Asian horses deepen the MSY phylogeny

Abstract

Humans have shaped the population history of the horse ever since domestication about 5500 years ago. Comparative analyses of the Y chromosome can illuminate the paternal origin of modern horse breeds. This may also reveal different breeding strategies that led to the formation of extant breeds. Recently, a horse Y-chromosomal phylogeny of modern horses based on 1.46 Mb of the male-specific Y (MSY) was generated. We extended this dataset with 52 samples from five European, two American and seven Asian breeds. As in the previous study, almost all modern European horses fall into a crown group, connected via a few autochthonous Northern European lineages to the outgroup, the Przewalski's Horse. In total, we now distinguish 42 MSY haplotypes determined by 158 variants within domestic horses. Asian horses show much higher diversity than previously found in European breeds. The Asian breeds also introduce a deep split to the phylogeny, preliminarily dated to 5527 ± 872 years. We conclude that the deep splitting Asian Y haplotypes are remnants of a far more diverse ancient horse population, whose haplotypes were lost in other lineages.

Chinese Mongolian horses may retain early domestic male genetic lineages yet to be discovered

“…(a) MSY haplotype network for 97 male horses [60 Chinese Mongolian horses from this study; 36 domestic horses and Przewalski's horse from Felkel et al . () and Wallner et al . ()].…”

“…; Felkel et al . ). Using these resources and taking into account the retention of ancient Y chromosome variation in Asian male horses (Felkel et al .…”

“…Using these resources and taking into account the retention of ancient Y chromosome variation in Asian male horses (Felkel et al . ), we tested the hypothesis that assessment of MSY variation in these long‐standing landrace populations may reveal a signature of ancient paternal variation that is now absent in many modern lineages.…”

“…Based on the allelic states at these 43 loci we inferred haplogroup clustering according to the network identified by Felkel et al . () by manually imputing the allelic state at 155 markers (Table ). The number of horses exhibiting each MSY haplotype and the frequencies of the MSY haplotypes in five Chinese Mongolian populations are provided in Fig.…”

“…The observed Chinese Mongolian MSY haplotypes were visualised using a median‐joining network generated with network 4.6.1.6 and by applying the MSY phylogeny generated by Felkel et al . () as a framework (Fig. a).…”