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Ancient Goat Genomes Reveal Multiple Source Populations During Domestication

NEW YORK (GenomeWeb) – A genomic analysis that included dozens of goat samples stretching back 8,000 years has offered a better look at the domestication processes and genetic diversity behind goat relationships with humans over more than 10,000 years.

Using mitochondrial and/or genome-wide sequence data for 83 wild and domestic goat remains from Southwest Asia's Fertile Crescent, researchers from the UK, Germany, Denmark, and elsewhere examined parts of the Capra genome that have been subject to selection during goat domestication. Their results, published online today in Science, also revealed several wild goat sources for populations of goats that were domesticated in different areas in and around the region.

"Goat domestication was a mosaic rather than a singular process with continuous recruitment from local wild populations," co-first author Pierpaolo Maisano Delser, a genetics and zoology researcher affiliated with Trinity College Dublin and the University of Cambridge, said in a statement. "This process generated a distinctive genetic pool which evolved across time and still characterizes the different goat populations of Asia, Europe and Africa today."

Past research has placed the domestication of goats, sheep, cattle, pigs, and other animals in and around the Fertile Crescent, the team noted. But in the case of goats, which were domesticated roughly 10,000 years ago, it remains unclear whether domestication occurred just once or from multiple populations.

With that in mind, the researchers did mitochondrial sequencing on 83 pre-Stone Age to Medieval goats from eastern, western, and southern sites surrounding the Fertile Crescent, including locations in Iran, Turkmenistan, Anatolia, the Balkans, Jordan, and Israel, generating nearly 71-fold average coverage from enriched mitochondrial genome samples. For the 51 ancient samples with the best DNA preservation, they also generated whole-genome sequences covered to depths of around 0.01- to almost 15-fold, on average.

When the team analyzed these sequences alongside those from ancient and modern samples from Africa, Europe, Asia, and the Middle East, it found that most of the domesticated ancient goats belonged to mitochondrial haplogroups that still exist in modern goats. In contrast, mitochondrial haplogroups appeared far more diverse in the oldest ancient goats from wild populations.

And from the haplogroup structures found in goats from early domestic populations, the researchers concluded that domestication involved wild goats from several distinct sites in the Fertile Crescent region over time — results supported by the genetic clusters formed with the available nuclear genome sequence data for the ancient goats.

"Our findings demonstrate that multiple divergent ancient wild goat sources were domesticated in a dispersed process that resulted in genetically and geographically distinct Neolithic goat populations, echoing contemporaneous human divergence across the region," the authors reported, noting that the "early goat populations contributed differently to modern goats in Asia, Africa, and Europe."

The researchers also compared sequences for half a dozen Neolithic goat genomes from the eastern part of this zone and four western Neolithic goat genomes, with sequences from 16 bezoar goat genomes from present-day goat populations, to search for domestication-related signs of selection.

That search highlighted 18 parts of the goat genome with enhanced divergence in the ancient and modern goats and increased diversity in the time since domestication — sites that included pigmentation or coat color-related genes such as KIT, KITLG, ASIP, and MITF, as well as genes linked to stature, milk production, and other reproductive or metabolic traits.

"We found evidence that at least as far back as 8,000 years ago, herders were interested in or valued the coat color of their animals, based on selection signals at pigmentation genes," first author Kevin Daly, a molecular population genetics researcher at Trinity College Dublin's Smurfit Institute of Genetics, said in a statement.

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