MTAXI: A COMPARATIVE TOOL FOR TAXON IDENTIFICATION OF ULTRA LOW COVERAGE ANCIENT GENOMES

Date

2023-9-17

Author

Atağ, Gözde

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Taxon identification of closely related species based on morphology using skeletal remains is a challenging task, especially when the remains are fragmented. If the species pair to be identified both have similarly good quality nuclear reference genomes, ancient DNA (aDNA) extracted from the remains can be shotgun sequenced, and a comparative alignment to both references can be of use. However, this may also fail with low coverage data. Here, we present a novel, alternative method, MTaxi, which works with highly accessible mitochondrial DNA (mtDNA). MTaxi utilizes mitochondrial transversion type substitutions in order to assign the sequence reads of candidate species pairs to one of the taxa, does a binomial test to the proportion of reads and determines the sample taxon. Sheep/goat and horse/donkey data are suitable to test MTaxi on, as their zooarcheological classification can be problematic in ways that exemplify the case. On simulated ancient genomes, MTaxi was successful with down to 0.3x mtDNA coverage for both species, without any false positives. We also tested our tool on real ancient sheep/goat and horse/donkey samples, which again yielded 100% accuracy. Overall, MTaxi provides a simple but effective approach for the classification of closely related species pairs, using ultra low coverage aDNA data.

Subject Keywords

Ancient DNA, Bioinformatics, Mitochondrial DNA, Taxon identification

URI

https://hdl.handle.net/11511/105524

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Graduate School of Natural and Applied Sciences, Thesis