Horse had multiple domestication events (ancient equine mtDNA)

German researchers have successfully retrieved mtDNA from 85 ancient specimens from diverse Eurasian regions and periods, ranging from c. 12,000 BCE to the Middle Ages. They have found that most of the extant mtDNA diversity in the species existed before domestication.

M. Cieslak et al., Origin and History of Mitochondrial DNA Lineages in Domestic Horses. PLoS ONE 2010. Open access. 

Abstract

Domestic horses represent a genetic paradox: although they have the greatest number of maternal lineages (mtDNA) of all domestic species, their paternal lineages are extremely homogeneous on the Y-chromosome. In order to address their huge mtDNA variation and the origin and history of maternal lineages in domestic horses, we analyzed 1961 partial d-loop sequences from 207 ancient remains and 1754 modern horses. The sample set ranged from Alaska and North East Siberia to the Iberian Peninsula and from the Late Pleistocene to modern times. We found a panmictic Late Pleistocene horse population ranging from Alaska to the Pyrenees. Later, during the Early Holocene and the Copper Age, more or less separated sub-populations are indicated for the Eurasian steppe region and Iberia. Our data suggest multiple domestications and introgressions of females especially during the Iron Age. Although all Eurasian regions contributed to the genetic pedigree of modern breeds, most haplotypes had their roots in Eastern Europe and Siberia. We found 87 ancient haplotypes (Pleistocene to Mediaeval Times); 56 of these haplotypes were also observed in domestic horses, although thus far only 39 haplotypes have been confirmed to survive in modern breeds. Thus, at least seventeen haplotypes of early domestic horses have become extinct during the last 5,500 years. It is concluded that the large diversity of mtDNA lineages is not a product of animal breeding but, in fact, represents ancestral variability.

The paper provides ample insight on the various haplotypes and where they are found first. Not all lineages are from the putative area of first domestication (the Eurasian steppe) but they are also from other regions (East Asia, mainland Europe, Iberia).

Fig. 2 - Ancient horse mtDNA haplotypes with timeline and region

Pottoka

They also researched primitive horse breeds. 39 haplotypes were confined to one of these breeds. Among them are notable those of the Iberian peninsula (Lusitano, Marismeño, Cartujano, Garrano), which appear to have roots in pre-Neolithic local wild horses. Similarly the Basque pony known as pottoka also has roots in ancient mainland European horses (X1, derived from D). [Correction (Apr 6 2011): Pottoka's matrilineage X1 is of apparent Siberian origins: C - only attested in one individual. X1 as such is only documented since the Iron Age, in mainland Europe].

Other primitive breeds with unique haplotypes are Arabian, Cheju, Akhal Teke, Sicilian Oriental, Yakut, Debao and Fulani. The authors argue that the Altai Mountains and the Takla Maklan and Gobi deserts were barriers partly impeding the genetic flow from the Eurasian steppe to East Asia, where several of these breeds belong.


Update (Apr 6 2011): see also to this more recent post: Horse's double origins, on new research supporting by means of autosomal DNA diversity the double origin in the steppes and SW Europe of modern horses.