Estimating the proportion of spurious alignments in ancient DNA as described in: de Filippo, Meyer and Prüfer, "Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences" BMC Biology 2018 16:121.
Although the method is applied directly to hominin DNA, it works with any spiecies as long as there is a close reference genome and some data of the variation within spieces.
For the time being have a look at the following link https://bioinf.eva.mpg.de/SpAl/ for a full description of the procedure.