European Domestic Horses Originated in Two Holocene Refugia

Abstract

The role of European wild horses in horse domestication is poorly understood. While the fossil record for wild horses in Europe prior to horse domestication is scarce, there have been suggestions that wild populations from various European regions might have contributed to the gene pool of domestic horses. To distinguish between regions where domestic populations are mainly descended from local wild stock and those where horses were largely imported, we investigated patterns of genetic diversity in 24 European horse breeds typed at 12 microsatellite loci. The distribution of high levels of genetic diversity in Europe coincides with the distribution of predominantly open landscapes prior to domestication, as suggested by simulation-based vegetation reconstructions, with breeds from Iberia and the Caspian Sea region having significantly higher genetic diversity than breeds from central Europe and the UK, which were largely forested at the time the first domestic horses appear there. Our results suggest that not only the Eastern steppes, but also the Iberian Peninsula provided refugia for wild horses in the Holocene, and that the genetic contribution of these wild populations to local domestic stock may have been considerable. In contrast, the consistently low levels of diversity in central Europe and the UK suggest that domestic horses in these regions largely derive from horses that were imported from the Eastern refugium, the Iberian refugium, or both.

Mitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication

“…Moreover, its nucleotide (0.0070 ± 0.0003) and haplotype (0.809 ± 0.011) diversities in Europe are virtually identical to those diversities observed for the same haplogroup in Asia (0.0071 ± 0.0004 and 0.848 ± 0.016, respectively). These observations raise the possibility that at least one horse domestication event occurred in Western Europe, possibly in the Iberian Peninsula, which was also suggested by autosomal microsatellite variation in European horse breeds (36). …”

The Evolutionary Origin and Genetic Makeup of Domestic Horses

“…Interestingly, these regions still represent hotspots of genetic diversity for horses, as measured by heterozygosity levels and allelic richness at 12 autosomal microsatellites from 24 "traditional" breeds (e.g., native from specific regions). This continuity in the spatial patterns of genetic diversity suggests that local populations of wild horses from Iberia and the Pontic-Caspian steppes could have contributed to some extent to the genetic pool of modern-day European breeds (Warmuth et al 2011).…”

“…Only at that time, the horse population started to exhibit a certain degree of substructure within the Eurasian steppes and the Iberian Peninsula (Cieslak et al 2010). This ancient substructure is still faint but detectable today from autosomal microsatellites (Warmuth et al 2011), but recent selective breeding likely contributed to erode the corresponding signature at the mtDNA level. This is indirectly reflected by the Bayesian-skyline-plot (BSP) reconstructions (Drummond et al 2005), which show an almost constant effective population size over time, until the domestication started, and led to a continuous expansion (Lippold et al 2011a;Achilli et al 2012).…”

“…Fitting explicit stepping-stone scenarios of horse radiation to 26 microsatellite loci genotyped on 322 nonbreed animals, Warmuth et al (2012) found strongest support for domestication starting in the western Eurasian steppes (Warmuth et al 2012), in agreement with the earliest archaeological evidence (Outram et al 2009). The discovery of a second hotspot of microsatellite diversity among Iberian breeds recently revived the question of Iberia as a possible second domestication center (Warmuth et al 2011). It has been proposed, for instance, that the mtDNA haplogroup D1, which is the most-commonly found among Iberian and North-African barb horses, reflects local domestication in the Iberian Peninsula (Jansen et al 2002).…”

Twenty-five thousand years of fluctuating selection on leopard complex spotting and congenital night blindness in horses

“…It has previously been suggested that the genetic diversity of domestic animal species has been augmented through backcrossing with their wild ancestors [29], and a replacement of the original domestic mtDNA genomes with those from local wild boar populations has been demonstrated in early domestic pigs from Europe [30]. After their initial domestication, probably around 3500 BC in the North Caspian region [31], domestic horses were distributed very rapidly all over Eurasia, allowing incorporating of local genetic diversity of the respective wild populations into the domestic gene pool.…”