Genome-wide analysis of cold adaptation in indigenous Siberian populations.
Following the dispersal out of Africa, where hominins evolved in warm environments for millions of years, our species has colonised different climate zones of the world, including high latitudes and cold environments. The extent to which human habitation in (sub-)Arctic regions has been enabled by cultural buffering, short-term acclimatization and genetic adaptations is not clearly understood. Present day indigenous populations of Siberia show a number of phenotypic features, such as increased basal metabolic rate, low serum lipid levels and increased blood pressure that have been attributed to adaptation to the extreme cold climate. In this study we introduce a dataset of 200 individuals from ten indigenous Siberian populations that were genotyped for 730,525 SNPs across the genome to identify genes and non-coding regions that have undergone unusually rapid allele frequency and long-range haplotype homozygosity change in the recent past. At least three distinct population clusters could be identified among the Siberians, each of which showed a number of unique signals of selection. A region on chromosome 11 (chr11:66-69 Mb) contained the largest amount of clustering of significant signals and also the strongest signals in all the different selection tests performed. We present a list of candidate cold adaption genes that showed significant signals of positive selection with our strongest signals associated with genes involved in energy regulation and metabolism (CPT1A, LRP5, THADA) and vascular smooth muscle contraction (PRKG1). By employing a new method that paints phased chromosome chunks by their ancestry we distinguish local Siberian-specific long-range haplotype signals from those introduced by admixture.
Department of Archaeology and Anthropology, University of Cambridge, Cambridge, United Kingdom.
Alexia
A
Cardona
Department of Archaeology and Anthropology, University of Cambridge, Cambridge, United Kingdom; Wellcome Trust Sanger Institute, Hinxton, United Kingdom.
Luca
L
Pagani
The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
Tiago
T
Antao
Department of Mathematics, University of Bristol, Bristol, United Kingdom.
Daniel J
DJ
Lawson
Department of Archaeology and Anthropology, University of Cambridge, Cambridge, United Kingdom.
Christina A
CA
Eichstaedt
Department of Archaeology and Anthropology, University of Cambridge, Cambridge, United Kingdom.
Bryndis
B
Yngvadottir
National Cancer Centre Singapore, Singapore, Singapore.
Ma Than Than
MT
Shwe
National Cancer Centre Singapore, Singapore, Singapore.
Joseph
J
Wee
Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America.
Irene Gallego
IG
Romero
Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America.
Srilakshmi
S
Raj
Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia; Estonian Biocentre, Tartu, Estonia.
Mait
M
Metspalu
Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia; Estonian Biocentre, Tartu, Estonia.
Richard
R
Villems
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
Eske
E
Willerslev
Wellcome Trust Sanger Institute, Hinxton, United Kingdom.
Chris
C
Tyler-Smith
Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia.
Boris A
BA
Malyarchuk
Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia.
Miroslava V
MV
Derenko
Department of Archaeology and Anthropology, University of Cambridge, Cambridge, United Kingdom; Estonian Biocentre, Tartu, Estonia.
Toomas
T
Kivisild
D000064:Acclimatization / Q000235:genetics*; D003081:Cold Climate; D019143:Evolution, Molecular; D023281:Genomics; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D044382:Population Groups / Q000208:ethnology / Q000235:genetics*; D012641:Selection, Genetic; D012800:Siberia / Q000208:ethnology