Widespread signals of convergent adaptation to high altitude in Asia and America

Abstract

Living at high altitude is one of the most difficult challenges that humans had to cope with during their evolution. Whereas several genomic studies have revealed some of the genetic bases of adaptations in Tibetan, Andean, and Ethiopian populations, relatively little evidence of convergent evolution to altitude in different continents has accumulated. This lack of evidence can be due to truly different evolutionary responses, but it can also be due to the low power of former studies that have mainly focused on populations from a single geographical region or performed separate analyses on multiple pairs of populations to avoid problems linked to shared histories between some populations. We introduce here a hierarchical Bayesian method to detect local adaptation that can deal with complex demographic histories. Our method can identify selection occurring at different scales, as well as convergent adaptation in different regions. We apply our approach to the analysis of a large SNP data set from low-and high-altitude human populations from America and Asia. The simultaneous analysis of these two geographic areas allows us to identify several candidate genome regions for altitudinal selection, and we show that convergent evolution among continents has been quite common. In addition to identifying several genes and biological processes involved in high-altitude adaptation, we identify two specific biological pathways that could have evolved in both continents to counter toxic effects induced by hypoxia.

Metabolic basis to Sherpa altitude adaptation

“…This finding suggests an alternative strategy to supply the TCA cycle with succinate. Intriguingly, recent analysis of a large SNP dataset from low-and high-altitudeadapted populations in the Americas and Asia (31) aimed to identify pathways of convergent evolution, and highlighted fatty acid ω-oxidation as the most significant cluster of overlapping gene sets between high-altitude groups (32). ω-Oxidation is normally a minor pathway in vertebrates, becoming more important when β-oxidation is defective (33); through successive cycles, it oxidizes fatty acids to adipate and succinate in the endoplasmic reticulum, after which succinate enters the mitochondria with anaplerotic regulation of the TCA cycle (34).…”

Genetic signature of natural selection in first Americans

“…Two versions of BayeScan (16,35) were used to identify candidate targets for positive selection. Both versions assume an island model in which the subpopulations' allele frequencies are correlated through a common migrant gene pool from which they may differ in varying degrees.…”

Identifying genomic changes associated with insecticide resistance in the dengue mosquito Aedes aegypti by deep targeted sequencing

“…Searching for selection footprints using a Bayesian approach taking into account population structure (Foll et al 2014) identified 156 outlier loci significantly associated with deltamethrin resistance. These outlier loci included 31 nonsynonymous variants and affected multiple supercontigs spread over all chromosomes.…”

“…Searching for selection footprint using a hierarchical Bayesian approach BayeScan3 was used for identifying loci under natural selection through a hierarchical Bayesian model, taking into account population structure and usable on pools of individuals (Foll et al 2014). This approach estimates the probability that each locus is subject to selection by discriminating population-specific and locus-specific components of the fixation index using a logistic regression.…”