Biology subjects

Arbuckle, B. S.

Publications and source records attributed to Arbuckle, B. S..

3 recordsLinked to original sources

bioRxiv2023

The first complete genome of the extinct European wild ass (Equus hemionus hydruntinus)

We present paleogenomes of three morphologically-unidentified Anatolian equids dating to the 1st millennium BCE, sequenced to coverages of 0.6-6.4X. Mitochondrial DNA haplotypes of the Anatolian individuals clustered with those of Equus hydruntinus (or Equus hemionus hydruntinus), the extinct European wild ass. The Anatolian wild ass whole genome profiles fall outside the genomic diversity of other extant and past Asiatic wild ass (E.hemionus) lineages. These observations strongly suggest that the three Anatolian wild asses represent E.hydruntinus, making them the latest recorded survivors of this lineage, about a millennium later than the latest observations in the zooarchaeological record. Comparative genomic analyses suggest that E.hydruntinus was a sister clade to all ancient and present-day E.hemionus lineages, representing an early split. We also find indication of gene flow between hydruntines and Middle Eastern wild asses. Analyses of genome-wide heterozygosity and runs of homozygosity reveal that the Anatolian wild ass population had severely lost genetic diversity by the mid-1st millennium BCE, a likely omen of its eventual demise.

genomics↗

bioRxiv2022

A novel lineage of the Capra genus discovered in the Taurus Mountains of Turkey using ancient genomics.

AO_SCPLOWBSTRACTC_SCPLOWDirekli Cave, located in the Taurus Mountains of southern Turkey, was occupied by Late Epipaleolithic hunters-gatherers for the seasonal hunting and processing of game including large numbers of wild goats. We report genomic data from new and published Capra specimens from Direkli Cave and, supplemented with historic genomes from multiple Capra species, find a novel lineage best represented by a [~]14,000 year old 2.59X genome sequenced from specimen Direkli4. This newly discovered Capra lineage is a sister clade to the Caucasian tur species (Capra cylindricornis and Capra caucasica), both now limited to the Caucasus region. We identify genomic regions introgressed in domestic goats with high affinity to Direkli4, and find that West Eurasian domestic goats in the past, but not those today, appear enriched for Direkli4-specific alleles at a genome-wide level. This forgotten "Taurasian tur" likely survived Late Pleistocene climatic change in a Taurus Mountain refugia and its genomic fate is unknown.

genomics↗

bioRxiv2016

Taming the Late Quaternary phylogeography of the Eurasiatic wild ass through ancient and modern DNA

Taxonomic over-splitting of extinct or endangered taxa, due to an incomplete knowledge of both skeletal morphological variability and the geographical ranges of past populations, continues to confuse the link between isolated extant populations and their ancestors. This is particularly problematic with the genus Equus. To more reliably determine the evolution and phylogeographic history of the endangered Asiatic wild ass, we studied the genetic diversity and inter-relationships of both extinct and extant populations over the last 100,000 years, including samples throughout its previous range from Western Europe to Southwest and East Asia. Using 229 bp of the mitochondrial hypervariable region, an approach which allowed the inclusion of information from extremely poorly preserved ancient samples, we classify all non-African wild asses into nine clades that show a clear phylogeographic structure revealing their phylogenetic history. This study places the extinct European wild ass, E. hydruntinus, the phylogeny of which has been debated since the end of the 19th century, into its phylogenetic context within the Asiatic wild asses and reveals recent gene flow events between populations currently regarded as separate species. The phylogeographic organization of clades resulting from these efforts can be used not only to improve future taxonomic determination of a poorly characterized group of equids, but also to identify historic ranges, interbreeding events between various populations, and the impact of ancient climatic changes. In addition, appropriately placing extant relict populations into a broader phylogeographic and genetic context can better inform ongoing conservation strategies for this highly endangered species.

evolutionary biology↗