Via West Hunter, from bioRxiv, news of an important new genome analysis technique, Singleton Density Score (SDS), that focuses on Darwinian selection among humans over the last 100 generations (e.g., during historic times).
This is a big deal breakthrough made possible by having thousands of genomes sequenced. This first round focuses upon recent selection pressures upon the British, but everybody else can eventually be analyzed.
Yair Field, Evan A Boyle, Natalie Telis, Ziyue Gao, Kyle J Gaulton, David Golan, Loic Yengo, Ghislain Rocheleau, Philippe Froguel, Mark I McCarthy, Jonathan K Pritchard
This article is a preprint and has not been peer-reviewed
Detection of recent natural selection is a challenging problem in population genetics, as standard methods generally integrate over long timescales. Here we introduce the Singleton Density Score (SDS), a powerful measure to infer very recent changes in allele frequencies from contemporary genome sequences. When applied to data from the UK10K Project, SDS reflects allele frequency changes in the ancestors of modern Britons during the past 2,000 years. We see strong signals of selection at lactase and HLA, and in favor of blond hair and blue eyes. Turning to signals of polygenic adaptation we find, remarkably, that recent selection for increased height has driven allele frequency shifts across most of the genome. Moreover, we report suggestive new evidence for polygenic shifts affecting many other complex traits. Our results suggest that polygenic adaptation has played a pervasive role in shaping genotypic and phenotypic variation in modern humans.
They looked at a database of the genomes of 3,195 individuals with deep ancestral roots in Britain.
The single largest peak is at the lactase locus, with a maximum SDS score of 10.0 (p=1×10-23; Fig. 3B, fig. S8). Lactase is a well-known target of selection in Europeans [4,24], however our data show that strong selection persisted well into the last 2,000 years. …
We see strong signals of selection at lactase and HLA, and in favor of blond hair and blue eyes.
Turning to signals of polygenic adaptation we find, remarkably, that recent selection for increased height has driven allele frequency shifts across most of the genome.
Moreover, we report suggestive new evidence for polygenic shifts affecting many other complex traits. Our results suggest that polygenic adaptation has played a pervasive role in shaping genotypic and phenotypic variation in modern humans.
… We speculate that recent selection in favor of blond hair and blue eyes may reflect sexual selection for phenotypes in the ancestors of the British, as opposed to the longer-term trend toward lighter skin pigmentation in non-Africans, generally thought to have been driven by the need for Vitamin D production.
Thus far we have described strong selection signals at individual loci. However, it has been proposed that another major mechanism of adaptation may be through polygenic selection on complex traits. This mode of selection would act through small, directed shifts in allele frequencies at many loci. Polygenic selection can potentially change phenotypes rapidly, but would leave only weak signals at individual loci. The best evidence of polygenic adaptation is for height, which shows a signal of differential selection on height in northern Europeans relative to southern Europeans [17–19,33]. A recent study of prehistoric Europeans found selection both for decreased height in southern Europeans, and a weak signal of an increase in steppe populations that contributed to northern Europeans, within the past ~5,000 years.
While height has the strongest signal, we also see signals for a variety of other traits. These include additional anthropometric traits such as selection toward increased infant head circumference and birth weight, and increases in female hip size; as well as selection on variants underlying metabolic traits including levels of insulin and glycated hemoglobin.
Some of the results hint at sexually dimorphic adaptations: in addition to the female-specific signal for increased hip size, we observe a male specific signal for decreased BMI; we further see a signal in favor of later sexual maturation in women, but not in men. While many of these signals are highly intriguing, and some match known phenotypes of modern British (SOM), it remains to fully determine the confounding role—if any—of population structure in contributing to these signals.
Until Cochran and Harpending started beating the drums for the concept of accelerated recent human evolution in this century, the conventional wisdom was increased cultural change in recent millennia meant less absolute genetic change. But this was a logical mistake driven in part by the human predilection to anthropomorphize everything into Who Would Win in a Fight? Nature or a Nurture? If cultural change had become relatively more important, it was assumed that genetic change had become absolutely less important, because genes were Losers.
In reality, however, the world doesn’t work that way. Increased cultural change (due say to colonizing new latitudes and even continents and developing new economies, such as agriculture) would increase the novel selection pressures and thus, all else being equal, speed up genetic evolution and diversification, thus increasing racial differences.
I had this discussion with Jared Diamond in 2002 about his G uns, Germs, and Steel bestseller. We had been chatting amicably I pointed out that his documentation of environmental differences among the continents would imply more selection for genetic differences. He then quickly gathered his papers and vamoosed.
P.S., Razib goes with Rosamund Pike as his illustration.