Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse

Abstract

The rich fossil record of equids has made them a model for evolutionary processes. Here we present a 1.12-times coverage draft genome from a horse bone recovered from permafrost dated to approximately 560-780 thousand years before present (kyr BP). Our data represent the oldest full genome sequence determined so far by almost an order of magnitude. For comparison, we sequenced the genome of a Late Pleistocene horse (43 kyr BP), and modern genomes of five domestic horse breeds (Equus ferus caballus), a Przewalski's horse (E. f. przewalskii) and a donkey (E. asinus). Our analyses suggest that the Equus lineage giving rise to all contemporary horses, zebras and donkeys originated 4.0-4.5 million years before present (Myr BP), twice the conventionally accepted time to the most recent common ancestor of the genus Equus. We also find that horse population size fluctuated multiple times over the past 2 Myr, particularly during periods of severe climatic changes. We estimate that the Przewalski's and domestic horse populations diverged 38-72 kyr BP, and find no evidence of recent admixture between the domestic horse breeds and the Przewalski's horse investigated. This supports the contention that Przewalski's horses represent the last surviving wild horse population. We find similar levels of genetic variation among Przewalski's and domestic populations, indicating that the former are genetically viable and worthy of conservation efforts. We also find evidence for continuous selection on the immune system and olfaction throughout horse evolution. Finally, we identify 29 genomic regions among horse breeds that deviate from neutrality and show low levels of genetic variation compared to the Przewalski's horse. Such regions could correspond to loci selected early during domestication.

Biologically and diagenetically derived peptide modifications in moa collagens

“…Consistent with previous analyses of ancient bone [8,14,15], we observe deamidation for both glutamine and asparagine (figure 4; electronic supplementary material, figure S4) that is incomplete (e.g. electronic supplementary material, figure S4) and may be, in part, derived from sample preparation.…”

“…Now, recent advances in high-resolution mass spectrometry have resulted in a renewed interest in the utility of proteins preserved in fossils (reviewed in [9]). Ancient proteomic studies have extended the age for which biomolecules and phylogenetically informative molecular sequences can be recovered to well beyond the hypothesized limit for DNA preservation [8,[10][11][12][13][14][15][16][17].…”

“…The first investigations into biomolecular preservation in fossils focused on proteins [1][2][3][4][5]; however, polymerase chain reaction (PCR) and other technological advances [6][7][8] resulted in genomic studies superseding those of proteins. Now, recent advances in high-resolution mass spectrometry have resulted in a renewed interest in the utility of proteins preserved in fossils (reviewed in [9]).…”

Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne

“…LC-MS/MS analysis was conducted on three (SI Appendix, Fig. S1) of the hominin bone specimens, as published previously for nonhominin bone specimens (19), as well as two additional analyses of one palaeoproteomic extract generated following a modified protein extraction protocol (52). We took measures to avoid and detect protein contamination throughout our palaeoproteomic workflow.…”

Human evolution: The Neanderthal in the family

“…Orlando and his team found that the preparation lost vast quantities of fragments. But with a few tweaks to the experimental protocol, such as reducing the extraction temperature, the researchers captured ten times more scraps of DNA than before -and produced a draft of the oldest genome on record 2 .…”