Abstract
The UK and Ireland have many native pony breeds with historical and cultural importance as well as being a source of uncharacterized genetic diversity. However, there is a lack of comprehensive research investigating their genetic diversity and phylogenetic interrelationships. Many studies contain a limited number of pony breeds or small sample sizes for these breeds. This may result in erroneous grouping of pony breeds that otherwise have intricate interrelationships with each other and are not evaluated correctly when placed as a token subset of a larger dataset. This is the first study that specifically investigates the genetic diversity within and between British and Irish native pony breeds using large sample numbers from locations of their native origin.This study used a panel of microsatellite markers and sequence analysis of the mitochondrial control region to analyze the genetic diversity within and between 11 pony breeds from Britain and Ireland. A large dataset was collected (a total of 485 animals were used for mtDNA analysis and 450 for microsatellite analysis), and previously published data were used to place the British and Irish ponies in a global context.The native ponies of Britain and Ireland were found to have had a complex history, and the interrelationships between the breeds were revealed. Overall, high levels of genetic diversity were maintained in native breeds, although some reduction was evident in small or isolated populations (Shetland, Carneddau, and Section C). Unusual mitochondrial diversity distribution patterns were apparent for the Carneddau and Dartmoor, although among breeds and global haplogroups there was a high degree of haplotype sharing evident, well‐represented within British and Irish ponies. Ancestral maternal diversity was maintained by most populations, particularly the Fells and Welsh ponies, which exhibited rare and ancient lineages. The maternal and paternal histories of the breeds are distinct, with male‐biased crossings between native breeds, and other shared influences, likely Arabs and Thoroughbreds, are apparent. The data generated herein provide valuable information to guide and implement the conservation of increasingly rare native genetic resources.
Highlights
Evidence has been found of horses present in Britain as early as the Middle Pleistocene, but horse and human populations seem to have become established following the last ice age during the middle Devensian period (Currant & Jacobi, 2001; Hosfield, 2011; Schreve, 2001)
The results revealed lower autosomal genetic differentiation according to breed (8%) compared to previously reported data of other horse breeds worldwide, in which 10%–17% of the genetic diversity could be partitioned this way (Aberle, Hamann, Drögemüller, & Distl, 2004; Glowatzki-Mullis et al, 2006; Plante et al, 2007; Prystupa, Juras, et al, 2012)
This may be because this study consists solely of pony breeds originating from Britain and Ireland and recent interbreeding must be considered more widely during their historical development than the more distantly related breeds analyzed in other studies
Summary
Evidence has been found of horses present in Britain as early as the Middle Pleistocene, but horse and human populations seem to have become established following the last ice age during the middle Devensian period (Currant & Jacobi, 2001; Hosfield, 2011; Schreve, 2001). It is not clear when the ancestors of the modern native ponies of Britain and Ireland arrived, or how the currently recognized populations relate to each other in terms of their deep ancestral lineages. This study determines the genetic diversity and history of British and Irish pony breeds, by examining them as populations in their own right and in relation to each other
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