> In modern horses, the Y chromosomes in stallions are almost identical, reflecting the breeding technique of using a single stallion with desired characteristics to father many offspring.
Could that be true? I mean, could all modern domesticated stallions have "almost identical" Y chromosomes?
Edit: Perhaps over generalizing?
> ... Lippold based his findings on the results of a 2004 Swedish study that showed a particular DNA sequence in the Y chromosomes of 52 modern-day stallions representing 15 different breeds was absolutely identical.
> This doesn't mean modern stallions have no diversity of all, Lippold cautioned. The researchers only studied one part of the Y chromosome ...
Domestication leads to heavy inbreeding and a depression in genetic diversity genome-wide.
Furthermore, the Y chromosome recombines at a much slower rate compared to the autosome, resulting in less diversity. This should be balanced by a higher mutation rate, but again, domestication depresses that.
(Source: ~25 years experience working with horses as a hobby)
At least in the US, inbreeding is indeed extensive. The vast majority of male horses are castrated at a young age, since intact males are considered more difficult to train and control (therefore more dangerous to humans) and more expensive to house than castrated males or intact females. Therefore, a small percentage of males end up fathering all the offspring. There are American Quarter Horse stallions with literally thousands of offspring (sometimes to their detriment, as when a popular stallion was belatedly discovered to carry a recessive genetic disease[0]).
It's therefore interesting to a modern horse person to read that "the Scythians maintained the natural herd structure" (a "harem" structure in which one male tends to sexually dominate several females - but several, not thousands, and not generally for his entire life).
Scythians probably put a lot more value on an slow ugly horse that would live 30 years rather than a pretty horse that could sprint but died when it saw its shadow.
If you're trying to malign quarter horses, be aware that many can't even sprint anymore (they're being bred more for "western pleasure" e.g. extremely slow, mechanical movements ;-)
> In fact, a screening for single-nucleotide polymorphisms (SNPs) in 14.3 kb of noncoding Y chromosome sequence among 52 male horses of 15 different breeds did not identify a single segregation site.
That's just part of the Y chromosome.
But this is a better cite:
> 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.
Wallner et al. (2013) Identification of Genetic Variation on the Horse Y Chromosome and the Tracing of Male Founder Lineages in Modern Breeds
> So yes, it seems that all domestic stallions descend from just one ancestor stallion. That's amazing!
I once a class on population genetics in which the instructor commented that the "mitochondrial Eve" idea is kind of over-played. Basically, if you look at any genetic locus, you're going to find some most-recent common ancestor, but that most-recent common ancestor isn't going to be the same for all loci. (So yes, there might be a "mitochrondrial Eve", but there's also a "cytochrome Sam" and they're not necessarily the same person.)
"""Because of recombination, different gene loci follow different pathways of ancestry, resulting in different gene genealogies. The coalescent is also relevant to phylogenetics, as incomplete lineage sorting between speciation events results in conflict among gene-loci in phylogenetic relationships inferred among species."""
(I'm no expert, but sometimes I think population genetics has one of the most interesting mathematical structures of all the natural processes I know about.)
But still, Wallner et al. (2013) only found six versions of the Y chromosome in modern horses, and argued that five of them "apparently arose on the background of HT1 by mutation or gene conversion after domestication".
So yes, it looks like one ancestral stallion. But then, all commercial bananas are clones.
Could that be true? I mean, could all modern domesticated stallions have "almost identical" Y chromosomes?
Edit: Perhaps over generalizing?
> ... Lippold based his findings on the results of a 2004 Swedish study that showed a particular DNA sequence in the Y chromosomes of 52 modern-day stallions representing 15 different breeds was absolutely identical.
> This doesn't mean modern stallions have no diversity of all, Lippold cautioned. The researchers only studied one part of the Y chromosome ...
http://www.thehorse.com/articles/28083/researchers-examine-a...