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Low Paternal Genetic Diversity in Domestic Horses Likely Due to Selective Breeding

NEW YORK (GenomeWeb) – Today's domestic horses are genetically diverse on the maternal side, as indicated by their mitochondrial DNA, but their genetic diversity is extremely limited on the paternal side, represented by their Y chromosomes.

A team led by researchers at the Leibniz Institute for Zoo and Wildlife Research in Berlin, Germany, has now shed new light on how the domestication of horses over the last few thousand years led to this decrease in Y chromosome variability.

In a paper published in Science Advances today, the researchers, led by senior author Arne Ludwig in the Leibniz Institute's Department of Evolutionary Genetics, describe the results of a Y chromosome genotyping study of almost 100 ancient DNA samples from stallions across Eurasia that span the last 5,000 years.    

For their study, they analyzed 350 ancient horse DNA samples from China; Mongolia; Siberia; eastern, middle, and northern Europe; and the Iberian Peninsula. The age of the samples, which ranged from the Neolithic and Copper Age to the Middle Ages, was determined by radiocarbon dating or from the archeological context. Using PCR-based amplification and either Illumina MiSeq or Sanger sequencing, the researchers successfully genotyped 16 single nucleotide polymorphism loci on the Y chromosome in 96 of the samples.

Besides the Y-HT-1 haplotype that dominates current domestic horses, they found two new haplotypes — Y-HT-3 and Y-HT-4 — and, somewhat to their surprise, the Y-HT-2 haplotype that is also found in the Przewalski wild horse.

To gauge how Y-chromosome variation changed over time, the team divided the samples into four time periods: older than 2,200 BC; 2,200 BC to 900 BC; 900 BC to 400 AD; and younger than 400 AD.

The first time period had all haplotypes except Y-HT-1 present, which might be explained by the fact that it only included samples from Europe and not farther East. The Y-HT-2 haplotype was most frequent during that period. Over time, the Y-HT-1 haplotype became more common, getting to be the most frequent haplotype during the third period and almost completely taking over in the last period. Haplotypes Y-HT-3 and Y-HT-4, which were present in the first three periods, disappeared completely in the fourth, whereas Y-HT-2 disappeared during the third period but was present in one sample from the last period.

While the data did not allow the researchers to pinpoint the geographical origin of the Y-HT-1 haplotype, it might have either emerged in the domestic horse population by mutation or entered it through wild horses at the beginning or during domestication, the authors wrote. The fact that the estimated age of this haplotype is the same as the start of horse domestication — around 4,000 BC to 3,500 BC — suggests, though, that the Y-HT-1 haplotype came from within the domestic population.

Y-HT-1 took over starting in the Bronze Age, when humans migrated across Eurasia, "undoubtedly facilitated by the spread of horses as a means of transport and warfare," they wrote, and during the Iron Age, when the Roman Empire ruled Europe and changed breeding customs from female-based to male-based selective breeding.

The start of the Y-HT-1 expansion, they noted, correlated with the spread of the Yamnaya culture from the Pontic-Caspian steppe, which has been called the center of horse domestication. "Given the importance of domestic horses, it appears that deliberate selection/rejection of certain stallions by these people might have contributed to the loss of paternal diversity," they wrote.

Several additional analyses, assuming different demographic scenarios, further showed that the loss of paternal diversity was most likely caused by deliberate breeding rather than by genetic drift.

Presumably, Y-HT-1 offered some advantage over Y-HT-4, to which it is similar. "With Y-HT-4 probably being older than Y-HT-1, it seems possible that the selective advantage of Y-HT-4 was retained in Y-HT-1, which then acquired its own additional advantageous mutations and, consequently, an even higher selective value," the authors speculated, noting that future research could try to explain what phenotypic traits the two haplotypes possibly exhibited that breeders could select for.