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"Deciphering the domestication and speciation of horses through next-generation paleogenomics using Pleistocene specimens, modern breeds and the domesticated donkey"

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Genome of the ancient horse revealed

EU research has funded the analysis of the genome of a horse that lived 700 thousand years ago, around the time when many large mammals became extinct.

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Horses have a rich fossil record and offer a unique opportunity to understand the genetic processes behind domestication as well as new species formation in the wild. Palaeogenetic information could lead the way to conservation of Przewalski's horses, the last surviving subspecies of wild horse, now threatened by extinction. Currently, there are about 250 horses living wild. The NGP (Deciphering the domestication and speciation of horses through next-generation paleogenomics using Pleistocene specimens, modern breeds and the domesticated donkey) project used the latest massively parallel sequencing technologies available. Third generation sequencing analysed not only the 700 kilo years before present (KYBP) horse from the mid-Pleistocene but six modern horse genomes including Przewalski's horse, five domestic breeds and a modern donkey. Authenticity of the genomes was confirmed using data from autosomal and Y chromosomes as well as from mitochondrial DNA. A tool, mapDamage, was the theme of a peer-reviewed paper published by the project. The system distinguishes between ancient DNA in the fossil and genetic material from microbes as well as nucleotides from post mortem damage. Analysis of the mid-Pleistocene DNA allowed the researchers to recalibrate the time when the most recent common ancestor of the horse and the donkey roamed the plains. In reality, this ranged from four to four and a half million years ago. This is twice the time commonly used. Przewalski's horse genome showed that it diverged from domestic horses as long ago as 72 KYBP and moreover, didn't show recent signs of interbreeding with its modern counterparts. This one remaining wild horse has a genetic diversity comparable with domestic breeds. Most of the 1 500 Przewalski's horses live in captivity and this data justifies current conservation efforts and reintroduction into the wild. NGP has shown that accessing palaeogenomes from as far back in time as the mid-Pleistocene is feasible. Application of state-of-the-art sequencing methods will lead to the next generation of palaeogenomes that have so far been inaccessible. This has significant implications for deciphering the mysteries of evolutionary biology.

Keywords

Genome, ancient horse, Przewalski's horses, mid-Pleistocene, conservation

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