by the scale of patchiness of prey. In Chapter 2, I correlated scale- dependent prey patchiness and predator feeding rates to predict predator movement in a heterogeneous prey environment. I then compared these predictions to observed movement of a predatory intertidal whelk Nucella ostrina over a 3-month period. I found that combining prey patchiness and predator feeding rates sufficiently explains predator movement rates, highlighting a tradeoff between prey heterogeneity and individual energetic demands in determining predator foraging behavior.\n\nForaging behavior can maintain variation in individual diet, with differential habitat use and prey selection correlated with different foraging strategies. Optimal search strategies for a foraging predator depend on the abundance and predictability of prey, therefore differences in individual diet breadth are thought to produce different foraging patterns. In Chapter 3, I connected the broad-scale movement patterns found in Chapter 2 with variation in individual foraging behavior by quantifying variation in individual foraging patterns and correlating these patterns to habitat use and diet breadth. I found evidence for variation in individual behaviors, habitat use, and diet diversity. However, there was an overwhelming influence of tidal cycles on movement patterns, rather than associations with prey choice or habitat occupancy. This is likely due to the high degree of prey productivity at my focal study site, making random search patterns and small foraging movements sufficiently efficient for finding prey.\n\nWhile prey heterogeneity and individual behaviors within a population can maintain variation in individual diet at local scales, the processes that establish individual diet variation requires further study. The lack of environmental predictability has been posited to promote inter-individual differences on both ecological and evolutionary timescales, as tradeoffs between being a prey specialist versus a generalist result in one being favored over the other in certain environmental predictability regimes. In Chapter 4, I used manipulative laboratory experiments to investigate the role of site-specific environmental unpredictability on the relative contributions of learning and heritable diet plasticity in shaping the foraging efficiency of whelk hatchlings. My results indicated the importance of learning in individual foraging and prey handling efficiency. Additionally, there is suggestive evidence that prey predictability at the population source location decreases foraging times as well. However, site attributes or behavioral modification may play a larger role than prey predictability in determining individual foraging abilities I detected. ","tags":["Intraspecific variation","Intertidal"],"title":"The influence of prey predictability on the foraging behavior and movement of intertidal predators","type":"publication"},{"authors":["Bruce Menge","Jenn Caselle","Jack Barth","Carol Blanchette","Mark Carr","Francis Chan","Sarah Gravem","Tarik Gouhier","Jane Lubchenco","Margaret McManus","Kirsten Milligan","Mark Novak","Pete Raimondi","Libe Washburn","Will White"],"categories":[],"content":"","date":1546300800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371663,"objectID":"c2d84c328299e3e5cf282b5d2af6ab29","permalink":"https://novaklabosu.github.io/publication/menge-2019-aa/","publishdate":"2021-04-02T13:54:23.326542Z","relpermalink":"/publication/menge-2019-aa/","section":"publication","summary":" A major goal of the Partnership for Interdisciplinary Studies of Coastal Oceans (PISCO) has been to understand the impacts of climate change and variability on the coastal ecosystems of the inner shelf of the California Current Large Marine System in particular, and other marine and even nonmarine systems more generally. Insights can result from determination of impacts of climatic perturbations such as the El Niño-Southern Oscillation, the North Pacific Gyre Oscillation, and the Pacific Decadal Oscillation, as well as impacts of climate-related surprises on populations, communities, and ecosystems. To gain insight into warming impacts at organismal levels, we also investigated mechanistic suborganismal (physiological, molecular) responses to thermal conditions. Warmer water was connected to changes in ecological subsidies, growth of dominant space occupiers (mussels and barnacles), and heightened physiological stress impacts. Fortuitously, PISCO researchers were ideally positioned to document ecosystem vulnerability and resilience to an unprecedented ecological surprise—coast-wide collapse of keystone predator (sea star) populations—and to investigate its consequences. As these examples suggest, long-term sampling is critically important for helping society anticipate and adapt to present and future disruptions caused by global change. ","tags":["Subtidal","Intertidal"],"title":"Community Responses to Climate-Related Variability and Disease: The Critical Importance of Long-Term Research","type":"publication"},{"authors":["Dan Preston","Landon Falke","Jeremy Henderson","Mark Novak"],"categories":[],"content":"","date":1546300800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371667,"objectID":"6a74ecb804b056d444f8f0dd37aa353f","permalink":"https://novaklabosu.github.io/publication/preston-2019-ab/","publishdate":"2021-04-02T13:54:27.073999Z","relpermalink":"/publication/preston-2019-ab/","section":"publication","summary":" Species interactions in food webs are usually recognized as dynamic, varying across species, space, and time because of biotic and abiotic drivers. Yet food webs also show emergent properties that appear consistent, such as a skewed frequency distribution of interaction strengths (many weak, few strong). Reconciling these two properties requires an understanding of the variation in pairwise interaction strengths and its underlying mechanisms. We estimated stream sculpin feeding rates in three seasons at nine sites in Oregon to examine variation in trophic interaction strengths both across and within predator–prey pairs. Predator and prey densities, prey body mass, and abiotic factors were considered as putative drivers of within‐pair variation over space and time. We hypothesized that consistently skewed interaction strength distributions could result if individual interaction strengths show relatively little variation, or alternatively, if interaction strengths vary but shift in ways that conserve their overall frequency distribution. Feeding rate distributions remained consistently and positively skewed across all sites and seasons. The mean coefficient of variation in feeding rates within each of 25 focal species pairs across surveys was less than half the mean coefficient of variation seen across species pairs within a survey. The rank order of feeding rates also remained conserved across streams, seasons and individual surveys. On average, feeding rates on each prey taxon nonetheless varied by a hundredfold, with some feeding rates showing more variation in space and others in time. In general, feeding rates increased with prey density and decreased with high stream flows and low water temperatures, although for nearly half of all species pairs, factors other than prey density explained the most variation. Our findings show that although individual interaction strengths exhibit considerable variation in space and time, they can nonetheless remain relatively consistent, and thus predictable, compared to the even larger variation that occurs across species pairs. These results highlight how the ecological scale of inference can strongly shape conclusions about interaction strength consistency and help reconcile how the skewed nature of interaction strength distributions can persist in highly dynamic food webs. ","tags":["Interaction strength","Food webs","Streams","Observational approach"],"title":"Food-web interaction strength distributions are conserved by greater variation between than within predator--prey pairs","type":"publication"},{"authors":["Bruce Menge","Jenn Caselle","Kirsten Milligan","Sarah Gravem","Tarik Gouhier","Will White","Jack Barth","Carol Blanchette","Mark Carr","Francis Chan","Jane Lubchenco","Margaret McManus","Mark Novak","Pete Raimondi","Libe Washburn"],"categories":[],"content":"","date":1546300800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371663,"objectID":"51cbc4e6e104004542f9ea991096ed68","permalink":"https://novaklabosu.github.io/publication/menge-2019-ab/","publishdate":"2021-04-02T13:54:23.555307Z","relpermalink":"/publication/menge-2019-ab/","section":"publication","summary":" As the reality of climate change became obvious during the late 1900s, the need for understanding ecosystem pattern and dynamics at large scales and for long periods became increasingly evident. This realization inspired the genesis of the Partnership for Interdisciplinary Studies of Coastal Oceans (PISCO). PISCO research aimed to quantify intertidal and subtidal biogeographic patterns of community structure and ecological subsidies, create a mooring network to document inner-shelf oceanic conditions, and conduct coordinated, coast-wide experiments testing hypotheses on the relative influences of top-down, bottom-up, non-trophic, and ecological subsidy processes. To date, insights include (1) at large scales, bottom-up and related processes drive species interactions and thereby dominate in structuring benthic communities, (2) local-to-latitudinal variation in these processes is ultimately determined by upwelling interacting with coastal geomorphology, and (3) these and similar systems are thus prime examples of “meta-ecosystems” or local-scale ecosystems that are linked by flows of propagules, particulates, and nutrients. ","tags":["Subtidal","Intertidal"],"title":"Integrating Coastal Oceanic and Benthic Ecological Approaches for Understanding Large-Scale Meta-Ecosystem Dynamics","type":"publication"},{"authors":["Bruce Menge","Kirsten Milligan","Jenn Caselle","Jack Barth","Carol Blanchette","Mark Carr","Francis Chan","Bob Cowen","Mark Denny","Steve Gaines","Gretchen Hofmann","Kristy Kroeker","Jane Lubchenco","Margaret McManus","Mark Novak","Steve Palumbi","Pete Raimondi","George Somero","Robert Warner","Libe Washburn","Will White"],"categories":[],"content":"","date":1546300800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371663,"objectID":"51df9781a6ebacb7e93b486f3f0d51d9","permalink":"https://novaklabosu.github.io/publication/menge-2019-ac/","publishdate":"2021-04-02T13:54:23.763891Z","relpermalink":"/publication/menge-2019-ac/","section":"publication","summary":" To support conservation practices, societal demand for understanding fundamental coastal ocean ecosystem mechanisms has grown in recent decades. Globally, these regions are among the world’s most productive, but they are highly vulnerable to extractive and non-extractive stresses. In 1999, we established the Partnership for Interdisciplinary Studies of Coastal Oceans (PISCO) to perform basic and use-inspired, long-term ecological research at local to large marine ecosystem (LME) scales. Coordinated investigations of ecosystem patterns and dynamics focused on nearshore coastal waters and hard-bottom habitats (rocky intertidal and kelp forests) in the California Current Large Marine Ecosystem. Communicating relevant scientific discoveries to inform decision-making was an integral component, as was commitment to training new generations of interdisciplinary marine scientists, thereby building scientific capacity and expertise in marine conservation science and policy. Issues of climate change and ocean acidification, wildlife disease outbreaks, oil spills, and conservation strategies such as marine protected areas have spotlighted the immense value of long-term monitoring and research at the LME scale. Here, we reflect on PISCO’s approach and progress in linking science, conservation, management, and policy using 20 years of experience in the formation and operation of this research network. ","tags":["Subtidal","Intertidal"],"title":"PISCO: Advances Made Through the Formation of a Large-Scale, Long-Term Consortium for Integrated Understanding of Coastal Ecosystem Dynamics","type":"publication"},{"authors":["Kristy Kroeker","Mark Carr","Pete Raimondi","Jenn Caselle","Libe Washburn","Steve Palumbi","Jack Barth","Francis Chan","Bruce Menge","Kirsten Milligan","Mark Novak","Will White"],"categories":[],"content":"","date":1546300800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371663,"objectID":"4e96428d024037fb2aa8b7ef9a639d4f","permalink":"https://novaklabosu.github.io/publication/kroeker-2019-aa/","publishdate":"2021-04-02T13:54:22.981178Z","relpermalink":"/publication/kroeker-2019-aa/","section":"publication","summary":" Despite progressive policies and continued advances in ocean management, numerous shifts associated with global changes have been observed in marine ecosystems in recent years, including warming, ocean acidification, and deoxygenation. As global change accelerates, science is needed to inform evidence-based management strategies for continued ecosystem services. Resilience management, in which actions are undertaken to promote the resistance and recovery responses of populations and ecosystems to disturbance, has been suggested as a possible strategy. However, empirical evidence for effective resilience management is still limited. To inform effective management strategies, mechanisms that underlie resilience to global change that can be influenced by management-ready actions must be identified and tested through observations, experiments, and modeling. Here, we discuss the potential links between three common management strategies (i.e., spatial restrictions such as marine protected areas, coordinated spatial protections, and fisheries management approaches) and potential mechanisms of resilience for marine populations and ecosystems, and provide guidance for future research on resilience management for a changing ocean drawing on insight gained by the Partnership for Interdisciplinary Studies of Coastal Oceans’ work at the science-policy interface in the California Current Large Marine Ecosystem. ","tags":["Subtidal","Intertidal"],"title":"Planning for Change: Assessing the Potential Role of Marine Protected Areas and Fisheries Management Approaches for Resilience Management in a Changing Ocean","type":"publication"},{"authors":["Leah Segui"],"categories":[],"content":"","date":1546300800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617376893,"objectID":"b000eea7ac7e3d55de88efb4b53983ad","permalink":"https://novaklabosu.github.io/publication/segui-2019-aa/","publishdate":"2021-04-02T15:21:32.998191Z","relpermalink":"/publication/segui-2019-aa/","section":"publication","summary":" A central challenge for ecology is to understand the dynamic nature of species interactions. A classic approach to community ecology assumes that individuals within a species are functionally identical and that consumer-resource dynamics can be predicted solely by using species abundances. However, one species can consist of multiple functional groups, as diet differences among life stages of a single species may be greater than the diet differences among species. Because of variation in diets over a lifetime, we must ask: under what circumstances can individuals be simplified into a collective species, and when does it matter to focus on intraspecific variation? I examined the role of stage structure in species interactions and its consequences across levels of biological organization.\n\nIn chapter 2, I conducted a functional response experiment in the laboratory to examine the role of body size, temperature, ontogenetic stage, and larval stonefly density on crayfish feeding rates. I found that the effect of temperature was stage-dependent as juveniles increased feeding with temperature, whereas adult feeding rate was similar across temperature treatments. Adult crayfish reduced their attack rate with increased stonefly density, which is either reflective of their biology or an artifact of experimental\n\ndesign. Nonetheless, size- and temperature- dependent functional response models that included stage structure performed better than models without stage structure, highlighting the importance of incorporating stage structure into measures of species interaction strengths.\n\nIn chapter 3, I used metacommunity theory as a lens to explore how crayfish ontogenetic stage and sex alter the effect of diet on gut microbial communities. There was little overlap in the microbial community between crayfish in the lab and those in the wild, indicating that gut microbes are transient. The similarities in microbial community composition between food items and crayfish suggest that their gut microbes are mainly from their food and not from the surrounding environment. There were stage- and sex- dependent effects on gut microbial communities, likely due to differences in behavior and physiology between the stages and sexes. Though stage, sex, and diet influenced gut microbial communities, they had low explanatory power. Addressing connectivity between hosts or feedbacks between the host and the environment on gut microbial communities are potential avenues for future work. Species introductions can alter the relationship between trophic interactions and ecosystem processes. Often, introduced species reduce the abundance and diversity of biota in recipient food webs. However, ontogenetic diet shifts in the introduced species can alter the presence, degree or direction of these impacts on native species, making it difficult for scientists and managers to predict the ecological consequences of species introductions. In chapter 4, I conducted a manipulative field experiment to assess the effects of crayfish species identity and ontogenetic stage on benthic invertebrate composition and abundance as well as leaf litter breakdown by native signal crayfish (Pacifastacus leniusculus) and introduced ringed crayfish (Faxonius neglectus neglectus). Treatments with signal crayfish or adult crayfish had higher reductions in leaf litter relative to treatments with introduced crayfish and juvenile crayfish. Alpha and beta diversity of benthic invertebrates was similar among treatments, but there were fewer shredders in treatments with adult crayfish. Thus, I show that ontogenetic stage and native vs. non-native status both matter for understanding the impact of species introductions on local ecological communities and ecosystem processes.\n\nIn Chapter 5, I presented the challenges of uniting ecological theory and empirical data. I designed an experiment that investigated the roles of consumer body size and ontogenetic stage, environmental temperature, and resource quality on consumer-resource interactions. My goal was to bridge the Metabolic Theory of Ecology and Ecological Stoichiometry to describe how the balance leaf litter nutrient availability and crayfish elemental demand govern their feeding rates and nutrient cycling over ontogeny, but my models did not fit the data well. This developed into a philosophical dilemma: as scientists, do we choose to work in systems that will produce data that we know will fit our model, or do we test a model in various systems to see how generalizable our predictions can be? I explored the culture of science, focusing on the existence of paradigms in ecology that discourage “negative results” and the obstacles one might face in conducting functional response experiments. Specifically, I reviewed experimental design and statistical methods used in functional response literature and how they can be biased to maintain paradigms in ecology.\n\nMy dissertation contributes to our understanding on the role of intraspecific variation in ecology. I examined consumer-resource interactions (Ch. 2), community structure (Ch. 3), and ecosystem processes (Ch. 4 and 5) to assess the effect of stage structure on species interactions and their consequences across multiple scales of organization. I illustrated the challenges of bridging ecological theory and empirical data and the approaches that hinder or advance the field. Overall, my work has demonstrated the importance of incorporating stage structure in ecological studies and that this information advances both ecological theory and applied efforts. ","tags":["Intraspecific variation","Streams","Functional response"],"title":"State-structured species interactions and their consequences across levels of biological organization","type":"publication"},{"authors":["Frank Pennekamp","Alison Iles","Joshua Garland","Georgina Brennan","Ulrich Brose","Ursula Gaedke","Ute Jacob","Pavel Kratina","Blake Matthews","Steve Munch","Mark Novak","Gian Marco Palamara","Björn Rall","Benjamin Rosenbaum","Andrea Tabi","Colette Ward","Rich Williams","Hao Ye","Owen Petchey"],"categories":[],"content":"","date":1546300800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371666,"objectID":"3b75c66b7626aebea848d0cc3d72b653","permalink":"https://novaklabosu.github.io/publication/pennekamp-2019-uq/","publishdate":"2021-04-02T13:54:26.39242Z","relpermalink":"/publication/pennekamp-2019-uq/","section":"publication","summary":"Successfully predicting the future states of systems that are complex, stochastic, and potentially chaotic is a major challenge. Model forecasting error (FE) is the usual measure of success; however model predictions provide no insights into the potential for improvement. In short, the realized predictability of a specific model is uninformative about whether the system is inherently predictable or whether the chosen model is a poor match for the system and our observations thereof. Ideally, model proficiency would be judged with respect to the systems? intrinsic predictability, the highest achievable predictability given the degree to which system dynamics are the result of deterministic vs. stochastic processes. Intrinsicredictability may be quantified with permutation entropy (PE), a model-free, information-theoretic measure of the complexity of a time series. By means of simulations, we show that a correlation exists between estimated PE and FE and show how stochasticity, process error, and chaotic dynamics affect the relationship. This relationship is verified for a data set of 461 empirical ecological time series. We show how deviations from the expected PE?FE relationship are related to covariates of data quality and the nonlinearity of ecological dynamics. These results demonstrate a theoretically grounded basis for a model-free evaluation of a system's intrinsic predictability. Identifying the gap between the intrinsic and realized predictability of time series will enable researchers to understand whether forecasting proficiency is limited by the quality and quantity of their data or the ability of the chosen forecasting model to explain the data. Intrinsic predictability also provides a model-free baseline of forecasting proficiency against which modeling efforts can be evaluated.","tags":["Dynamics","Time-series"],"title":"The intrinsic predictability of ecological time series and its potential to guide forecasting","type":"publication"},{"authors":["Kyle Coblentz"],"categories":[],"content":"","date":1514764800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617376892,"objectID":"a78290927653e91fd9c7fb593820103c","permalink":"https://novaklabosu.github.io/publication/coblentz-2018-aa/","publishdate":"2021-04-02T15:21:28.098015Z","relpermalink":"/publication/coblentz-2018-aa/","section":"publication","summary":" Diet variation among individuals within populations is widespread. Often diet dierences among individuals are attributable to obvious differences among individuals such as age, sex, or morphology. However, growing evidence suggests that individual diet variation is also common among seemingly identical individuals within populations. This phenomenon has been termed individual diet specialization. Individual diet specialization has been documented across a variety of taxa and biomes and theory suggests that diet specialization can potentially alter the structure and strength of predator-prey interactions. This raises two important questions: 1) What are the causes of individual diet specialization?, and 2) What are the potential consequences of diet specialization for populations and communities? In this dissertation, I attempt to address these two questions by combining mathematical theory, the novel application of statistical methods, and field and laboratory experiments with the intertidal whelk, Nucella ostrina.\n\nA potential ultimate cause of variation among individuals is disruptive selection in which natural selection favors individuals with more extreme trait values over individuals with intermediate trait values. Theory has suggested that the availability of alternative resources and intraspecific competition for those resources can drive disruptive selection in consumers and lead to increased diet variation. However, this theory makes several ecologically unrealistic assumptions. In particular, this theory assumes that consumers have linear functional responses and that the trait of the consumer under selection only influences the consumer’s attack rates on resources. In Chapter 2, I alleviate these assumptions and show that nonlinear functional responses and traits influencing multiple functional response parameters simultaneously can influence the strength and likelihood of disruptive selection. My results suggest the characteristics of consumers in which disrup- tive selection in resource-use traits may occur and diet specialization through this mechanism may be most likely.\n\nTo empirically evaluate hypotheses on the causes and consequences of individ- ual diet specialization, we need to be able to accurately quantify diet specialization. In Chapter 3, I apply Bayesian hierarchical models to the problem of estimating diet specialization and compare the performance of the Bayesian hierarchical models to currently used methods for estimating diet specialization. Currently used methods infer individual prey preferences using the observed proportion of prey in individuals’ diets whereas the Bayesian hierarchical models instead estimate these proportions. I find that the currently used approach tends to overestimate diet specialization compared to the Bayesian hierarchical approach. This is especially the case when sample sizes per individual are low or heterogeneous. In addition, the Bayesian hierarchical approach provides estimates of prey proportions, their variability, and the uncertainty on these estimates in ways that are inaccessible to current methods. These results suggest that the Bayesian hierarchical method can provide an improved method for quantifying diet specialization.\n\nIn Chapter 4, I present the results from a field caging experiment examining the proximate ecological mechanisms determining individual diet specialization and its consequences in the intertidal whelk, Nucella ostrina. Many of the hypotheses on the ecological causes of diet specialization assume that individuals differ from one another in their prey preferences. However, these hypotheses ignore the potential influence of stochasticity in the foraging process in generating diet variation among individuals. The results of this chapter suggest that changes in the magnitude of diet variation with changes in prey community composition in Nucella ostrina can largely be explained by stochastic foraging by individuals with shared prey pref- erences. In this chapter, I also estimate the consequences of this diet variation for estimates of predator feeding rates through nonlinear averaging (Jensen’s inequality) of predator attack rates. The results suggest that nonlinear averaging alters the perceived strength of predator-prey interactions in this system providing one of the first empirical estimates of the potential consequences of diet variation.\n\nOverall, my dissertation provides several insights into the potential causes of diet specialization, provides one of the first empirical estimates of a possibly widespread consequence of diet specialization for populations and communities, and suggests improved statistical methodology for quantifying diet specialization. I believe that this dissertation will lead to a critical assessment of definitions of individual diet specialization, provide guidance towards systems in which diet specialization is the most likely to occur, and encourage further empirical research estimating the e↵ects of diet specialization on populations and communities. ","tags":["Intraspecific variation","Intertidal","Interaction strength"],"title":"Candidate causes, consequences, and estimation of individual diet specialization","type":"publication"},{"authors":["David Koslicki","Mark Novak"],"categories":[],"content":"","date":1514764800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371662,"objectID":"50efc86de60f6374876f752490926c57","permalink":"https://novaklabosu.github.io/publication/koslicki-2018-zm/","publishdate":"2021-04-02T13:54:22.792016Z","relpermalink":"/publication/koslicki-2018-zm/","section":"publication","summary":"We consider the goal of predicting how complex networks respond to chronic (press) perturbations when characterizations of their network topology and interaction strengths are associated with uncertainty. Our primary result is the derivation of exact formulas for the expected number and probability of qualitatively incorrect predictions about a system's responses under uncertainties drawn form arbitrary distributions of error. Additional indices provide new tools for identifying which links in a network are most qualitatively and quantitatively sensitive to error, and for determining the volume of errors within which predictions will remain qualitatively determinate (i.e. sign insensitive). Together with recent advances in the empirical characterization of uncertainty in networks, these tools bridge a way towards probabilistic predictions of network dynamics.","tags":["Networks","Dynamics","Community matrix","Press perturbations"],"title":"Exact probabilities for the indeterminacy of complex networks as perceived through press perturbations","type":"publication"},{"authors":["Dan Preston","Jeremy Henderson","Landon Falke","Leah Segui","Tamara Layden","Mark Novak"],"categories":[],"content":"","date":1514764800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371667,"objectID":"19fa7fff6447dea4dda8f2fe0c0ff7d8","permalink":"https://novaklabosu.github.io/publication/preston-2018-kt/","publishdate":"2021-04-02T13:54:26.904951Z","relpermalink":"/publication/preston-2018-kt/","section":"publication","summary":"Describing the mechanisms that drive variation in species interaction strengths is central to understanding, predicting, and managing community dynamics. Multiple factors have been linked to trophic interaction strength variation, including species densities, species traits, and abiotic factors. Yet most empirical tests of the relative roles of multiple mechanisms that drive variation have been limited to simplified experiments that may diverge from the dynamics of natural food webs. Here, we used a field-based observational approach to quantify the roles of prey density, predator density, predator-prey body-mass ratios, prey identity, and abiotic factors in driving variation in feeding rates of reticulate sculpin (Cottus perplexus). We combined data on over 6,000 predator-prey observations with prey identification time functions to estimate 289 prey-specific feeding rates at nine stream sites in Oregon. Feeding rates on 57 prey types showed an approximately log-normal distribution, with few strong and many weak interactions. Model selection indicated that prey density, followed by prey identity, were the two most important predictors of prey-specific sculpin feeding rates. Feeding rates showed a positive relationship with prey taxon densities that was inconsistent with predator saturation predicted by current functional response models. Feeding rates also exhibited four orders-of-magnitude in variation across prey taxonomic orders, with the lowest feeding rates observed on prey with significant anti-predator defenses. Body-mass ratios were the third most important predictor variable, showing a hump-shaped relationship with the highest feeding rates at intermediate ratios. Sculpin density was negatively correlated with feeding rates, consistent with the presence of intraspecific predator interference. Our results highlight how multiple co-occurring drivers shape trophic interactions in nature and underscore ways in which simplified experiments or reliance on scaling laws alone may lead to biased inferences about the structure and dynamics of species-rich food webs.","tags":["Interaction strength","Food webs","Streams","Functional response","Observational approach"],"title":"What drives interaction strengths in complex food webs? A test with feeding rates of a generalist stream predator","type":"publication"},{"authors":["Chris Wolf","Mark Novak","Alix Gitelman"],"categories":[],"content":"","date":1483228800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371668,"objectID":"4105b5db07d4720d0f50e512bd99af52","permalink":"https://novaklabosu.github.io/publication/wolf-2017-rq/","publishdate":"2021-04-02T13:54:28.789439Z","relpermalink":"/publication/wolf-2017-rq/","section":"publication","summary":"Considerable effort has been devoted to the estimation of species interaction strengths. This effort has focused primarily on statistical significance testing and obtaining point estimates of parameters that contribute to interaction strength magnitudes, leaving the characterization of uncertainty associated with those estimates unconsidered. We consider a means of characterizing the uncertainty of a generalist predator’s interaction strengths by formulating an observational method for estimating a predator’s prey-specific per capita attack rates as a Bayesian statistical model. This formulation permits the explicit incorporation of multiple sources of uncertainty. A key insight is the informative nature of several so-called non-informative priors that have been used in modeling the sparse data typical of predator feeding surveys. We introduce to ecology a new neutral prior and provide evidence for its superior performance. We use a case study to consider the attack rates in a New Zealand intertidal whelk predator, and we illustrate not only that Bayesian point estimates can be made to correspond with those obtained by frequentist approaches, but also that estimation uncertainty as described by 95% intervals is more useful and biologically realistic using the Bayesian method. In particular, unlike in bootstrap confidence intervals, the lower bounds of the Bayesian posterior intervals for attack rates do not include zero when a predator–prey interaction is in fact observed. We conclude that the Bayesian framework provides a straightforward, probabilistic characterization of interaction strength uncertainty, enabling future considerations of both the deterministic and stochastic drivers of interaction strength and their impact on food webs.","tags":["Interaction strength","Functional response","Intertidal","Observational approach"],"title":"Bayesian characterization of uncertainty in species interaction strengths","type":"publication"},{"authors":["Tamara Layden"],"categories":[],"content":"","date":1483228800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617376892,"objectID":"fd2c6fbe2d08e30a1a69372c52bce4e9","permalink":"https://novaklabosu.github.io/publication/layden-2017/","publishdate":"2021-04-02T15:21:28.098015Z","relpermalink":"/publication/layden-2017/","section":"publication","summary":" Parasites are increasingly recognized for their significant roles in shaping community structure and ecosystem dynamics. Due to their cryptic nature, however, they are often neglected in measurements of energy flow and biomass in ecosystems. Past studies have demonstrated that parasites directly contribute to the flow of energy through marine estuaries and freshwater wetlands, yet it remains unknown how broadly applicable these findings are across other ecosystems. The aim of our study was to quantify the role of trematode parasites in the flow of energy through freshwater streams, using biomass as a proxy for energy flow. To accomplish this, we quantified the density and size distributions of aquatic organisms using quadrat and surber samplers within three Oregon steams (n = 9 field sites total) during the summer months. We then used length-to-mass regressions to estimate the free-living biomass of each organism per unit area. To estimate trematode biomass, we dissected freshwater snail hosts, Juga plicifera, quantifying infection prevalence and trematode mass as a function of host body size for each trematode taxon. \n\nJuga snails dominated the standing crop biomass of aquatic invertebrates, constituting an average of 87.5% of the total invertebrate biomass across the three streams (mean = 3.77 g m2). The other most important groups included Coleoptera (0.0315 g m2), Plecoptera (0.0138 g m2), Trichoptera (0.0129 g m2), and Odonata (0.0128 g m2). We identified five trematode taxa that infected Juga snails at our field sites (Metagonimoides oregonensis, Nanophyetus salmincola, Acanthatrium oregonense, Derogenidae spp., and Opecoilidae spp.). Trematode tissue comprised an average of 31% of the total body mass of each infected snail at the individual level, with a positive correlation between snail size and percent trematode mass. Trematode biomass ranged from 4% to 17% of the total population-level snail biomass, averaging 0.392 g m2 across the sites. Trematode biomass exceeded all taxon-specific and total free-living insect biomass (mean = 0.096 g m2). Our results suggest that trematodes are capable of surpassing the roles of many major free-living invertebrates in the movement of energy through these stream food webs. Furthermore, because few aquatic predators consume Juga snails, trematodes potentially alter pathways of energy flow by routing snail production through parasites and into other components of the aquatic food web. ","tags":["Streams","Interaction strength"],"title":"Contributions of parasites to energy flow through a stream food web","type":"publication"},{"authors":["Jon Witman","Franz Smith","Mark Novak"],"categories":[],"content":"","date":1483228800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371668,"objectID":"26c3be46efafaa64df7cca3cee1b8214","permalink":"https://novaklabosu.github.io/publication/witman-2017-jm/","publishdate":"2021-04-02T13:54:28.582235Z","relpermalink":"/publication/witman-2017-jm/","section":"publication","summary":"In diverse tropical webs, trophic cascades are presumed to be rare, as species interactions may dampen top-down control and reduce their prevalence. To test this hypothesis, we used an open experimental design in the Galápagos rocky subtidal that enabled a diverse guild of fish species, in the presence of each other and top predators (sea lions and sharks), to attack two species of sea urchins grazing on benthic algae. Time-lapse photography of experiments on natural and experimental substrates revealed strong species identity effects: only two predator species–blunthead triggerfish (Pseudobalistes naufragium) and finescale triggerfish (Balistes polylepis)–drove a diurnal trophic cascade extending to algae, and they preferred large pencil urchins (Eucidaris galapagensis) over green urchins (Lytechinus semituberculatus). Triggerfish predation effects were strong, causing a 24-fold reduction of pencil urchin densities during the initial 21 hours of a trophic cascade experiment. A trophic cascade was demonstrated for pencil urchins, but not for green urchins, by significantly higher percent cover of urchin-grazed algae in cages that excluded predatory fish than in predator access (fence) treatments. Pencil urchins were more abundant at night when triggerfish were absent, suggesting that this species persists by exploiting a nocturnal predation refuge. Time-series of pencil urchin survivorship further demonstrated per capita interference effects of hogfish and top predators. These interference effects respectively weakened and extended the trophic cascade to a fourth trophic level through behavioral modifications of the triggerfish-urchin interaction. We conclude that interference behaviors capable of modifying interaction strength warrant greater attention as mechanisms for altering top-down control, particularly in speciose food webs.","tags":["Interaction strength","Subtidal","Time-series","Higher-order effects","Functional response"],"title":"Experimental demonstration of a trophic cascade in the Galápagos rocky subtidal:  Effects of consumer identity and behavior","type":"publication"},{"authors":["Brent Hughes","Rodrigo Beas-Luna","Allie Barner","Kimberly Brewitt","Dan Brumbaugh","Liz Cerny-Chipman","Sarah Close","Kyle Coblentz","Kristin de Nesnera","Sarah Drobnitch","Jared Figurski","Becky Focht","Maya Friedman","Jan Freiwald","Kristen Heady","Walter Heady","Annaliese Hettinger","Angela Johnson","Kendra Karr","Brenna Mahoney","Monica Moritsch","Ann-Marie Osterback","Jessica Reimer","Jonathan Robinson","Tully Rohrer","Jeremy Rose","Megan Sabal","Leah Segui","Chenchen Shen","Jenna Sullivan","Rachel Zuercher","Pete Raimondi","Bruce Menge","Kirsten Grorud-Colvert","Mark Novak","Mark Carr"],"categories":[],"content":"","date":1483228800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371662,"objectID":"8077edf6ad81a0aad7b5651e9f692d77","permalink":"https://novaklabosu.github.io/publication/hughes-2017-uq/","publishdate":"2021-04-02T13:54:22.21664Z","relpermalink":"/publication/hughes-2017-uq/","section":"publication","summary":" As the contribution for long-term ecological and environmental studies (LTEES) to our understanding of how species and ecosystems respond to a changing global climate becomes more urgent, the relative number and investment in LTEES are declining. To assess the value of LTEES to advancing the field of ecology, we evaluated relationships between citation rates and study duration, as well as the representation of LTEES with the impact factors of 15 ecological journals. We found that the proportionate representation of LTEES increases with journal impact factor and that the positive relationship between citation rate and study duration is stronger as journal impact factor increases. We also found that the representation of LTEES in reports written to inform policy was greater than their representation in the ecological literature and that their authors particularly valued LTEES. We conclude that the relative investment in LTEES by ecologists and funders should be seriously reconsidered for advancing ecology and its contribution to informing environmental policy. ","tags":["Time-series"],"title":"Long-Term Studies Contribute Disproportionately to Ecology and Policy","type":"publication"},{"authors":["Mark Novak","Chris Wolf","Kyle Coblentz","Isaac Shepard"],"categories":[],"content":"","date":1483228800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371666,"objectID":"0737eb86279d4e1c238eafb08226efc8","permalink":"https://novaklabosu.github.io/publication/novak-2017-mo/","publishdate":"2021-04-02T13:54:26.054074Z","relpermalink":"/publication/novak-2017-mo/","section":"publication","summary":" A long‐standing debate concerns how functional responses are best described. Theory suggests that ratio dependence is consistent with many food web patterns left unexplained by the simplest prey‐dependent models. However, for logistical reasons, ratio dependence and predator dependence more generally have seen infrequent empirical evaluation and then only so in specialist predators, which are rare in nature. Here we develop an approach to simultaneously estimate the prey‐specific attack rates and predator‐specific interference (facilitation) rates of predators interacting with arbitrary numbers of prey and predator species in the field. We apply the approach to surveys and experiments involving two intertidal whelks and their full suite of potential prey. Our study provides strong evidence for predator dependence that is poorly described by the ratio dependent model over manipulated and natural ranges of species abundances. It also indicates how, for generalist predators, even the qualitative nature of predator dependence can be prey‐specific. ","tags":["Functional response","Intertidal","Interaction strength","Functional response","Higher-order effects","Observational approach"],"title":"Quantifying predator dependence in the functional response of generalist predators","type":"publication"},{"authors":["Jameal Samhouri","Adrian Stier","Shannon Hennessey","Mark Novak","Ben Halpern","Phil Levin"],"categories":[],"content":"","date":1483228800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371667,"objectID":"19e90262f794c23658bdf851e04ef663","permalink":"https://novaklabosu.github.io/publication/samhouri-2017-om/","publishdate":"2021-04-02T13:54:27.416016Z","relpermalink":"/publication/samhouri-2017-om/","section":"publication","summary":" One of the twenty-first century’s greatest environmental challenges is to recover and restore species, habitats and ecosystems. The decision about how to initiate restoration is best-informed by an understanding of the linkages between ecosystem components and, given these linkages, an appreciation of the consequences of choosing to recover one ecosystem component before another. However, it remains difficult to predict how the sequence of species’ recoveries within food webs influences the speed and trajectory of restoration, and what that means for human well-being. Here, we develop theory to consider the ecological and social implications of synchronous versus sequential (species-by-species) recovery in the context of exploited food webs. A dynamical systems model demonstrates that synchronous recovery of predators and prey is almost always more efficient than sequential recovery. Compared with sequential recovery, synchronous recovery can be twice as fast and produce transient fluctuations of much lower amplitude. A predator-first strategy is particularly slow because it counterproductively suppresses prey recovery. An analysis of real-world predator–prey recoveries shows that synchronous and sequential recoveries are similarly common, suggesting that current practices are not ideal. We highlight policy tools that can facilitate swift and steady recovery of ecosystem structure, function and associated services.","tags":["Dynamics","Theory","Press perturbations","Ecosystem stability","Time-series","Community matrix"],"title":"Rapid and direct recoveries of predators and prey through synchronized ecosystem management","type":"publication"},{"authors":["Kyle Coblentz","Adam Rosenblatt","Mark Novak"],"categories":[],"content":"","date":1483228800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371661,"objectID":"18c6ca5d6856bf81546163f295036631","permalink":"https://novaklabosu.github.io/publication/coblentz-2017-gq/","publishdate":"2021-04-02T13:54:21.234884Z","relpermalink":"/publication/coblentz-2017-gq/","section":"publication","summary":" Intraspecific variation in ecologically relevant traits is widespread. In generalist predators in particular, individual diet specialization is likely to have important consequences for food webs. Understanding individual diet specialization empirically requires the ability to quantify individual diet preferences accurately. Here we compare the currently used frequentist maximum likelihood approach, which infers individual preferences using the observed prey proportions to Bayesian hierarchical models that instead estimate these proportions. Using simulated and empirical data, we find that the approach of using observed prey proportions consistently overestimates diet specialization relative to the Bayesian hierarchical approach when the number of prey observations per individual is low or the number of prey observations vary among individuals, two common features of empirical data. Furthermore, the Bayesian hierarchical approach permits the estimation of point estimates for both prey proportions and their variability within and among levels of organization (i.e., individuals, experimental treatments, populations), while also characterizing the uncertainty of these estimates in ways inaccessible to frequentist methods. The Bayesian hierarchical approach provides a useful framework for improving the quantification and understanding of intraspecific variation in diet specialization studies. ","tags":["Intraspecific variation","Intertidal"],"title":"The application of Bayesian hierarchical models to quantify individual diet specialization","type":"publication"},{"authors":["Dan Preston","Jeremy Henderson","Landon Falke","Mark Novak"],"categories":[],"content":"","date":1483228800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371666,"objectID":"109eafd4fd69fdf83f14a8a787a4d661","permalink":"https://novaklabosu.github.io/publication/preston-2017-bh/","publishdate":"2021-04-02T13:54:26.648091Z","relpermalink":"/publication/preston-2017-bh/","section":"publication","summary":" Estimates of predator feeding rates are important for understanding trophic dynamics. One common method for quantifying feeding rates in fishes combines mass‐based diet data with gastric evacuation times to estimate prey mass consumed per predator. An alternative approach is to estimate the rates of prey individuals consumed using prey identification time—the time period over which prey remain identifiable in a predator's stomach. One challenge with the analysis of prey identification times, however, is that the response variable is likely to be censored because the “true” prey identification time cannot be observed directly. Here, we applied survival analysis that can incorporate censored data to estimate the effects of predator body size, water temperature, and prey characteristics (type, count, and body size) on identification times in Reticulate Sculpin Cottus perplexus. We focused on seven types of prey that are common in this generalist predator's diet: mayflies (Ephemeroptera), caddisflies (Trichoptera), stoneflies (Plecoptera), true flies (Diptera), beetles (Coleoptera), worms (Annelida), and sculpin eggs. An information‐theoretic model comparison approach indicated that an accelerated failure time Weibull model with all five covariates provided the best relative fit to the full data set. Prey type had a strong effect on prey identification time, with annelid worms having the shortest times (15 h). Water temperature decreased prey identification time (7.5% per 1°C increase), whereas prey count (i.e., meal size) increased prey identification time (15.5% per additional prey item). Predator body size had a weak negative effect on prey identification time (0.04% per 1‐mm increase). Body sizes of some prey taxa, including mayflies, caddisflies, and stoneflies, increased prey identification times, leading to an interaction between prey type and prey size. Our study highlights the utility of survival analysis for quantifying variation in prey identification times in the diets of generalist predators. ","tags":["Interaction strength","Food webs","Streams","Observational approach"],"title":"Using Survival Models to Estimate Invertebrate Prey Identification Times in a Generalist Stream Fish","type":"publication"},{"authors":["Mark Novak","Justin Yeakel","Andrew Noble","Dan Doak","Mark Emmerson","Jim Estes","Ute Jacob","Tim Tinker","Tim Wootton"],"categories":[],"content":"","date":1451606400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371666,"objectID":"98c8f46d32db4592bf2041b32576aea0","permalink":"https://novaklabosu.github.io/publication/novak-2016-og/","publishdate":"2021-04-02T13:54:25.845195Z","relpermalink":"/publication/novak-2016-og/","section":"publication","summary":" The community matrix is among ecology's most important mathematical abstractions, formally encapsulating the interconnected network of effects that species have on one another's populations. Despite its importance, the term “community matrix” has been applied to multiple types of matrices that have differing interpretations. This has hindered the application of theory for understanding community structure and perturbation responses. Here, we clarify the correspondence and distinctions among the Interaction matrix, the Alpha matrix, and the Jacobian matrix, terms that are frequently used interchangeably as well as synonymously with the term “community matrix.” We illustrate how these matrices correspond to different ways of characterizing interaction strengths, how they permit insights regarding different types of press perturbations, and how these are related by a simple scaling relationship. Connections to additional interaction strength characterizations encapsulated by the Beta matrix, the Gamma matrix, and the Removal matrix are also discussed. Our synthesis highlights the empirical challenges that remain in using these tools to understand actual communities. ","tags":["Theory","Interaction strength","Community matrix","Dynamics","Press perturbations","Networks"],"title":"Characterizing species interactions to understand press perturbations: What is the community matrix?","type":"publication"},{"authors":["Wendy Saepharn"],"categories":[],"content":"","date":1451606400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617376892,"objectID":"3a8cfe0453089cd18958088e3396f257","permalink":"https://novaklabosu.github.io/publication/saepharn-2017/","publishdate":"2021-04-02T15:21:28.098015Z","relpermalink":"/publication/saepharn-2017/","section":"publication","summary":" Invasive species are one of the greatest threats to biodiversity around the world.  Although a seemingly harmless act, species introduction into a new ecosystem can have detrimental effects. Once introduced, invasive species may disrupt the existing ecosystem by competing with native species for limited resources.Freshwater ecosystems are heavily invaded, with native species at risk of being removed. Crayfish are one of the most widespread aquatic invaders around the world. They are introduced into freshwater ecosystems by fishermen who use them as bait and by schools who use them for scientific experiments. Crayfish affect stream food webs by competing with fishes and other invertebrates for food and shelter.\n\nThe invasive ringed crayfish (_Orconectes neglectus_), which are native to the Ozark region, appeared in the Willamette River basin for the first time in 2015. They have replaced the native signal crayfish (_Pacifastacus leniusculus_) in other river systems around Oregon. However, there have been no studies surrounding the interactions between ringed and signal crayfish. I am interested in the mechanisms that allow establishment of ringed crayfish in Oregon's freshwater ecosystems. Specifically, I will test the competitive ability of both juvenile and adult ringed and signal crayfish in obtaining food and shelter. I hypothesize that ringed crayfish will outcompete signal crayfish for limited resources and that this behavior may explain why ringed crayfish have replaced signal crayfish in other rivers in Oregon.\n\nI will independently conduct laboratory experiments to test the competitive behaviors of ringed and signal crayfish. I will collect both juveniles and adults of each crayfish species from streams in the Willamette River basin. The crayfish will be sustained in lab conditions one week before the experimental trials. Lab conditions will consist of a 14:10 hr light-dark cycle at 15°C. One ringed crayfish and one signal crayfish of similar size will be placed together in a tank for both food and shelter trials. Prior to the food competition experiment, the pair will be starved for 24 hours. After crayfish acclimate to the tank for 1 hour, I will place a worm in the tank and note which crayfish obtained the worm. If a trial lasts longer than 20 minutes, I will record it as a tie. The experimental trials for shelter will consist of the different crayfish pairs that were used for the food competition trials. A PVC half-tube shelter will be placed in the experimental tank. A pair consisting of a ringed crayfish and a signal crayfish will acclimate in the tank overnight. The following day, I will note how often each crayfish use the shelter every hour for 8 hours. Usage of the shelter will only be noted if 3/4 of the body are within the pipe. After the shelter experiment, I will also observe how often each species uses its shelter when put in a tank alone. Individual shelter usage will be noted every hour for 8 hours. ","tags":["Streams"],"title":"Competitive mechanisms underlying the displacement of native crayfish by non-native crayfish","type":"publication"},{"authors":["Alison Iles","Mark Novak"],"categories":[],"content":"","date":1451606400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371662,"objectID":"bedc3f2f52de84525f9f937005be8357","permalink":"https://novaklabosu.github.io/publication/iles-2016-br/","publishdate":"2021-04-02T13:54:22.383843Z","relpermalink":"/publication/iles-2016-br/","section":"publication","summary":" All ecosystems are subjected to chronic disturbances, such as harvest, pollution, and climate change. The capacity to forecast how species respond to such press perturbations is limited by our imprecise knowledge of pairwise species interaction strengths and the many direct and indirect pathways along which perturbations can propagate between species. Network complexity (size and connectance) has thereby been seen to limit the predictability of ecological systems. Here we demonstrate a counteracting mechanism in which the influence of indirect effects declines with increasing network complexity when species interactions are governed by universal allometric constraints. With these constraints, network size and connectance interact to produce a skewed distribution of interaction strengths whose skew becomes more pronounced with increasing complexity. Together, the increased prevalence of weak interactions and the increased relative strength and rarity of strong interactions in complex networks limit disturbance propagation and preserve the qualitative predictability of net effects even when pairwise interaction strengths exhibit substantial variation or uncertainty. ","tags":["Community matrix","Networks","Press perturbations"],"title":"Complexity increases predictability in allometrically constrained food webs","type":"publication"},{"authors":["Adrian Stier","Jameal Samhouri","Mark Novak","Kristin Marshall","Eric Ward","Robert Holt","Phil Levin"],"categories":[],"content":"","date":1451606400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371667,"objectID":"25d7cf1f6c23b01f917c02243cdaeb50","permalink":"https://novaklabosu.github.io/publication/stier-2016-yj/","publishdate":"2021-04-02T13:54:27.625534Z","relpermalink":"/publication/stier-2016-yj/","section":"publication","summary":" Habitat loss, overexploitation, and numerous other stressors have caused global declines in apex predators. This “trophic downgrading” has generated widespread concern because of the fundamental role that apex predators can play in ecosystem functioning, disease regulation, and biodiversity maintenance. In attempts to combat declines, managers have conducted reintroductions, imposed stricter harvest regulations, and implemented protected areas. We suggest that full recovery of viable apex predator populations is currently the exception rather than the rule. We argue that, in addition to well-known considerations, such as continued exploitation and slow life histories, there are several underappreciated factors that complicate predator recoveries. These factors include three challenges. First, a priori identification of the suite of trophic interactions, such as resource limitation and competition that will influence recovery can be difficult. Second, defining and accomplishing predator recovery in the context of a dynamic ecosystem requires an appreciation of the timing of recovery, which can determine the relative density of apex predators and other predators and therefore affect competitive outcomes. Third, successful recovery programs require designing adaptive sequences of management strategies that embrace key environmental and species interactions as they emerge. Consideration of recent research on food web modules, alternative stable states, and community assembly offer important insights for predator recovery efforts and restoration ecology more generally. Foremost among these is the importance of a social-ecological perspective in facilitating a long-lasting predator restoration while avoiding unintended consequences. ","tags":["Dynamics","Theory","Time-series"],"title":"Ecosystem context and historical contingency in apex predator recoveries","type":"publication"},{"authors":["Kurt Ingeman"],"categories":[],"content":"","date":1451606400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617376892,"objectID":"a8eaddc2ff442479e43b74fad600161f","permalink":"https://novaklabosu.github.io/publication/ingeman-2016-aa/","publishdate":"2021-04-02T15:21:32.794903Z","relpermalink":"/publication/ingeman-2016-aa/","section":"publication","summary":" There is increasing awareness that human activities are altering the ways that natural systems operate and that local shifts in species composition and abundance can lead to abrupt and irreversible global change. Therefore, understanding the processes that buffer biological communities from critical shifts and how our actions affect natural stabilizing feedbacks are important goals of ecology. One human activity with far reaching consequences for global ecosystems is the introduction of exotic species outside of their native ranges. Introduced predators, whose effects may be exacerbated by lack of shared evolutionary history with native prey, can have particularly strong effects on recipient communities. As trophic interactions play a central role in both population regulation and community persistence, it is essential to determine the extent to which introduction of novel predators can alter the function of stabilizing mechanisms.\n\nThe goals of this dissertation were to use a combination of manipulative field experiments and theoretical modeling to explore how introduced predators influence invaded communities through their effects on the processes that naturally maintain bounded prey population dynamics and promote community coexistence. Density- dependent predation can regulate prey populations by providing a negative feedback in response to changes in population size. In my first experiment (Chapter 2), I investigated the effects of invasive Indo-Pacific red lionfish (Pterois volitans) on density-dependent mortality patterns previously documented to regulate a common native Atlantic prey species, the fairy basslet (Gramma loreto) on coral reefs in the Bahamas. By repeating a pre-invasion density-manipulation experiment, now in the context of predation by both native piscivores and lionfish, I demonstrated that per capita loss of fairy basslet remained density-dependent in the presence of lionfish, but the overall magnitude of loss was substantially greater compared to pre-invasion rates. Per capita loss was higher in 13 out of 16 basslet populations with an average increase of over 60% in the presence of the invader. The before-and-after design provided no evidence for a change in the intensity of density dependence between experiments, indicating the addition of destabilizing density-independent mortality caused by lionfish.\n\nIn my second experiment (Chapter 3), I employed a split-plot, cross-factored experimental design, manipulating both fairy basslet density and lionfish presence/absence such that differences in per capita loss rates were attributable only to predation by the invader. Over four weeks, mortality of fairy basslet was far greater on lionfish reefs compared to reefs with only native predators, displaying 2.4 times higher net loss on recruitment-enhanced fairy basslet populations and a five- fold increase in net loss at unmanipulated prey populations. Per capita loss was density-dependent in both predator treatments, but high mortality rates at low prey density on lionfish reefs resulted in extirpation of 15% of unmanipulated fairy basslet populations. In contrast, no prey populations were extirpated on reefs with only native predators.\n\nIn addition to field experiments, this dissertation includes a theoretical model (Chapter 4) that explored the effects of predator novelty on the coexistence of an intraguild predation web with adaptive antipredator defense in the shared prey. Adaptive prey responses can promote multi-predator coexistence by creating a stabilizing tradeoff in the allocation of predator-specific defense effort. Yet to date, all such theory has assumed that prey have accurate perception of predation risk and appropriate antipredator responses, assumptions that may not be justified when considering a novel predator. The model showed that the parameter region of IGP coexistence is dramatically reduced by an exotic predator but that effects of novelty on community persistence are complex and context-dependent. Specifically, the model predicts that predator novelty can weaken the effect of adaptive defense, causing exclusion of native predators that would persist in the absence of novelty. Coexistence is predicted to be more sensitive to the effects of suboptimal defense compared to naïveté and differentially leads to exclusion of native predators in highly productive environments and when defense costs are low. Moderate novelty of the omnivore can increase resource density via a trophic cascade, while consumer novelty can either lead to omnivore exclusion or facilitate three-species coexistence by providing a subsidy to the otherwise excluded native omnivore. The results suggest that models of adaptive defense are sensitive to assumptions regarding predator-prey eco-evolutionary experience and that predator novelty has significant implications for food web dynamics.\n\nOverall, the research described in this dissertation illuminates the mechanisms by which introduced predators can disrupt the boundedness and persistence of otherwise stable systems and provides insight into how predator novelty can alter biological communities via novel trophic and non-trophic interactions. As natural systems across the globe face multiple stressors that can alter their functioning, it is increasingly vital to understand the stabilizing mechanisms that buffer these systems from change, and how species introductions may modify the capacity for communities to respond to natural and human-caused disturbance.","tags":["Dynamics","Subtidal","Theory"],"title":"Effects of predator introductions on population and community dynamics","type":"publication"},{"authors":["Kira Krumhansl","Dan Okamoto","Andy Rassweiler","Mark Novak","John Bolton","Kyle Cavanaugh","Sean Connell","Craig Johnson","Brenda Konar","Scott Ling","Fio Micheli","Kjell Norderhaug","Alejandro Pérez-Matus","Isabel Sousa-Pinto","Dan Reed","Anne Salomon","Nick Shears","Thomas Wernberg","Robert Anderson","Nevell Barrett","Alejandro Buschmann","Mark Carr","Jenn Caselle","Sandrine Derrien-Courtel","Graham Edgar","Matt Edwards","Jim Estes","Claire Goodwin","Mike Kenner","David Kushner","Frithjof Moy","Julia Nunn","Robert Steneck","Julio Vásquez","Jane Watson","Jon Witman","Jarrett Byrnes"],"categories":[],"content":"  ","date":1451606400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371663,"objectID":"618dd0537702e8fb8e1d9d6f02883440","permalink":"https://novaklabosu.github.io/publication/krumhansl-2016-sb/","publishdate":"2021-04-02T13:54:23.146872Z","relpermalink":"/publication/krumhansl-2016-sb/","section":"publication","summary":" Kelp forests (Order Laminariales) form key biogenic habitats in coastal regions of temperate and Arctic seas worldwide, providing ecosystem services valued in the range of billions of dollars annually. Although local evidence suggests that kelp forests are increasingly threatened by a variety of stressors, no comprehensive global analysis of change in kelp abundances currently exists. Here, we build and analyze a global database of kelp time series spanning the past half-century to assess regional and global trends in kelp abundances. We detected a high degree of geographic variation in trends, with regional variability in the direction and magnitude of change far exceeding a small global average decline (instantaneous rate of change = −0.018 y−1). Our analysis identified declines in 38% of ecoregions for which there are data (−0.015 to −0.18 y−1), increases in 27% of ecoregions (0.015 to 0.11 y−1), and no detectable change in 35% of ecoregions. These spatially variable trajectories reflected regional differences in the drivers of change, uncertainty in some regions owing to poor spatial and temporal data coverage, and the dynamic nature of kelp populations. We conclude that although global drivers could be affecting kelp forests at multiple scales, local stressors and regional variation in the effects of these drivers dominate kelp dynamics, in contrast to many other marine and terrestrial foundation species. ","tags":["Times-series","Dynamics","Subtidal"],"title":"Global patterns of kelp forest change over the past half-century","type":"publication"},{"authors":["Julia Bingham"],"categories":[],"content":"","date":1451606400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617376892,"objectID":"228e25864601c675827bb7b814419849","permalink":"https://novaklabosu.github.io/publication/bingham-2016/","publishdate":"2021-04-02T15:21:28.098015Z","relpermalink":"/publication/bingham-2016/","section":"publication","summary":" Current human – ocean relationships are dominated by unsustainable extraction of marine resources having both ecological and socio-economic consequences. Sustainable fishery management utilizing stakeholder collaboration must become a proactive strategy to prevent or reduce further long-lasting impacts. In Oregon, USA, a newly developing fishery for gooseneck barnacle (Pollicipes polymerus) presents a real-world opportunity to reframe fisheries management. Commercial gooseneck fishing in Oregon requires the development of harvest management to prevent patterns of gooseneck overharvest seen historically in Europe, but relevant scientific information on the natural population dynamics and life-history of Oregon goosenecks is lacking. To begin filling this need, I studied the spatial and temporal variability of life history patterns and population structure of _Pollicipes polymerus_ at several sites along the central Oregon coast. I documented (i) significant correlation between regional differences in oceanography and gooseneck population density (ii) site-specific variation in the size-frequency distribution of individuals, particularly in the fraction of individuals of harvestable size, (iii) seasonality in population brooding patterns, and (iv) slow rates of population recovery spanning multiple years in a manipulative harvest simulation experiment on natural substrates. These findings suggest future necessary scientific investigations of P. polymerus populations and support preliminary sustainable harvest management design in Oregon. ","tags":["Intertidal"],"title":"Sensitive barnacles - A case study for collaborative sustainable fishery development","type":"publication"},{"authors":["Isaac Shepard"],"categories":[],"content":"","date":1451606400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617376892,"objectID":"ffe5dd7885862ceb012f7fd29a8d938e","permalink":"https://novaklabosu.github.io/publication/shepard-2016/","publishdate":"2021-04-02T15:21:28.098015Z","relpermalink":"/publication/shepard-2016/","section":"publication","summary":" Understanding ecological interaction strengths is one of the main objectives of ecology. Recently, two methods for estimating interaction strengths of predator- prey interactions in nature have been proposed: a field observation approach proposed by Novak and Wootton (2008) and stable isotope analysis. The field observation method estimates feeding rates based on feeding observations, handling times and prey abundances. Stable isotope analysis estimates diet proportions using mixing models of ratios of heavy to light carbon and nitrogen isotopes in body tissues of predators and their prey. However, because these two methods are relatively new, few studies have been conducted to understand and contrast their estimates of interaction strengths. I sought to quantify the correlation between the estimates of interaction strength made by the two methods. Both methods were conducted simultaneously in a rocky intertidal community on the Oregon coast with the whelk Nucella ostrina as the focal predator and the barnacle Balanus glandula and the mussel Mytilus trossulus as the two primary prey species. I documented a non-significant and weak correlation between the two method’s estimates of interaction strength. I hypothesize that this lack of correspondence between the methods may be explained by abnormal δ13C enrichment in the whelks compared to their prey, and a lack of variation in observed predator diets between replicate sample populations. ","tags":["Intertidal","Stable isotopes","Interaction strength"],"title":"Using stable isotopes to quantify species interaction strengths","type":"publication"},{"authors":["Jonathan Borrelli","Stefano Allesina","Priyanga Amarasekare","Roger Arditi","Ivan Chase","John Damuth","Robert Holt","Dmitrii Logofet","Mark Novak","Rudolf Rohr","Axel Rossberg","Matthew Spencer","Khai Tran","Lev Ginzburg"],"categories":[],"content":"","date":1420070400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371661,"objectID":"50606e2c2c0bb9e00d793d36fc00ba90","permalink":"https://novaklabosu.github.io/publication/borrelli-2015-cy/","publishdate":"2021-04-02T13:54:21.066942Z","relpermalink":"/publication/borrelli-2015-cy/","section":"publication","summary":" Much of the focus in evolutionary biology has been on the adaptive differentiation among organisms. It is equally important to understand the processes that result in similarities of structure among systems. Here, we discuss examples of similarities occurring at different ecological scales, from predator–prey relations (attack rates and handling times) through communities (food-web structures) to ecosystem properties. Selection among systemic configurations or patterns that differ in their intrinsic stability should lead generally to increased representation of relatively stable structures. Such nonadaptive, but selective processes that shape ecological communities offer an enticing mechanism for generating widely observed similarities, and have sparked new interest in stability properties. This nonadaptive systemic selection operates not in opposition to, but in parallel with, adaptive evolution. ","tags":["Dynamics","Ecosystem stability","Theory"],"title":"Selection on stability across ecological scales","type":"publication"},{"authors":["Mark Novak","Tim Tinker"],"categories":[],"content":"","date":1420070400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371665,"objectID":"dd7e78599d390713c1b990070c5da48e","permalink":"https://novaklabosu.github.io/publication/novak-2015-ef/","publishdate":"2021-04-02T13:54:25.657571Z","relpermalink":"/publication/novak-2015-ef/","section":"publication","summary":" Many populations consist of individuals that differ substantially in their diets. Quantification of the magnitude and temporal consistency of such intraspecific diet variation is needed to understand its importance, but the extent to which different approaches for doing so reflect instantaneous vs. time-aggregated measures of individual diets may bias inferences. We used direct observations of sea otter individuals (_Enhydra lutris nereis_) to assess how: (1) the timescale of sampling, (2) under-sampling, and (3) the incidence- vs. frequency-based consideration of prey species affect the inferred strength and consistency of intraspecific diet variation. Analyses of feeding observations aggregated over hourly to annual intervals revealed a substantial bias associated with time aggregation that decreases the inferred magnitude of specialization and increases the inferred consistency of individuals’ diets. Time aggregation also made estimates of specialization more sensitive to the consideration of prey frequency, which decreased estimates relative to the use of prey incidence; time aggregation did not affect the extent to which under-sampling contributed to its overestimation. Our analyses demonstrate the importance of studying intraspecific diet variation with an explicit consideration of time and thereby suggest guidelines for future empirical efforts. Failure to consider time will likely produce inconsistent predictions regarding the effects of intraspecific variation on predator–prey interactions. ","tags":["Subtidal","Intraspecific variation"],"title":"Timescales alter the inferred strength and temporal consistency of intraspecific diet specialization","type":"publication"},{"authors":["Rebecca Terry","Mark Novak"],"categories":[],"content":"","date":1420070400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371668,"objectID":"4cc503a0dcd7325b3b0b489010559d13","permalink":"https://novaklabosu.github.io/publication/terry-2015-lb/","publishdate":"2021-04-02T13:54:28.003869Z","relpermalink":"/publication/terry-2015-lb/","section":"publication","summary":" Knowing how time is distributed within a fossil record is fundamental to paleobiology. Many efforts to quantify temporal resolution have estimated rates of specimen decay from the frequency distribution of specimen ages in near-surface assemblages. The implicit assumption has been that the shape of these distributions is invariant with depth and thus decay-rate estimates reflect the temporal resolution of a fossil record’s deeper layers as well. Here we present a new model that predicts how age-frequency distribution shape will change with depth due to the interplay of burial, mixing, and decay. Unlike previous models, this model distinguishes the dimensions of time, specimen age, and depth, and predicts a right-to-left shift in age-frequency distribution skewness, and a decrease in kurtosis, with increasing stratigraphic depth. We find support for these predictions with the accelerator mass spectrometry 14C dating of 80 small mammal specimens spanning the Quaternary fossil record of Homestead Cave, Utah (United States). Our study indicates (1) that previous models overestimate rates of specimen decay, (2) that the acuity of ecological information captured in near-surface assemblages is higher than previously inferred, and (3) how time-averaging can alter the apparent dynamics of biodiversity over time. We thereby offer a new quantitative framework to account for time-averaging, to merge modern and paleontological archives, and to place ecological systems within the context of their past dynamics. ","tags":["Paleontology"],"title":"Where does the time go?: Mixing and the depth-dependent distribution of fossil ages","type":"publication"},{"authors":["Rodrigo Beas-Luna","Mark Novak","Mark Carr","Tim Tinker","August Black","Jenn Caselle","Michael Hoban","Dan Malone","Alison Iles"],"categories":["Data"],"content":"","date":1388534400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371660,"objectID":"e6b4506d46ebcf0ca32415eec440b92c","permalink":"https://novaklabosu.github.io/publication/beas-luna-2014-cv/","publishdate":"2021-04-02T13:54:15.711257Z","relpermalink":"/publication/beas-luna-2014-cv/","section":"publication","summary":" Ecological network models and analyses are recognized as valuable tools for understanding the dynamics and resiliency of ecosystems, and for informing ecosystem-based approaches to management. However, few databases exist that can provide the life history, demographic and species interaction information necessary to parameterize ecological network models. Faced with the difficulty of synthesizing the information required to construct models for kelp forest ecosystems along the West Coast of North America, we developed an online database ([http://kelpforest.ucsc.edu/](http://kelpforest.ucsc.edu/)) to facilitate the collation and dissemination of such information. Many of the database's attributes are novel yet the structure is applicable and adaptable to other ecosystem modeling efforts. Information for each taxonomic unit includes stage-specific life history, demography, and body-size allometries. Species interactions include trophic, competitive, facilitative, and parasitic forms. Each data entry is temporally and spatially explicit. The online data entry interface allows researchers anywhere to contribute and access information. Quality control is facilitated by attributing each entry to unique contributor identities and source citations. The database has proven useful as an archive of species and ecosystem-specific information in the development of several ecological network models, for informing management actions, and for education purposes (e.g., undergraduate and graduate training). To facilitate adaptation of the database by other researches for other ecosystems, the code and technical details on how to customize this database and apply it to other ecosystems are freely available and located at the following link ([https://github.com/kelpforest-cameo/databaseui](https://github.com/kelpforest-cameo/databaseui)). ","tags":["Subtidal","Food webs","Networks"],"title":"An Online Database for Informing Ecological Network Models: http://kelpforest.ucsc.edu","type":"publication"},{"authors":["Hamza Moulvi"],"categories":[],"content":"","date":1388534400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617376892,"objectID":"5c93b4151e7d2d82ae00c6b93ee15563","permalink":"https://novaklabosu.github.io/publication/moulvi-2014/","publishdate":"2021-04-02T15:21:28.098015Z","relpermalink":"/publication/moulvi-2014/","section":"publication","summary":" Kelp forests serve as an integral abode for aquatic species. Kelp forests are one of the most productive terrestrial systems, providing its denizens the conditions necessary for growth. Wave action allows for the constant motion of the seaweed, which provides maximum sunlight exposure and contact with nutrients.\n\nThe kelp forest ecosystem is a complex one. The understanding of the interactions between members of this unique ecosystem can be facilitated through the use of data visualization, a mode through which big data sets — such as the kelp forest — can be better understood.\n\nThis particular research project focuses on the kelp forests off the California coast, work that is funded by the NSF/NOAA CAMEO program, and is being conducted by OSU in conjunction with the UCSC, USGS, PISCO, and NOAA.\n\nPrevious work has looked at the visualization of this data through the use of D3.js — a javascript library that allows for the creation of dynamic data visualizations — which led to the creation of a network visualization that illustrated the relationship amongst the diverse species found in the kelp forest. While this visualization highlights all the different types of interactions between species, the sheer number of species existent in the SQL database presented a large visualization, one that resulted in a slow load time, as well as a degree of difficulty in parsing the visualization to gain useful insights.\n\nOne of the goals with this work was to improve the load time with this particular visualization. Another was to expand the visualizations available through the exploration of a matrix visualization, which would contribute an increased understanding regarding the relationships between species. ","tags":["Networks"],"title":"Complex networks in kelp forest ecosystems - Visualizing big data","type":"publication"},{"authors":["Mike Kenner","Jim Estes","Tim Tinker","James Bodkin","Bob Cowen","Chris Harrold","Brian Hatfield","Mark Novak","Andy Rassweiler","Dan Reed"],"categories":["Data"],"content":"","date":1356998400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371662,"objectID":"aa0bf97616bfb52b6515f3454d99b17f","permalink":"https://novaklabosu.github.io/publication/kenner-2013-co/","publishdate":"2021-04-02T13:54:22.606886Z","relpermalink":"/publication/kenner-2013-co/","section":"publication","summary":" San Nicolas Island is surrounded by broad areas of shallow subtidal habitat, characterized by dynamic kelp forest communities that undergo dramatic and abrupt shifts in community composition. Although these reefs are fished, the physical isolation of the island means that they receive less impact from human activities than most reefs in Southern California, making San Nicolas an ideal place to evaluate alternative theories about the dynamics of these communities. Here we present monitoring data from seven sampling stations surrounding the island, including data on fish, invertebrate, and algal abundance. These data are unusual among subtidal monitoring data sets in that they combine relatively frequent sampling (twice per year) with an exceptionally long time series (since 1980). Other outstanding qualities of the data set are the high taxonomic resolution captured and the monitoring of permanent quadrats and swaths where the history of the community structure at specific locations has been recorded through time. Finally, the data span a period that includes two of the strongest ENSO events on record, a major shift in the Pacific decadal oscillation, and the reintroduction of sea otters to the island in 1987 after at least 150 years of absence. These events provide opportunities to evaluate the effects of bottom‐up forcing, top‐down control, and physical disturbance on shallow rocky reef communities. ","tags":["Dynamics","Time-series","Subtidal"],"title":"A multi-decade time series of kelp forest community structure at San Nicolas Island, California (USA)","type":"publication"},{"authors":["Mark Novak"],"categories":[],"content":"","date":1356998400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371665,"objectID":"842c1c5a6a95cb8030933820556560fa","permalink":"https://novaklabosu.github.io/publication/novak-2013-qg/","publishdate":"2021-04-02T13:54:25.440318Z","relpermalink":"/publication/novak-2013-qg/","section":"publication","summary":" Intraguild predation theory centres on two predictions: (i) for an omnivore and an intermediate predator (IG-prey) to coexist on shared resources, the IG-prey must be the superior resource competitor, and (ii) increasing resource productivity causes the IG-prey's equilibrium abundance to decline. I tested these predictions with a series of species-rich food webs along New Zealand's rocky shores, focusing on two predatory whelks, _Haustrum haustorium_, a trophic omnivore, and _Haustrum scobina_, the IG-prey. In contrast to theory, the IG-prey's abundance increased with productivity. Furthermore, feeding rates and allometric considerations indicate a competitive advantage for the omnivore when non-shared prey are considered, despite the IG-prey's superiority for shared prey. Nevertheless, clear and regular cross-gradient changes in network structure and interaction strengths were observed that challenge the assumptions of current theory. These insights suggest that the consideration of consumer-dependent functional responses, non-equilibrium dynamics, the dynamic nature of prey choice and non-trophic interactions among basal prey will be fruitful avenues for theoretical development. ","tags":["Intertidal","Interaction strength","Functional response","Theory","Observational approach","Intraguild predation and trophic omnivory"],"title":"Trophic omnivory across a productivity gradient: intraguild predation theory and the structure and strength of species interactions","type":"publication"},{"authors":["Justin Yeakel","Paulo Guimarães","Mark Novak","Kena Fox-Dobbs","Paul Koch"],"categories":[],"content":"","date":1325376000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371669,"objectID":"99cd7ff413b9de8f3b60a911dda2792d","permalink":"https://novaklabosu.github.io/publication/yeakel-2012-vm/","publishdate":"2021-04-02T13:54:29.325429Z","relpermalink":"/publication/yeakel-2012-vm/","section":"publication","summary":" Patterns of species interactions affect the dynamics of food webs. An important component of species interactions that is rarely considered with respect to food webs is the strengths of interactions, which may affect both structure and dynamics. In natural systems, these strengths are variable, and can be quantified as probability distributions. We examined how variation in strengths of interactions can be described hierarchically, and how this variation impacts the structure of species interactions in predator–prey networks, both of which are important components of ecological food webs. The stable isotope ratios of predator and prey species may be particularly useful for quantifying this variability, and we show how these data can be used to build probabilistic predator–prey networks. Moreover, the distribution of variation in strengths among interactions can be estimated from a limited number of observations. This distribution informs network structure, especially the key role of dietary specialization, which may be useful for predicting structural properties in systems that are difficult to observe. Finally, using three mammalian predator–prey networks (two African and one Canadian) quantified from stable isotope data, we show that exclusion of link-strength variability results in biased estimates of nestedness and modularity within food webs, whereas the inclusion of body size constraints only marginally increases the predictive accuracy of the isotope-based network. We find that modularity is the consequence of strong link-strengths in both African systems, while nestedness is not significantly present in any of the three predator–prey networks. ","tags":["Theory","Interaction strength","Food webs","Networks"],"title":"Probabilistic patterns of interaction: the effects of link-strength variability on food web structure","type":"publication"},{"authors":["Tim Tinker","Paulo Guimarães","Mark Novak","Flavia Marquitti","James Bodkin","Michelle Staedler","Gena Bentall","Jim Estes"],"categories":[],"content":"","date":1325376000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371668,"objectID":"b2ec2e686c8fec6ed998aa493db111c8","permalink":"https://novaklabosu.github.io/publication/tinker-2012-xd/","publishdate":"2021-04-02T13:54:28.172316Z","relpermalink":"/publication/tinker-2012-xd/","section":"publication","summary":" Studies of consumer‐resource interactions suggest that individual diet specialisation is empirically widespread and theoretically important to the organisation and dynamics of populations and communities. We used weighted networks to analyze the resource use by sea otters, testing three alternative models for how individual diet specialisation may arise. As expected, individual specialisation was absent when otter density was low, but increased at high‐otter density. A high‐density emergence of nested resource‐use networks was consistent with the model assuming individuals share preference ranks. However, a density‐dependent emergence of a non‐nested modular network for ‘core’ resources was more consistent with the ‘competitive refuge’ model. Individuals from different diet modules showed predictable variation in rank‐order prey preferences and handling times of core resources, further supporting the competitive refuge model. Our findings support a hierarchical organisation of diet specialisation and suggest individual use of core and marginal resources may be driven by different selective pressures. ","tags":["Subtidal","Intraspecific variation","Networks"],"title":"Structure and mechanism of diet specialisation: testing models of individual variation in resource use with sea otters","type":"publication"},{"authors":["Laura Twardochleb","Mark Novak","Jon Moore"],"categories":[],"content":"","date":1325376000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371668,"objectID":"e3a9892c2d986c509fc5034048fbc505","permalink":"https://novaklabosu.github.io/publication/twardochleb-2012-ii/","publishdate":"2021-04-02T13:54:28.35861Z","relpermalink":"/publication/twardochleb-2012-ii/","section":"publication","summary":" Predators sometimes provide biotic resistance against invasions by nonnative prey. Understanding and predicting the strength of biotic resistance remains a key challenge in invasion biology. A predator's functional response to nonnative prey may predict whether a predator can provide biotic resistance against nonnative prey at different prey densities. Surprisingly, functional responses have not been used to make quantitative predictions about biotic resistance. We parameterized the functional response of signal crayfish (Pacifastacus leniusculus) to invasive New Zealand mud snails (Potamopyrgus antipodarum; NZMS) and used this functional response and a simple model of NZMS population growth to predict the probability of biotic resistance at different predator and prey densities. Signal crayfish were effective predators of NZMS, consuming more than 900 NZMS per predator in a 12‐h period, and Bayesian model fitting indicated their consumption rate followed a type 3 functional response to NZMS density. Based on this functional response and associated parameter uncertainty, we predict that NZMS will be able to invade new systems at low crayfish densities (0.2 crayfish/m2), we predict that low densities of NZMS will be able to establish in new communities; however, once NZMS reach a threshold density of ∼2000 NZMS/m2, predation by crayfish will drive negative NZMS population growth. Further, at very high densities, NZMS overwhelm predation by crayfish and invade. Thus, interacting thresholds of propagule pressure and predator densities define the probability of biotic resistance. Quantifying the shape and uncertainty of predator functional responses to nonnative prey may help predict the outcomes of invasions. ","tags":["Interaction strength","Functional response","Streams"],"title":"Using the functional response of a consumer to predict biotic resistance to invasive prey","type":"publication"},{"authors":["Justin Yeakel","Dirk Stiefs","Mark Novak","Thilo Gross"],"categories":[],"content":"","date":1293840000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371669,"objectID":"ef1cb25f300c2eee1d60c9a8a2f0041f","permalink":"https://novaklabosu.github.io/publication/yeakel-2011-uy/","publishdate":"2021-04-02T13:54:28.988805Z","relpermalink":"/publication/yeakel-2011-uy/","section":"publication","summary":" Over the past 7 years, several authors have used the approach of generalized modeling to study the dynamics of food chains and food webs. Generalized models come close to the efficiency of random matrix models, while being as directly interpretable as conventional differential-equation-based models. Here, we present a pedagogical introduction to the approach of generalized modeling. This introduction places more emphasis on the underlying concepts of generalized modeling than previous publications. Moreover, we propose a shortcut that can significantly accelerate the formulation of generalized models and introduce an iterative procedure that can be used to refine existing generalized models by integrating new biological insights. ","tags":["Theory","Dynamics","Ecosystem stability"],"title":"Generalized modeling of ecological population dynamics","type":"publication"},{"authors":["Justin Yeakel","Mark Novak","Paulo Guimarães","Nate Dominy","Paul Koch","Eric Ward","Jon Moore","Brice Semmens"],"categories":[],"content":"","date":1293840000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371669,"objectID":"8a26a654acbf9bcf4aa13430c0e29a60","permalink":"https://novaklabosu.github.io/publication/yeakel-2011-ib/","publishdate":"2021-04-02T13:54:29.163489Z","relpermalink":"/publication/yeakel-2011-ib/","section":"publication","summary":" Bayesian mixing models have allowed for the inclusion of uncertainty and prior information in the analysis of trophic interactions using stable isotopes. Formulating prior distributions is relatively straightforward when incorporating dietary data. However, the use of data that are related, but not directly proportional, to diet (such as prey availability data) is often problematic because such information is not necessarily predictive of diet, and the information required to build a reliable prior distribution for all prey species is often unavailable. Omitting prey availability data impacts the estimation of a predator's diet and introduces the strong assumption of consumer ultrageneralism (where all prey are consumed in equal proportions), particularly when multiple prey have similar isotope values. ","tags":["Stable isotopes","Interaction strength","Intertidal"],"title":"Merging Resource Availability with Isotope Mixing Models: The Role of Neutral Interaction Assumptions","type":"publication"},{"authors":["Mark Novak","Jon Moore","Robert Leidy"],"categories":[],"content":"","date":1293840000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371665,"objectID":"1d778a97055d383b91ea489b742b4e23","permalink":"https://novaklabosu.github.io/publication/novak-2011-ed/","publishdate":"2021-04-02T13:54:25.10578Z","relpermalink":"/publication/novak-2011-ed/","section":"publication","summary":" Many factors contribute to the nonrandom processes of extinctions and invasions that are changing the structure of ecological communities worldwide. These factors include the attributes of the species, their abiotic environment, and the interactions and feedbacks between them. The relative importance of these factors has been difficult to quantify. We used nested subset theory and a novel permutation‐based extension of gradient analysis to disentangle the direct and indirect pathways by which these factors affect the metacommunity structure of freshwater fishes inhabiting the streams tributary to the San Francisco Bay. Our analyses provide quantitative measures of how species and stream attributes may influence extinction vulnerability and invasion risk, highlight the need for considering the multiple interacting drivers of community change concurrently, and indicate that the ongoing disassembly and assembly of Bay Area freshwater fish communities are not fully symmetric processes. Fish communities are being taken apart and put back together in only partially analogous trajectories of extinction and invasion for which no single explanatory hypothesis is sufficient. Our study thereby contributes to the forecasting of continued community change and its effects on the functioning of freshwater ecosystems. ","tags":["Streams","Dynamics"],"title":"Nestedness patterns and the dual nature of community reassembly in California streams: a multivariate permutation-based approach","type":"publication"},{"authors":["Mark Novak","Tim Wootton","Dan Doak","Mark Emmerson","Jim Estes","Tim Tinker"],"categories":[],"content":"","date":1293840000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371665,"objectID":"70f37f36d841e893609055a3d883b2b1","permalink":"https://novaklabosu.github.io/publication/novak-2011-qh/","publishdate":"2021-04-02T13:54:25.278468Z","relpermalink":"/publication/novak-2011-qh/","section":"publication","summary":" How best to predict the effects of perturbations to ecological communities has been a long‐standing goal for both applied and basic ecology. This quest has recently been revived by new empirical data, new analysis methods, and increased computing speed, with the promise that ecologically important insights may be obtainable from a limited knowledge of community interactions. We use empirically based and simulated networks of varying size and connectance to assess two limitations to predicting perturbation responses in multispecies communities: (1) the inaccuracy by which species interaction strengths are empirically quantified and (2) the indeterminacy of species responses due to indirect effects associated with network size and structure. We find that even modest levels of species richness and connectance (∼25 pairwise interactions) impose high requirements for interaction strength estimates because system indeterminacy rapidly overwhelms predictive insights. Nevertheless, even poorly estimated interaction strengths provide greater average predictive certainty than an approach that uses only the sign of each interaction. Our simulations provide guidance in dealing with the trade‐offs involved in maximizing the utility of network approaches for predicting dynamics in multispecies communities. ","tags":["Theory","Dynamics","Community matrix","Press perturbations","Networks"],"title":"Predicting community responses to perturbations in the face of imperfect knowledge and network complexity","type":"publication"},{"authors":["Donald DeAngelis","Gail Wolkowicz","Yuan Lou","Yuexin Jiang","Mark Novak","Richard Svanbäck","Márcio Araújo","YoungSeung Jo","Erin Cleary"],"categories":[],"content":"","date":1293840000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371661,"objectID":"111ee8b9730167a35a81c41da8bd4975","permalink":"https://novaklabosu.github.io/publication/de-angelis-2011-vp/","publishdate":"2021-04-02T13:54:21.448312Z","relpermalink":"/publication/de-angelis-2011-vp/","section":"publication","summary":"A key assumption of the ideal free distribution (IFD) is that there are no costs in moving between habitat patches. However, because many populations  exhibit more or less continuous population movement between patches and traveling  cost is a frequent factor, it is important to determine the effects of costs on  expected population movement patterns and spatial distributions. We consider a food  chain (tritrophic or bitrophic) in which one species moves between patches, with  energy cost or mortality risk in movement. In the two-patch case, assuming forced  movement in one direction, an evolutionarily stable strategy requires bidirectional movement, even if costs during movement are high. In the N-patch case, assuming  that at least one patch is linked bidirectionally to all other patches, optimal  movement rates can lead to source-sink dynamics where patches with negative growth  rates are maintained by other patches with positive growth rates. As well, dispersal  between patches is not balanced (even in the two-patch case), leading to a deviation  from the IFD. Our results indicate that cost-associated forced movement can have  important consequences for spatial metapopulation dynamics. Relevance to marine reserve design and the study of stream communities subject to drift is discussed.","tags":["Intraspecific variation","Theory"],"title":"The Effect of Travel Loss on Evolutionarily Stable Distributions of Populations in Space","type":"publication"},{"authors":["Dan Bolnick","Priyanga Amarasekare","Márcio Araújo","Reinhold Bürger","Jonathan Levine","Mark Novak","Volker Rudolf","Sebastian Schreiber","Mark Urban","David Vasseur"],"categories":[],"content":"","date":1293840000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371661,"objectID":"5564982e2d7c24156d7ebdd6cbfd8a29","permalink":"https://novaklabosu.github.io/publication/bolnick-2011-zf/","publishdate":"2021-04-02T13:54:20.896427Z","relpermalink":"/publication/bolnick-2011-zf/","section":"publication","summary":" Natural populations consist of phenotypically diverse individuals that exhibit variation in their demographic parameters and intra- and inter-specific interactions. Recent experimental work indicates that such variation can have significant ecological effects. However, ecological models typically disregard this variation and focus instead on trait means and total population density. Under what situations is this simplification appropriate? Why might intraspecific variation alter ecological dynamics? In this review we synthesize recent theory and identify six general mechanisms by which trait variation changes the outcome of ecological interactions. These mechanisms include several direct effects of trait variation per se and indirect effects arising from the role of genetic variation in trait evolution. ","tags":["Intraspecific variation"],"title":"Why intraspecific trait variation matters in community ecology","type":"publication"},{"authors":["Mark Novak"],"categories":[],"content":"","date":1262304000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371664,"objectID":"aab5ddf932fed5858db322f0f5ad07d3","permalink":"https://novaklabosu.github.io/publication/novak-2010-ch/","publishdate":"2021-04-02T13:54:24.765643Z","relpermalink":"/publication/novak-2010-ch/","section":"publication","summary":" The complexity of food webs poses a significant hurdle for our growing understanding of the structure and dynamics of ecological communities. Empirical methods that measure the per capita strengths of trophic species interactions offer a means to identify keystone species and bridge mathematical models and data to synthesize our knowledge of population dynamics and predator feeding behaviors. Many such methods have been proposed, but few have seen independent validation of their estimates or underlying assumptions. This is particularly so with respect to the nonlinear functional responses by which predators often respond to their prey. Here I describe an empirical test of a recently proposed observational method for estimating the nonlinear strength of predator–prey interactions in the field. By applying the method to two populations of a predatory intertidal whelk, Haustrum scobina, I estimated its per capita attack rates on all nine of its observed prey species. These spanned two orders of magnitude in per capita strength. Concurrent experimental manipulations of the two predator populations provided population time series for the response of a mussel prey species, Xenostrobus pulex. I obtained independent interaction strength estimates for this focal interaction by fitting a sequence of hypothesized predator–prey models to these time series. Overall, site‐specific models assuming linear functional responses performed better than all others. A direct comparison of the attack‐rate estimates from the observational method with those of the best‐performing nonlinear model nevertheless revealed high concordance between the two methods. The results of this study therefore support the use of the observational method in larger and more complex food webs and suggest that trophic interactions in the range of mean prey densities observed in nature are approximately linear. ","tags":["Intertidal","Interaction strength","Functional response","Observational approach"],"title":"Estimating interaction strengths in nature: experimental support for an observational approach","type":"publication"},{"authors":["Mark Novak","Tim Wootton"],"categories":[],"content":"","date":1262304000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371665,"objectID":"a2ad40de4d38af9c520288b21e0f4840","permalink":"https://novaklabosu.github.io/publication/novak-2010-km/","publishdate":"2021-04-02T13:54:24.938296Z","relpermalink":"/publication/novak-2010-km/","section":"publication","summary":" Few methods for demonstrating the effects of species interactions rival that of the manipulative experiment (Kareiva and Levin 2002). The now commonly performed removal or addition of predators, competitors, or mutualists to experimentally replicated populations of recipient species has irrefutably shown that species can have important effects on each other's populations, and that the strengths of these effects can vary considerably across environmental contexts and species identities. A large body of research is directed towards understanding this variation to forecast community dynamics and dissect how species interactions regulate community structure (Chesson 2000, McCann 2000, Stachowicz 2001, Duffy 2002). It has frequently been pointed out that progress in this field will require more explicit connections between ecological theory and the realities of nature (Laska and Wootton 1998, Parker et al. 1999, Berlow et al. 2004, Agrawal et al. 2007). This requires that interaction strengths measured experimentally be appropriate to the biology of our study systems and the mathematical abstractions we ascribe to them.\n\nHere we clarify some of the assumptions made in the application of the two most commonly used indices for measuring the strengths of species interactions with manipulative removal/addition experiments: Paine's index and the dynamic index. We explain how the values these indices are intended to measure – the per capita interaction strength between two species – are typically not estimated in common currencies. We then introduce extensions to these indices that alleviate a subset of previously made assumptions and limitations. These include a reformulation of Paine's index appropriate for an open‐recruitment system, and an extension of the dynamic index applicable to interactions of a particular nonlinear form. While we focus our language on predator–prey interactions, our discussions are pertinent to the measurement of species effects in other types of interactions as well (Mitchell and Wass 1996, Freckleton et al. 2009). ","tags":["Theory","Functional response","Interaction strength"],"title":"Using experimental indices to quantify the strength of species interactions","type":"publication"},{"authors":["Mark Novak","Tim Wootton"],"categories":[],"content":"","date":1199145600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371664,"objectID":"6427c7ea9ccc6a7ea04a8b6d0ccddbe7","permalink":"https://novaklabosu.github.io/publication/novak-2008-nw/","publishdate":"2021-04-02T13:54:24.280088Z","relpermalink":"/publication/novak-2008-nw/","section":"publication","summary":" Efforts to estimate the strength of species interactions in species‐rich, reticulate food webs have been hampered by the multitude of direct and indirect interactions such systems exhibit and have been limited by an assumption that pairwise interactions display linear functional forms. Here we present a new method for directly measuring, on a per capita basis, the nonlinear strength of trophic species interactions within such food webs. This is an observation‐based method, requiring three pieces of information: (1) species abundances, (2) predator and prey‐specific handling times, and (3) data from predator‐specific feeding surveys in which the number of individuals observed feeding on each of the predator's prey species has been tallied. The method offers a straightforward way to assess the completeness of one's sampling effort in accurately estimating interaction strengths through the construction of predator‐specific prey accumulation curves. The method should be applicable to a variety of systems in which empirical estimates of direct interaction strengths have thus far remained elusive. ","tags":["Interaction strength","Theory","Functional response","Observational approach"],"title":"Estimating nonlinear interaction strengths: an observation-based method for species-rich food webs","type":"publication"},{"authors":["Mark Novak"],"categories":[],"content":"","date":1199145600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371664,"objectID":"fdce7282882ba8af9c10d427b773d1cb","permalink":"https://novaklabosu.github.io/publication/novak-2008-wo/","publishdate":"2021-04-02T13:54:24.462548Z","relpermalink":"/publication/novak-2008-wo/","section":"publication","summary":" Two elements of food webs add significantly to their complexity:  The presence of trophic omnivores and the nonlinear nature of predator-prey interactions. I introduce a new observational method for estimating the strengths of species interactions that accounts for the indeterminacy of omnivorous indirect effects and the saturating functional responses that predators exhibit. I present an empirical validation of the method’s accuracy by applying it to two populations of the predatory whelk, Haustrum (= Lepsiella) scobina, that is common to the rocky intertidal shores of New Zealand, and comparing these interaction strength estimates with those derived from concurrently performed experimental manipulations of H. scobina’s populations.\n\nI then test two key predictions of intraguild predation theory by investigating how species abundances, food web structure and species interactions strengths change across six omnivorous food webs along a gradient of productivity present around New Zealand’s coastline. I find that the intermediate predator, H. scobina, is the superior competitor for shared prey species, as predicted by theory.  Counter to theory, however, I show that it is the omnivorous whelk, H. haustorium, that is the superior competitor when all prey are considered, and that H. scobina’s abundance increases with increasing productivity. My analyses nevertheless reveal clear and regular cross-gradient shifts in interactions that can be incorporated into future modeling efforts.\n\nFinally, I ask to what degree whelk feeding rates are saturated with respect to prey densities and, by extending and parameterizing the classic Rosenzweig-MacArthur model, ask whether empirical interactions are nonlinear enough to affect the stability of whelk-prey dynamics. Results indicate that whelk feeding rates are not strongly saturated and that increasing diet richness has a non-additive effect on a predator’s saturation such that alternative prey have a stabilizing effect on whelk-prey dynamics.  I thereby offer a new mechanism by which generalist predators stabilize the dynamics of their species-rich food webs that does not invoke prey switching.\n\nMy dissertation brings empirical data to bear on the importance of omnivory and the nonlinear nature of trophic interactions. Furthering our understanding of these food web features can contribute much to both the conceptual and applied goals of ecology. ","tags":["Intertidal","Theory","Interaction strength","Food webs","Networks","Observational approach"],"title":"Trophic omnivory and the structure, strength, and nonlinear nature of species interactions across a productivity gradient","type":"publication"},{"authors":["Dan Doak","Jim Estes","Ben Halpern","Ute Jacob","David Lindberg","James Lovvorn","Daniel Monson","Tim Tinker","Terri Williams","Tim Wootton","Ian Carroll","Mark Emmerson","Fio Micheli","Mark Novak"],"categories":[],"content":"","date":1199145600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371661,"objectID":"f4fc69b505a55836adfe617cdf9eddb5","permalink":"https://novaklabosu.github.io/publication/doak-2008-kx/","publishdate":"2021-04-02T13:54:21.774481Z","relpermalink":"/publication/doak-2008-kx/","section":"publication","summary":" Ecological surprises, substantial and unanticipated changes in the abundance of one or more species that result from previously unsuspected processes, are a common outcome of both experiments and observations in community and population ecology. Here, we give examples of such surprises along with the results of a survey of well‐established field ecologists, most of whom have encountered one or more surprises over the course of their careers. Truly surprising results are common enough to require their consideration in any reasonable effort to characterize nature and manage natural resources. We classify surprises as dynamic‐, pattern‐, or intervention‐based, and we speculate on the common processes that cause ecological systems to so often surprise us. A long‐standing and still growing concern in the ecological literature is how best to make predictions of future population and community dynamics. Although most work on this subject involves statistical aspects of data analysis and modeling, the frequency and nature of ecological surprises imply that uncertainty cannot be easily tamed through improved analytical procedures, and that prudent management of both exploited and conserved communities will require precautionary and adaptive management approaches. ","tags":["Dynamics"],"title":"Understanding and predicting ecological dynamics: are major surprises inevitable","type":"publication"},{"authors":["Mark Novak"],"categories":[],"content":"","date":1072915200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371664,"objectID":"57bcd829012bd7470d2cd90bb9016a20","permalink":"https://novaklabosu.github.io/publication/novak-2004-df/","publishdate":"2021-04-02T13:54:24.116711Z","relpermalink":"/publication/novak-2004-df/","section":"publication","summary":" The patterns of diel activity of four large decapod species in the shallow subtidal of the Isles of Shoals, Gulf of Maine, U.S.A. were investigated. During the summer of 1999 the diel abundance and size distribution of active decapod individuals were surveyed at three depth ranges at a sheltered site on Appledore Island. Densities of active American lobsters, _Homarus americanus_ H. Milne Edwards, 1837, were, as expected, highest at night. The crabs _Cancer borealis_ Stimpson, 1859 and _Carcinus maenas_ (L., 1758), however, were almost exclusively active during the day. _Cancer irroratus_ Say, 1817 were equally active during the day and the night, but the mean size of individuals was significantly larger during the day. Surveys at additional sites in 2003 confirmed that these same patterns of diel activity were present throughout the Isles of Shoals. An extensive review of the literature suggests that such diurnal activity is not only unusual for the three crab species of this study, but for the whole genus Cancer as well. ","tags":["Subtidal"],"title":"Diurnal activity in a group of Gulf of Maine decapods","type":"publication"},{"authors":["Mark Novak"],"categories":[],"content":"","date":946684800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1617371664,"objectID":"16ecde9b349bf6342cf1fca156b32273","permalink":"https://novaklabosu.github.io/publication/novak-2000-gd/","publishdate":"2021-04-02T13:54:23.944491Z","relpermalink":"/publication/novak-2000-gd/","section":"publication","summary":" On the rocky shores of the Gulf of Maine, the American lobster, Homarus americanus, the Jonah crab, Cancer borealis, the Rock crab, Cancer irroratus, and the Green crab, Carcinus maenas, compose a guild of highly mobile predators. Although the species are potential competitors that consume the same prey and utilize the same shelters, lobsters also prey on crabs (i.e., lobsters are intraguild predators of crabs). During daytime low tides, crabs are also preyed upon by Larus spp. gulls. In this study, I investigated the importance of avian and intraguild predation in influencing the diel and spatial (depth) patterns of decapod activity in the algal-covered lower intertidal and subtidal zones of Appledore Island, Maine, USA. During the summer months of 1999, the diel abundance and size distribution of active individuals was measured at several depths for each decapod species. Densities of active lobsters were highest at night and did not vary with depth. Contrary to prevailing knowledge, C. borealis and C. maenas were active almost exclusively during the day. While diurnal C. borealis were significantly more abundant in the deepest zone (9-11 m), C. maenas was not found at this depth and was most abundant in the shallowest zone (0-1 m). Day and night C. irroratus densities were not significantly different and showed no significant variation with depth. Only C. irroratus populations exhibited a diel difference in the mean size of individual crabs. The mean size of individuals observed during the day was larger than those observed at night. During the day, C. borealis were larger at depths of 9-11 m than at depths of 1-3 m, while C. maenas crabs were larger at depths of 5-7 m than at depths of 0-1 m.\nThe magnitude of avian predation was assessed by censuses of crab remains collected in the intertidal during periods of low tide. Results reinforce previous studies in suggesting that gulls are a major factor limiting the upper distribution of C. borealis. In the subtidal, the relative availability of potential shelters does not appear to account for the depth distributions observed among the species. The presence of a potentially sheltering Codium algal canopy at 1 to 7 m may be important for C. maenas and C. irroratus. A subtidal tethering experiment with C. borealis and C. irroratus revealed no diel or depth differences in crab survival. Overall, rates of predation were very low, but were significantly higher for small than for large crabs. Besides lobsters, no other predators were observed at the study site; predation on tethered crabs was therefore attributed to lobsters. In laboratory experiments exposing pairs of small and large C. borealis and C. irroratus to lobsters, small crabs were shown to be significantly more vulnerable to predation than large conspecifics; C. borealis and C. irroratus of similar size were equally vulnerable. Large crabs, however, were attacked 71 times more often than were small crabs. The results of this study reinforce concerns that traditional models of rocky shore community organization must be amended to include mobile predators. They indicate that competitive interactions between small crabs and lobsters may be unimportant relative to intraguild predation. For large crabs, perceived nocturnal intraguild predation pressures may be just as important as competitive interactions between guild members, especially in the recent absence of predatory fishes. These results underline the importance of understanding the ecological history of the community. They suggest that the overfishing of coastal fish populations has increased the relative importance of intraguild interactions and has thereby indirectly strengthened the link between marine and terrestrial ecosystems. ","tags":["Subtidal"],"title":"Intraguild and extraguild predations: implications for the diel activity and distribution of four large decapod species","type":"publication"},{"authors":null,"categories":null,"content":"","date":-62135596800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":-62135596800,"objectID":"f26b5133c34eec1aa0a09390a36c2ade","permalink":"https://novaklabosu.github.io/admin/config.yml","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/admin/config.yml","section":"","summary":"","tags":null,"title":"","type":"wowchemycms"},{"authors":null,"categories":null,"content":"Have you proposed a modeling chapter for your dissertation but need support getting things up and running? Will you soon be sitting on a complete data set ready for your planned analyses but don’t know how or where to begin? Maybe you’re far along in a series of analyses and feel “lost in the trees.”\nThis course will help you with these challenges by practicing the development and implementation of efficient, reproducible workflows for your projects. Every project should (and can) be modular and fully automated, hence reproducible, portable and easily modified. Rerunning an analysis with a different set of parameters should (and can) be as simple as a few keystrokes. Regenerating all figures and tables for your manuscript after finding a typo in your code or dataset should (and can) be painless.\nEfficient workflows start at project conception and end only if the project idea is itself a dead end. Thus, in this course, we’ll work to practice (1) refining and articulating project goals and benchmarks, (2) creating modular and automated analyses, and (3) using best practices in coding and project management. We’ll learn how to use Git, GitHub, LaTeX, Markdown, and high performance clusters (HPCs). The instructors will mostly use R within RStudio, but users of other programming languages and text editors are welcome and encouraged. You will need either (1) a dataset and a visualization or analysis goal, or (2) a model or simulation (or sufficiently well-developed ideas for one). The use of other people’s data or published models is also encouraged, as needed.\nAll teaching materials for this course are available on GitHub.\n","date":-62135596800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":-62135596800,"objectID":"95cf706f78daf24e44361c7e60cbda4f","permalink":"https://novaklabosu.github.io/courses/analyticalworkflows/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/courses/analyticalworkflows/","section":"courses","summary":"Tools and best-practices for efficient project managment","tags":["Graduate"],"title":"Analytical Workflows (IB516)","type":"courses"},{"authors":null,"categories":null,"content":"Course description A workshop-style short-course at the Rocky Mountain Biological Laboratory aiming to introduce basic concepts and tools for the statistical integration of the mathematical models and empirical data for characterizing species interactions.\nSee https://models4data2theory.github.io for details.\n","date":-62135596800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":-62135596800,"objectID":"bce093d309189278043d07240bd9fc00","permalink":"https://novaklabosu.github.io/courses/rmbl/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/courses/rmbl/","section":"courses","summary":"Workshop at RMBL on integrating theory and data on species interactions","tags":["Graduate"],"title":"Data-Theory Integration","type":"courses"},{"authors":null,"categories":null,"content":"Course description This ecology course consists of an introduction to the scientific study of the processes that shape the distribution, structure and dynamics of species and their communities. Topics include the methods and approaches of ecological research, the interactions between species and their abiotic and biotic environments, the distribution of biodiversity across the globe, the processes regulating population growth, species extinctions and invasions and their implications for conservation and the maintenance of ecosystem services, and the varied and profound impacts of humans on ecological systems.\nCourse objectives By the end of this course, you will be able to: (i) discuss how organisms interact with their biotic and abiotic environments, (ii) infer the processes that structure patterns of biodiversity from local to global scales, (iii) explain how ecological systems are dynamic in space and time based on knowledge of process, (iv) evaluate climate change and the future of biodiversity in the context of Earth’s past record of climate and life, (v) inform others of how anthropogenic activities are impacting the structure and functioning of natural systems, (vi) valuate alternative strategies for the conservation of biodiversity and ecosystem services, and (vii) describe the fundamental role of quantitative reasoning (statistics and modeling) in ecology.\n","date":-62135596800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":-62135596800,"objectID":"6764a8d12097e4d76e875337462c042a","permalink":"https://novaklabosu.github.io/courses/ecology/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/courses/ecology/","section":"courses","summary":"Distribution, structure and dynamics of species, communities and ecosystems","tags":["Undergraduate"],"title":"Ecology (BI370)","type":"courses"},{"authors":null,"categories":null,"content":"Course description This course consists of an introduction to the physical, chemical and biological aspects of life in the oceans, with an ecological emphasis. Topics include the methods of scientific inquiry, the interactions between organisms and their abiotic and biotic environments, the processes regulating populations and communities, local to global patterns of biodiversity, and the varied and profound impacts that we humans are having on all marine systems.\nCourse objectives By the end of this course, you will be able to: (i) disentangle the processes that structure patterns of marine biodiversity from local to global scales, (ii) evaluate ongoing environmental changes facing marine systems and their implications for future biodiversity, (iii) inform others of how anthropogenic activities are impacting the structure and functioning of marine systems, (iv) evaluate strategies for the conservation of marine biodiversity, and (v) appreciate and describe the amazing diversity of lifeforms that inhabit marine environments.\n","date":-62135596800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":-62135596800,"objectID":"827cbc4802deb24c2d590220de9c6e1c","permalink":"https://novaklabosu.github.io/courses/marineecology/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/courses/marineecology/","section":"courses","summary":"Physical, chemical and biological aspects of life in the oceans, with an ecological emphasis","tags":["Undergraduate"],"title":"Marine Ecology (BI351)","type":"courses"},{"authors":null,"categories":[],"content":" Quantitative Ecology (UCSC, w/ Tim Tinker) Long-term Ecology (seminar, w/ Bruce Menge) What is Systems Biology? (seminar, w/ Becky Vega-Thurber and Virginia Weis) Eco-Evolutionary Dynamics (seminar) Analytical Workflows (seminar w/ Ben Dalziel)  ","date":-62135596800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":-62135596800,"objectID":"2ad37993aacd016cf09d155eef630f77","permalink":"https://novaklabosu.github.io/courses/past/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/courses/past/","section":"courses","summary":"Courses and seminars of the past","tags":[],"title":"Past courses","type":"courses"},{"authors":null,"categories":null,"content":"Develop the skills and strategies for efficiently producing clear and effective scientific manuscripts. We’ll cover the full writing process, from establishing productive writing habits and managing writing workflows to selecting journals and navigating the peer review and publication process. We’ll examine writing habits, best practices, reference managers, and alternative writing and word-processing tools. And we’ll do all that while you work on writing your own scientific manuscript, emphasizing practical, hands-on learning and peer accountability.\nAll materials for this course are available on GitHub.\n","date":-62135596800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":-62135596800,"objectID":"061ca20893fac37ed88a94a684fae720","permalink":"https://novaklabosu.github.io/courses/scientificwriting/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/courses/scientificwriting/","section":"courses","summary":"Skills and strategies for scientific writing","tags":["Graduate"],"title":"Scientific Writing (IB514)","type":"courses"},{"authors":null,"categories":null,"content":"Undergraduate students who are interested in participating in this course should email me with a brief summary of their interests and goals for taking part.\nCourse description This course entails a quantitative treatment of the central concepts and applications of theoretical ecology. Emphasis is on the mathematical analysis and modeling of single populations and multi-species interactions, and the integration of models with data. Topics include discrete- and continuous-time models of population growth, stochastic and deterministic processes of unstructured populations, the sustainability of harvested populations, numerical and analytical investigations of population and community invasibility and stability, and an introduction to model-fitting and comparison in an information-theoretic framework.\nCourse objectives Our goals will be to (i) peel away at any apprehensions of mathematical equations you may have, (ii) enable you to independently interpret the classic and modern literature of theoretical ecology, and (iii) enable you to apply analytical and simulation-based approaches in evaluating ecological questions of your own interest and communicate these to an audience of your peers. You’ll complete the course with a working knowledge of R and Mathematica.\n","date":-62135596800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":-62135596800,"objectID":"374245b0f3f6cad0caed68d8137a6c8f","permalink":"https://novaklabosu.github.io/courses/theoreticalecology/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/courses/theoreticalecology/","section":"courses","summary":"Analysis of dynamical systems, from single populations to species-rich communities","tags":["Graduate"],"title":"Theoretical Ecology (IB592)","type":"courses"}]