MTaxi: A comparative tool for taxon identification of ultra low coverage ancient genomes

Abstract

A major challenge in zooarchaeology is to morphologically distinguish closely related species’ remains, especially using small bone fragments. Shotgun sequencing aDNA from archeological remains and comparative alignment to the candidate species’ reference genomes will only apply when reference nuclear genomes of comparable quality are available, and may still fail when coverages are low. Here, we propose an alternative method, MTaxi, that uses highly accessible mitochondrial DNA (mtDNA) to distinguish between pairs of closely related species from ancient DNA sequences. MTaxi utilises mtDNA transversion-type substitutions between pairs of candidate species, assigns reads to either species, and performs a binomial test to determine the sample taxon. We tested MTaxi on sheep/goat and horse/donkey data, between which zooarchaeological classification can be challenging in ways that epitomise our case. The method performed efficiently on simulated ancient genomes down to 0.3x mitochondrial coverage for both sheep/goat and horse/donkey, with no false positives. Trials on n=18 ancient sheep/goat samples and n=10 horse/donkey samples of known species identity also yielded 100% accuracy. Overall, MTaxi provides a straightforward approach to classify closely related species that are difficult to distinguish through zooarchaeological methods using low coverage aDNA data, especially when similar quality reference genomes are unavailable. MTaxi is freely available at https://github.com/goztag/MTaxi.

Archaeology meets environmental genomics: implementing sedaDNA in the study of the human past

“…Likewise, sedaDNA may help to increase spatial coverage of historical distribution maps of wild species, as well as -on a more local scale- assessment of their presence in the surroundings of humans. A drawback of using sedaDNA for the detection of specific domesticated or wild variants of a taxon is that such variants may be hard to distinguish in case of low DNA yields from a certain taxon, quality or availability of references, postmortem damage (Atağ et al 2022 ) and in some cases when samples have DNA from multiple closely related taxa.…”

Archaeology meets Environmental Genomics: implementing sedaDNA in the study of the human past

“…Likewise, sedaDNA may help to increase spatial coverage of historical distribution maps of wild species, as well as -on a more local scale-assessment of their presence in the surroundings of humans. A drawback of using sedaDNA for the detection of speci c domesticated or wild variants of a taxon is that such variants may be hard to distinguish in case of low DNA yields from a certain taxon, quality or availability of references, postmortem damage (Atağ et al, 2022) and in some cases when samples have DNA from multiple closely related taxa.…”