Archaeogenomics of Anatolian wild ass

Date

2023-7

Author

Özkan, Mustafa

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European wild ass (E. h. hydruntinus or hydruntines) puzzled scientists since their first discovery nearly a century ago. Taxonomy, population history, and extinction mechanisms of this species are not clear since they show a mixture of characteristics of other asses and ancient DNA research focusing on hydruntines utilized mitochondrial sequences so far. In this thesis, I present three nuclear genomes of hydruntines excavated from Iron Age Central Anatolia. The material of this work involves three equid genomes from Çadır Höyük and Çatalhöyük, of unknown species identity. I generated genomes of coverage 6.38x-0.57x. Using this data I defined their status as wild asses. The collective evidence showed that these three individuals were hydruntines. Because no nuclear genome data has yet been published for this species, this allowed me to study the phylogenetic and demographic history of this species for the first time. These analyses confirmed that hydruntines and hemiones/hemippes from Gobi/Tibet and the Middle East region were sister taxa. I next showed that hydruntines (as represented by the three Anatolian individuals) had a distinct gene pool from hemiones, onagers, and hemippus; with the latter, Asian asses sharing more genetic drift with each other than with hydruntines. Whole genome analyses also suggested that hydruntines from Anatolia and Middle Eastern subspecies of hemiones experienced a gene flow event. Next, I inspected homozygous tracks and heterozygosity levels of the Anatolian hydruntine genome to elucidate extinction dynamics. These analyses showed a decrease in heterozygosity and an increase in homozygous regions relative to extant Asian wild asses, in accordance with a declining population scenario. In this thesis, I thus shed light on the population genomics of hydruntines. I showed that these last known hydruntines experienced a population decline before going extinct, as zooarchaeologists predicted.

Subject Keywords

Ancient DNA, Equus hydruntinus, demography, taxonomy, population genetics

URI

https://hdl.handle.net/11511/104890

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Graduate School of Natural and Applied Sciences, Thesis