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

Abstract

23 A major challenge in zooarchaeology is to morphologically distinguish closely related species’ 24 remains, especially using small bone fragments. Shotgun sequencing aDNA from archeological 25 remains and comparative alignment to the candidate species’ reference genomes will only apply 26 when reference nuclear genomes of comparable quality are available, and may still fail when 27 coverages are low. Here, we propose an alternative method, MTaxi, that uses highly accessible 28 mitochondrial DNA (mtDNA) to distinguish between pairs of closely related species from 29 ancient DNA sequences. MTaxi utilises mtDNA transversion-type substitutions between pairs of 30 candidate species, assigns reads to either species, and performs a binomial test to determine the 31 sample taxon. We tested MTaxi on sheep/goat and horse/donkey data, between which 32 zooarchaeological classification can be challenging in ways that epitomise our case. The method 33 performed efficiently on simulated ancient genomes down to 0.5x mitochondrial coverage for 34 both sheep/goat and horse/donkey, with no false positives. Trials on n=18 ancient sheep/goat 35 samples and n=10 horse/donkey samples of known species identity with mtDNA coverages 0.1x 36 - 12x also yielded 100% accuracy. Overall, MTaxi provides a straightforward approach to 37 classify closely related species that are compelling to distinguish through zooarchaeological 38 methods using low coverage aDNA data, especially when similar quality reference genomes are 39 unavailable. MTaxi is freely available at https://github.com/goztag/MTaxi. 40 bioRxiv preprint doi: https://doi.org/10.1101/2022.06.06.491147; this version posted June 6, 2022. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. 41