Identifying Signatures of Natural Selection in Tibetan and Andean Populations Using Dense Genome Scan Data

We looked across each chromosome to identify genomic regions with previously unknown function with respect to altitude phenotypes

Abigail Bigham; Marc Bauchet; Dalila Pinto; Xianyun Mao; Joshua M. Akey; Rui Mei; Stephen W. Scherer; Colleen G. Julian; Megan J. Wilson; David López Herráez; Tom Brutsaert; Esteban J. Parra; Lorna G. Moore; Mark D. Shriver

2010

Scholarcy highlights

  • As human populations migrated across the globe, they encountered numerous environments each with unique ecological conditions
  • We found that the two distributions were not significantly different from one another, indicating that the hypoxia inducible transcription factor distribution is not enriched for SNPs falling in the 1% or 5% tail of the empirical locus specific branch length distribution in Andeans or Tibetans
  • We identified genomic regions showing evidence of recent positive selection in two high-altitude human populations, Andeans and Tibetans, using dense multilocus SNP genotype data
  • Putative natural selection candidate loci were detected in particular pathways with hypothesized roles in high-altitude adaptation as well as chromosomal regions with previously unknown involvement in altitude phenotypes
  • The whole genome long range haplotype test looks at patterns of linkage disequilibrium to identify genomic regions that exhibit longer than expected LD given their frequency in the population
  • These statistical tests should be considered as complementary tests that can be useful for the identification of regions under positive selection
  • To identify copy number polymorphisms that may be involved in adaptation to high altitude in Andeans or Tibetans, we compared population frequencies for each biallelic CNP using pairwise FST calculated in the same manner as described previously for SNPs

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