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Henn Lab for Population Genetics
Our official lab website is live!
Julie Granka (Feldman Lab, Stanford University) has successfully completed her PhD. Julie will soon join the Genetics Team at ancestry.com. We’ll miss you during field work this year. Congratulations!
hello world, this is a title
I’ve officially moved to Stony Brook as of January 2013. Just in time for the blizzard. The Henn Lab is up and running!
A Tale of Two Haplotypes: The EDA2R/AR Intergenic Region is the most Divergent Genomic Segment between Africans and East Asians in the Human Genome
Congratulations Amanda! Our manuscript on the X-chromosome is now accepted at Human Biology.
Amanda M. Casto, Brenna M. Henn, Jeffery M. Kidd, Carlos D. Bustamante, and Marcus W. Feldman
Single nucleotide polymorphisms (SNPs) with large allele frequency differences between human populations are relatively rare. The longest run of SNPs with an allele frequency difference of one between the Yoruba of Nigeria and the Han Chinese is found on the long arm of the X chromosome in the intergenic region separating the EDA2R and AR genes. It has been proposed that the unusual allele frequency distributions of these SNPs are the result of a selective sweep affecting African populations that occurred after the Out-of-Africa migration. To investigate the evolutionary history of the EDA2R/AR intergenic region, we characterized the haplotype structure of 52 of its highly-differentiated SNPs. Using a publicly-available dataset of 3,000 X chromosomes from 65 human populations, we found that nearly all human X chromosomes carry one of two modal haplotypes for these 52 SNPs. The predominance of two highly divergent haplotypes at this locus was confirmed using a subset of individuals sequenced to high coverage. The first of these haplotypes, the α haplotype, is at high frequencies in most of the African populations surveyed and likely arose prior to the separation of African populations into distinct genetic entities. The second, the β haplotype, is frequent or fixed in all non-African populations and likely arose in East Africa prior to the Out-of-Africa migration. We also observed a small group of rare haplotypes with no clear relationship to the α and β haplotypes. These haplotypes occur at relatively high frequencies in African hunter-gatherer populations, like the San and Mbuti Pygmies. Our analysis indicates that these haplotypes are part of a pool of diverse, ancestral haplotypes that have now been almost entirely replaced by the α and β haplotypes. We suggest that the rise of the α and β haplotypes was the result of the demographic forces that human populations experienced during the formation of modern African populations and the Out-of-Africa migration. However, we also present evidence that this region is the target of selection in the form of positive selection on the α and β haplotypes and of purifying selection against α/β recombinants.
Got to link to our cover photo for Genetics November 2012 before the month is up!
Limited Evidence for Classic Selective Sweeps in African Populations
The great human expansion
New Perspective piece by Marc Feldman, Luca Cavalli-Sforza and myself is out in the PNAS early edition. Stanford Report
The genetic prehistory of southern Africa
Congratulations to Joe Pickrell and colleagues on our latest Nature Communications paper!
Limited Evidence for Classic Selective Sweeps in African Populations
Congratulations to Julie! Our manuscript on selective sweeps in African populations is now online at Genetics. Julie M. Granka, Brenna M. Henn, Christopher R. Gignoux, Jeffrey M. Kidd, Carlos D. Bustamante, and Marcus W. Feldman While hundreds of loci have been identified as reflecting strong positive selection in human populations, connections between candidate loci and specific selective pressures often remain obscure. This study investigates broader patterns of selection in African populations, which are underrepresented despite their potential to offer key insights into human adaptation. We scan for hard selective sweeps using several haplotype and allele frequency statistics with a dataset of nearly 500,000 genome-wide single nucleotide polymorphisms in 12 highly diverged African populations that span a range of environments and subsistence strategies. We find that positive selection does not appear to be a strong determinant of allele frequency differentiation among these African populations. Haplotype statistics do identify putatively-selected regions that are shared across African populations. However, as assessed by extensive simulations, patterns of haplotype sharing between African populations follow neutral expectations and suggest that tails of the empirical distributions contain false positive signals. After highlighting several genomic regions where positive selection can be inferred with higher confidence, we use a novel method to identify biological functions enriched among populations’ empirical tail genomic windows, such as immune response in agricultural groups. In general, however, it seems that current methods for selection scans are poorly suited to populations which, like the African populations in this study, are affected by ascertainment bias, have low levels of linkage disequilibrium, possibly old selective sweeps, and potentially reduced phasing accuracy. Additionally, population history can confound the interpretation of selection statistics, suggesting greater care is needed in attributing broad genetic patterns to human adaptation.
