Sunday, January 24, 2010

Signatures of selection in dog breeds

10 breeds, 21,000 SNPs, breed-specific Fst.

Their most notable hits:
HMGA2 and IGF1R (size)
SILV, MITF (coat color and texture)
CDH9, DRD5, HTR2A (behavior)
SOX9 (skeletal morphology)
FTO, SLC2A9, SLC5A2 (physiology)

Unfortunately they only use Fst to detect evidence of selection. It would have been interesting to try out some haplotype or other tests of selection, but they were probably constrained by the total number of SNPs they had.

Most interestingly:
Similar to analyses of selection in natural populations (23), we find that genes involved in immunity and defense are also significantly overrepresented in the 155 candidate selection
regions. This is somewhat surprising, as natural and artificial selection would not necessarily be expected a priori to act on similar classes of genes, and suggests that immune related genes are pervasive targets of selection because of their critical role in pathogen defense or propensity for pleiotropic effects (24).
We note that as an initial foray into comparative selection mapping, of the 1,506 genes located in putatively selected regions in dogs, 169 overlap with genes located in well-supported selected regions in humans (10). Although this result should be interpreted with caution, as the specific targets of selection are generally not known with certainty in either dogs or humans, it does raise the intriguing possibility that recent selection has influenced common loci in both the human and dog lineages.
Tracking footprints of artificial selection in the dog genome
Joshua M. Akey, Alison L. Ruhe, Dayna T. Akey, Aaron K. Wong, Caitlin F. Connelly, Jennifer Madeoy, Thomas J. Nicholas, and Mark W. Neff
PNAS January 19, 2010 vol. 107 no. 3 1160-1165
Abstract: The size, shape, and behavior of the modern domesticated dog has been sculpted by artificial selection for at least 14,000 years. The genetic substrates of selective breeding, however, remain largely unknown. Here, we describe a genome-wide scan for selection in 275 dogs from 10 phenotypically diverse breeds that were genotyped for over 21,000 autosomal SNPs. We identified 155 genomic regions that possess strong signatures of recent selection and contain candidate genes for phenotypes that vary most conspicuously among breeds, including size, coat color and texture, behavior, skeletal morphology, and physiology. In addition, we demonstrate a significant association between HAS2 and skin wrinkling in the Shar-Pei, and provide evidence that regulatory evolution has played a prominent role in the phenotypic diversification of modern dog breeds. Our results provide a first-generation map of selection in the dog, illustrate how such maps can rapidly inform the genetic basis of canine phenotypic variation, and provide a framework for delineating the mechanistic basis of how artificial selection promotes rapid and pronounced phenotypic evolution.

Tuesday, January 19, 2010

More on the genetics of European farmers vs. hunter-gatherers

Continuing on the theme from the last post, here is a paper that just came out in PLoS Biology. It seems to come to the same conclusion as the Science one that used ancient mtDNA...sort of. The results conflict since the Bramanti one finds discontinuity in mtDNA lineages, while this paper doesn't. So the Bramanti paper finds little evidence for continuity in mtDNA lineages, while this one finds that there is some continuity in mtDNA lineages, at least compared to the Y-chromosome. The two papers use different sources of data and different methods, which could somehow explain the discrepancy.
Razib's already all over this.

A Predominantly Neolithic Origin for European Paternal Lineages
Patricia Balaresque, Georgina R. Bowden, Susan M. Adams, Ho-Yee Leung, Turi E. King, Zoë H. Rosser, Jane Goodwin, Jean-Paul Moisan, Christelle Richard, Ann Millward, Andrew G. Demaine, Guido Barbujani, Carlo Previderè, Ian J. Wilson, Chris Tyler-Smith, Mark A. Jobling
PLoS Biology 8(1): e1000285.
Abstract: The relative contributions to modern European populations of Paleolithic hunter-gatherers and Neolithic farmers from the Near East have been intensely debated. Haplogroup R1b1b2 (R-M269) is the commonest European Y-chromosomal lineage, increasing in frequency from east to west, and carried by 110 million European men. Previous studies suggested a Paleolithic origin, but here we show that the geographical distribution of its microsatellite diversity is best explained by spread from a single source in the Near East via Anatolia during the Neolithic. Taken with evidence on the origins of other haplogroups, this indicates that most European Y chromosomes originate in the Neolithic expansion. This reinterpretation makes Europe a prime example of how technological and cultural change is linked with the expansion of a Y-chromosomal lineage, and the contrast of this pattern with that shown by maternally inherited mitochondrial DNA suggests a unique role for males in the transition.

Saturday, January 09, 2010

Genetics of hunter-gatherers and early farmers in Europe

I'm back, and will try to be more regular about posting. This paper came out a few months ago in Science and I've been meaning to look at it for a while.
They examine the Fst in mtDNA sequence between hunter-gatherer samples (13,400 to 2,300 ago) in Central Europe, from more recent individuals (and modern Europeans). I guess they must use archaeological or other evidence to determine their subsistence pattern.
They get an Fst of 0.163, which is indeed remarkably high - although do we really know what to expect when comparing populations over time? To answer this, they perform some simulations, and reject the hypothesis that this Fst could have been due to a process of population continuity.
Along with their discussion of the haplotype differences betwee the hunter-gatherers and farmers, this result is pretty interesting and suggests a migration of early farmers into central Europe and replacement of hunter-gatherers.

Genetic discontinuity between local hunter-gatherers and central Europe's first farmers.
Bramanti B, Thomas MG, Haak W, Unterlaender M, Jores P, Tambets K, Antanaitis-Jacobs I, Haidle MN, Jankauskas R, Kind CJ, Lueth F, Terberger T, Hiller J, Matsumura S, Forster P, Burger J.
Science 2009 Oct 2;326(5949):137-40.
Abstract: After the domestication of animals and crops in the Near East some 11,000 years ago, farming had reached much of central Europe by 7500 years before the present. The extent to which these early European farmers were immigrants or descendants of resident hunter-gatherers who had adopted farming has been widely debated. We compared new mitochondrial DNA (mtDNA) sequences from late European hunter-gatherer skeletons with those from early farmers and from modern Europeans. We find large genetic differences between all three groups that cannot be explained by population continuity alone. Most (82%) of the ancient hunter-gatherers share mtDNA types that are relatively rare in central Europeans today. Together, these analyses provide persuasive evidence that the first farmers were not the descendants of local hunter-gatherers but immigrated into central Europe at the onset of the Neolithic.
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