title: A novel candidate region for genetic adaptation to high altitude in Andean populations.
abstract: Humans living at high altitude (≥ 2,500 meters above sea level) have acquired unique abilities to survive the associated extreme environmental conditions, including hypoxia, cold temperature, limited food availability and high levels of free radicals and oxidants. Long-term inhabitants of the most elevated regions of the world have undergone extensive physiological and/or genetic changes, particularly in the regulation of respiration and circulation, when compared to lowland populations. Genome scans have identified candidate genes involved in altitude adaption in the Tibetan Plateau and the Ethiopian highlands, in contrast to populations from the Andes, which have not been as intensively investigated. In the present study, we focused on three indigenous populations from Bolivia: two groups of Andean natives, Aymara and Quechua, and the low-altitude control group of Guarani from the Gran Chaco lowlands. Using pooled samples, we identified a number of SNPs exhibiting large allele frequency differences over 900,000 genotyped SNPs. A region in chromosome 10 (within the cytogenetic bands q22.3 and q23.1) was significantly differentiated between highland and lowland groups. We resequenced ~1.5 Mb surrounding the candidate region and identified strong signals of positive selection in the highland populations. A composite of multiple signals like test localized the signal to FAM213A and a related enhancer; the product of this gene acts as an antioxidant to lower oxidative stress and may help to maintain bone mass. The results suggest that positive selection on the enhancer might increase the expression of this antioxidant, and thereby prevent oxidative damage. In addition, the most significant signal in a relative extended haplotype homozygosity analysis was localized to the SFTPD gene, which encodes a surfactant pulmonary-associated protein involved in normal respiration and innate host defense. Our study thus identifies two novel candidate genes and associated pathways that may be involved in high-altitude adaptation in Andean populations.
authors.affiliation: Australian Centre for Ancient DNA, School of Earth & Environmental Sciences, The University of Adelaide, Adelaide, Australia.
authors.forename: Guido
authors.initials: G
authors.lastname: Valverde
authors.affiliation: Department of Computational Regulatory Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, China.
authors.forename: Hang
authors.initials: H
authors.lastname: Zhou
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Lippold
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
authors.forename: Cesare
authors.initials: C
authors.lastname: de Filippo
authors.affiliation: Department of Computational Regulatory Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, China.
authors.forename: Kun
authors.initials: K
authors.lastname: Tang
authors.affiliation: Department Effect-Directed Analysis, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.
authors.forename: David
authors.initials: D
authors.lastname: López Herráez
authors.affiliation: Department of Computational Regulatory Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Li
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
authors.forename: Mark
authors.initials: M
authors.lastname: Stoneking
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D000531:Altitude; D016022:Case-Control Studies; D002879:Chromosomes, Human, Pair 10 / Q000235:genetics; D005260:Female; D005787:Gene Frequency; D056426:Genetic Loci; D016678:Genome; D006239:Haplotypes; D006720:Homozygote; D006801:Humans; D008297:Male; D020641:Polymorphism, Single Nucleotide; D037663:Pulmonary Surfactant-Associated Protein D / Q000235:genetics
chemical_list: D037663:Pulmonary Surfactant-Associated Protein D