Comparative Mitochondrial Genomics and Phylogenetic Analysis

This task focuses on the comparative analysis of mitochondrial genomes from different species, primarily birds, mammals, and insects. The aim is to understand the evolutionary relationships between these species by analyzing and comparing their mitochondrial DNA, which is about 16,000 base pairs in length. You will use advanced computational methods to construct phylogenetic trees and delve into the ecological and anthropological insights that can be gleaned from this data. This project is designed to provide a comprehensive understanding of mitochondrial genomics, its importance in evolutionary biology, and its applications in broader scientific contexts.

You will learn:

• Techniques for aligning and comparing mitochondrial DNA sequences.
• How to construct and interpret phylogenetic trees using advanced computational methods.
• The application of mitochondrial genomics in understanding ecological interactions and human evolutionary history.

Task Roadmap

1. Mitochondrial Genome Comparison:

   • Align mitochondrial DNA sequences from the provided dataset.
   • Analyze these sequences to identify similarities and differences across species.

2. Phylogenetic Analysis Using Advanced Methods:

   • Apply Maximum Likelihood (ML) and Bayesian Inference methods, utilizing tools like ETE Toolkit, DendroPy, BEAST, or PyRate.
   • Compare the trees generated by these methods to understand how different approaches can lead to different interpretations of the data.

3. Cross-Disciplinary Applications (Bonus):

   • Ecology: Examine how mitochondrial DNA analysis can reveal information about species adaptation, migration, and conservation. This involves understanding how genetic variation within and between species can inform ecological strategies and conservation efforts.
   • Anthropology: Investigate the use of mitochondrial DNA in tracing human evolution and migration patterns. This includes studying the mitochondrial DNA of mammals in your dataset to draw parallels with human evolutionary studies.

Data Sources

The mitochondrial DNA data for birds, mammals, and insects will be provided to you. This dataset has been curated to facilitate a comprehensive comparative analysis and is essential for the completion of your phylogenetic studies.

Useful Resources and Material

• Mitochondrial DNA - Wikipedia: A general introduction to the structure, function, origin, and diversity of mitochondrial DNA, as well as its applications in various fields such as medicine, forensics, and anthropology.
• Mitochondrial DNA Analysis: Introduction, Methods, and Applications: An explanation of the basics of mitochondrial DNA sequencing, bioinformatics analysis, heteroplasmy, and advantages of mitochondrial DNA analysis over nuclear DNA analysis.
• Phylogenetic Tree- Definition, Types, Steps, Methods, Uses - Microbe Notes: A coverage of the concepts and methods of phylogenetic tree construction, including the types of phylogenetic trees, the steps involved in phylogenetic analysis, the main methods of phylogenetic inference, and the applications of phylogenetic trees in various disciplines.
• Phylogenetics - Wikipedia: An overview of the field of phylogenetics, which is the study of the evolutionary history and relationships among or within groups of organisms. It also discusses the data sources, models, algorithms, software, and challenges of phylogenetic analysis.
• ETE Toolkit: A Python library for manipulating, analyzing, and visualizing phylogenetic trees. It supports various formats, methods, and tools for phylogenetic analysis, such as alignment, tree inference, tree comparison, tree annotation, and tree visualization.
• DendroPy: Another Python library for phylogenetic computing. It provides a comprehensive API for working with phylogenetic data structures, such as trees, characters, and networks. It also offers a rich set of functions for simulation, manipulation, analysis, and annotation of phylogenetic data.