Asian horses deepen the MSY phylogeny

Area of Science:

• Genetics
• Animal Science
• Evolutionary Biology

Background:

• Human influence on horse population history dates back to domestication ~5500 years ago.
• Comparative Y chromosome analysis can reveal paternal origins and breeding strategies in modern horse breeds.
• Previous studies established a Y-chromosomal phylogeny for modern horses using male-specific Y (MSY) data.

Purpose of the Study:

• To extend the existing horse Y-chromosomal phylogeny with additional samples.
• To investigate the genetic diversity and paternal origins of Asian horse breeds.
• To understand the impact of different breeding strategies on horse population genetics.

Main Methods:

• Analysis of the male-specific Y (MSY) region from 52 additional horse samples across European, American, and Asian breeds.
• Phylogenetic analysis to construct a Y-chromosomal tree incorporating new and existing data.
• Identification and characterization of MSY haplotypes and genetic variants.

Main Results:

• Distinguished 42 MSY haplotypes based on 158 variants in domestic horses.
• Observed significantly higher genetic diversity in Asian horse breeds compared to European breeds.
• Identified a deep phylogenetic split in Asian haplotypes, dated to approximately 5527 ± 872 years ago.

Conclusions:

• Asian Y-chromosome haplotypes represent ancient lineages from a more diverse ancestral horse population.
• European horse breeds largely cluster into a crown group, with some Northern European connections to Przewalski's Horse.
• Genetic diversity patterns suggest significant loss of ancient haplotypes in non-Asian domestic horse lineages.