Two hotspots for genetic diversity in horses identified

April 2, 2011

by Neil Clarkson

Two areas provided wild horses with refuge during the Holocene epoch, when large tracts of Europe were forested, researchers have found.


An Exmoor pony. Researchers say traditional British breeds show less genetic diversity than breeds originating from Iberia and the Caspian Sea.
Vast tracts of Europe were densely forested during the Holocene epoch, from around 11,700 years ago to about 10,000 years ago, providing an unsuitable environment for wild horses.

Researchers found two genetic hotspots which they believe ultimately contributed signficantly to Europe's domestic horse breeds.

The findings of the researchers from Britain, Spain, the United States, Germany, Switzerland, Portugal and Poland are a result of genetic analysis of 24 different European horse breeds.

The findings of the researchers, led by Vera Warmuth, from the University of Cambridge in England, have been published in the open-access journal, PLoS ONE.

They found genetic evidence that pointed to the Eastern steppes and the Iberian Peninsula as providing refuge to wild horses during the Holocene.

The role of European wild horses in horse domestication is poorly understood, the researchers noted.

"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," they wrote.

To distinguish between regions where domestic populations were mainly descended from local wild stock and those where horses were largely imported, the researchers investigated patterns of genetic diversity in 24 European horse breeds genetically typed at 12 different locations.

The distribution of high levels of genetic diversity in Europe coincided with the distribution of predominantly open landscapes before domestication, with breeds from Iberia and the Caspian Sea region having significantly higher genetic diversity than breeds from central Europe and Britain, which were largely forested at the time the first domestic horses appear there.

Results suggest that not only the Eastern steppes, but also the Iberian Peninsula provided refugia - an area that escaped ecological changes occurring elsewhere - 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 Britain suggest that domestic horses in these regions largely derive from horses imported from the Eastern refugium, the Iberian refugium, or both.

The researchers noted that the domestication of horses was a fundamental step in the history of humankind, providing horse-centred societies with enormous advantages over agricultural societies with regard to long-distance travel, warfare and trade.

Consistent with the preference of horses for predominantly open landscapes, the earliest evidence for horse domestication appears in the Eurasian steppes around 3500 BCE.

Around the time when the first domesticated horses appeared in the Eurasian steppes, large parts of Europe were still covered by vast expanses of dense forest, a habitat that horses avoid.

Accordingly, the fossil record for wild horses at that time is extremely scarce, suggesting that European domestic horses largely descend from stock imported from elsewhere.

On the other hand, recent genetic analysis data from a large number of both pre-domestic and domestic horses has shown that European wild populations also contributed to the gene pool of domestic horses.

Unfortunately, the researchers noted, it is currently difficult to distinguish between regions in Europe where the genetic contribution of local wild horses to domestic stock was substantial, and regions where domestic stock was largely introduced, and backcrossing with local wild horses played only a minor role.


The Lusitano was one of the Iberian breeds studied.
To identify primary areas of horse domestication in Europe, the researchers investigated patterns of genetic diversity in horse breeds for which evidence demonstrates a historic origin in a distinct region of mainland Europe or Britain ("traditional breeds").

The researchers defined primary areas of horse domestication as regions where local domestic populations largely descend from local wild stock.

"If there were only a few, geographically restricted regions in Europe where the genetic contribution of local wild horses to domestic stock was substantial, and if domestic populations from such areas were imported into regions where local wild stock was scarce, we would expect the former areas to have retained high levels of genetic diversity, and the latter areas to be characterised by low levels of diversity," they wrote.

"The rationale behind this reasoning is that, as populations expand out of origins, genetic diversity will be lost as a consequence of the (usually) small population sizes involved in such expansions."

The researchers assembled a unique dataset of more than 1100 horses typed at 12 locations, using both new and previously published data.

The combined dataset represents the largest and most comprehensive microsatellite dataset on traditional European horse breeds to date.

They found that geographic variation in gene diversity revealed two hotspots of diversity - one in the Caspian region of western Asia, the researchers' easternmost sampling location, and one in the Iberian Peninsula.

"The Iberian hotspot coincides with the only region in central and western Europe that was characterised by appreciable expanses of open landscape in the mid-Holocene, suggesting that not only the Eurasian steppes but also the Iberian Peninsula served as refugia for wild horses in the early and mid Holocene, when vast expanses of forest would have rendered most of Europe unsuitable for this steppe-adapted species."

In a comparison of diversity between breeds from regions that were predominantly open versus those that were predominantly forested, the researchers found the latter group had significantly lower genetic diversity.

"Low levels of diversity in breeds from previously forested areas are consistent with a loss of diversity as small herds of domestic horses were imported into these areas, following their domestication in Iberia or the Eastern steppes.

"Estimating the relative contribution of the two refugial populations to individual breeds is not possible here due to the limited number of markers used."

The researchers found that the distribution of high genetic diversity in European horses coincided with the distribution of open vegetation in the mid-Holocene, suggesting that the two areas identified acted as a refugia for wild horses at a time when most of Europe was covered by dense forest.


A Caspian mare and foal. © Rutland and Stamford Mercury
"Although our lack of sampling locations in Central and East Asia prevents us from pinpointing primary areas of horse domestication in this region, high diversity in the Caspian area is in agreement with palaeontological data suggesting that E. ferus survived the Holocene in South-West Asia and Central Asia.

"Additional sampling further east will help establish whether there is a genuine hotspot of genetic diversity in the Caspian region or whether high diversity in this region merely reflects generally higher levels of diversity in the Eurasian steppes."

A hotspot of genetic diversity in the Iberian Peninsula indicates that E. ferus may have also survived in Iberia.

The Iberian Peninsula was the only region in central and western Europe in which appreciable expanses of open habitat persisted throughout the Holocene.

The presence of wild horses in the Iberian Peninsula before domestication is supported by findings of horse remains in Neolithic and Copper Age sites (sixth to fourth millennium BP).

More recently, it has been shown that several pre-domestic Iberian maternal lineages survive in modern horses of Iberian descent, thus documenting a genetic contribution of Iberian wild stock to local domestic horses.

The genetic contribution of Iberian wild stock to local domestic horses may have been substantial, the researchers noted. The high diversity in Iberian horses is consistent with the persistence of E. ferus in the Iberian Peninsula from the Pleistocene through the Holocene, and the subsequent extensive use of local Iberian wild horses in establishing and/or restocking local domestic populations.

Hypotheses of local domestication in other parts of Europe could not be confirmed in the study.

Levels of genetic diversity in breeds from previously forested areas are consistently low, suggesting a scenario whereby these areas primarily relied on an import of horses from either the Iberian or the Asian hotspot, or both.

"This is consistent with the fossil record for horses, which, in turn, reflects the ecology of this large, group-living animal.

"While our results do not imply that wild horses were entirely absent from forested parts of Holocene Europe, we suggest that their presence in these regions was spatially and temporally discontinuous, with local extinctions and re-colonisations occurring in response to natural forest gap dynamics."

They continued: "Our results suggest that primary areas of horse domestication were confined to regions where considerable expanses of open landscape persisted throughout the Holocene, and that previously forested regions in Europe primarily relied on an import of domestic horses.

"Whether the knowledge of how to successfully capture, tame and breed horses reached Iberia through cultural transmission, or whether this knowledge was acquired independently, is an open question that cannot be answered with genetic data."

Horse breeds included in the study:


Levels of admixture from three Middle Eastern breeds in Iberia and central Europe/Britain: (A-C) Relative genetic contribution of the (A) Arab, (B) Akhal Teke, and (C) Caspian breed to Iberian and cE/UK breeds based on the admixture coefficient mY. (D-F) Relative genetic contribution of the (D) Arab, (E) Akhal Teke, and (F) Caspian breed to Iberian and cE/UK breeds based on expected homozygosity FS.