The international team, which included researchers from University of Copenhagen, BGI and other institutes, has successfully sequenced and analyzed the short pieces of DNA preserved in bone-remnants from a horse frozen for the last 700,000 years in the permafrost of Yukon, Canada. This is the oldest genome reported so far, which is ten times as old as the ancient Denisovan genome reported in last year. The work here laid a solid foundation for researchers to further decode other extinct species and clarify biology evolution.
The Thistle Creek horse fossil, found by Dr. Duane Froese from the University of Alberta in 2003, was from an interglacial organic unit associated with the Gold Run volcanic ash, about 700,000 years old–representing some of the oldest known ice in the northern hemisphere. DNA molecules can be well reserved in species fossils, not as whole chromosomes but as short pieces, while theoretical and empirical evidence suggest the age of this horse fossil approaches the upper limit of DNA survival.
After analysis, the ancient horse bone revealed secondary ion signatures typical of collagen within the bone matrix, including blood-derived peptides. This is consistent with good biomolecular preservation thus possible DNA survival. The team then conducted larger-scale destructive sampling for Illumina and Helicos sequencing to identify molecular preservation niches in the bone and experimental conditions that enabled finishing the whole genome sequence.
Compared with the genomes of a pre-domestication horse, a modern donkey, five modern domestic samples and one modern Przewalski horse, researchers found all contemporary horses, zebras and donkeys originated 4.0~4.5 million years ago– twice the conventionally accepted time to the most recent common ancestor of genus Equus. The study also shows that there were many demographic fluctuations occurred in horse populations in the past two million years, especially during the period of major climatic changes.
The study suggests that the Przewalski and domestic horse populations may diverge 38,000-72,000 years ago, and there is no cross-breeding between the two types of horses. All these findings also provide the evidence that the Przewalski does represent the last survivor of wild horses. The team also fond the evidence supporting the continuous selection of the immune system and olfaction throughout horse evolution, and dozens of genomic regions that are likely to be taken as genetic markers during the domestication.
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