April 04, 2013

Horse Y chromosomes

PLoS ONE 8(4): e60015. doi:10.1371/journal.pone.0060015

Identification of Genetic Variation on the Horse Y Chromosome and the Tracing of Male Founder Lineages in Modern Breeds

Barbara Wallner et al.

The paternally inherited Y chromosome displays the population genetic history of males. While modern domestic horses (Equus caballus) exhibit abundant diversity within maternally inherited mitochondrial DNA, no significant Y-chromosomal sequence diversity has been detected. We used high throughput sequencing technology to identify the first polymorphic Y-chromosomal markers useful for tracing paternal lines. The nucleotide variability of the modern horse Y chromosome is extremely low, resulting in six haplotypes (HT), all clearly distinct from the Przewalski horse (E. przewalskii). The most widespread HT1 is ancestral and the other five haplotypes apparently arose on the background of HT1 by mutation or gene conversion after domestication. Two haplotypes (HT2 and HT3) are widely distributed at high frequencies among modern European horse breeds. Using pedigree information, we trace the distribution of Y-haplotype diversity to particular founders. The mutation leading to HT3 occurred in the germline of the famous English Thoroughbred stallion “Eclipse” or his son or grandson and its prevalence demonstrates the influence of this popular paternal line on modern sport horse breeds. The pervasive introgression of Thoroughbred stallions during the last 200 years to refine autochthonous breeds has strongly affected the distribution of Y-chromosomal variation in modern horse breeds and has led to the replacement of autochthonous Y chromosomes. Only a few northern European breeds bear unique variants at high frequencies or fixed within but not shared among breeds. Our Y-chromosomal data complement the well established mtDNA lineages and document the male side of the genetic history of modern horse breeds and breeding practices.



Annie Mouse said...

This paper is a nice cautionary lesson on understanding the breeding of domesticated animals.

All the modern domesticated horses are descended from arabian horses on the male line. Whereas arabians have a long history (~2,500 BCE) they are believed to have only started to permeate Europe during the crusades, about 1000 years ago.

Eclipse died in in 1789 and is the source of the spread of red major group HT3. Less than 300 years ago, but a a major chunk of the horse population is descended from his line.

We know this because we have the written histories. Without the written histories it would look like the domesticated horse originated in Arabia and there was an very early major expansion out of the British isles. This is rubbish of course.

Plus the diversity of species in places that control horse breed ing is always going to be a lot lower than places that dont, precisely because of effects like the above. In using total diversity data we have to compare essentially undisturbed wild populations to similar wild populations, which is not possible for any area that has bred horses in the present or past.

This has particular effect on understanding the domestication history of food species, draft species and companion/cohunter/sacred species like the dog and cat.

Mitochondrial DNA is less distortable but still problematic.

JDB said...

Eclipse is not the source of the spread of HT3. All of his descendants sampled trace through either his son King Fergus or his son Pot8os. The descendants of King Fergus were all HT2. The descendants of Pot8os were all HT3 but their most recent common ancestor in sire line is Pot8os' grandson Whalebone. The actual source of the spread of HT3 could be either of them, or Whalebone's sire Waxy.

For more information on Thoroughbred mitochondrial DNA see:

Shayan said...

Did they test farther east than Anatolia? Past DNA studies have shown Iran to be a genetic refuge during the Holocene. I'd guess Mongolian horses to have interesting results as well.