Colloquium paper: human adaptations to diet, subsistence, and ecoregion are due to subtle shifts in allele frequency.
Human populations use a variety of subsistence strategies to exploit an exceptionally broad range of ecoregions and dietary components. These aspects of human environments have changed dramatically during human evolution, giving rise to new selective pressures. To understand the genetic basis of human adaptations, we combine population genetics data with ecological information to detect variants that increased in frequency in response to new selective pressures. Our approach detects SNPs that show concordant differences in allele frequencies across populations with respect to specific aspects of the environment. Genic and especially nonsynonymous SNPs are overrepresented among those most strongly correlated with environmental variables. This provides genome-wide evidence for selection due to changes in ecoregion, diet, and subsistence. We find particularly strong signals associated with polar ecoregions, with foraging, and with a diet rich in roots and tubers. Interestingly, several of the strongest signals overlap with those implicated in energy metabolism phenotypes from genome-wide association studies, including SNPs influencing glucose levels and susceptibility to type 2 diabetes. Furthermore, several pathways, including those of starch and sucrose metabolism, are enriched for strong signals of adaptations to a diet rich in roots and tubers, whereas signals associated with polar ecoregions are overrepresented in genes associated with energy metabolism pathways.
Hancock
Angela M
AM
Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
Witonsky
David B
DB
Ehler
Edvard
E
Alkorta-Aranburu
Gorka
G
Beall
Cynthia
C
Gebremedhin
Amha
A
Sukernik
Rem
R
Utermann
Gerd
G
Pritchard
Jonathan
J
Coop
Graham
G
Di Rienzo
Anna
A
D000222:Adaptation, Physiological; D000818:Animals; D005075:Biological Evolution; D004032:Diet; D004463:Ecology; D005787:Gene Frequency; D005828:Genetics, Population; D006239:Haplotypes; D006720:Homozygote; D006801:Humans; D008954:Models, Biological; D008957:Models, Genetic; D012641:Selection, Genetic
Science. 2004 Jan 9;303(5655):223-6
14716012
J Theor Biol. 2005 Jul 21;235(2):207-19
15862590
Biochim Biophys Acta. 1996 Aug 16;1302(3):236-40
8765145
PLoS Genet. 2007 Oct;3(10):1827-37
17922574
Nature. 2007 Oct 18;449(7164):913-8
17943131
PLoS Biol. 2006 Mar;4(3):e72
16494531
Br Med J. 1954 Feb 6;1(4857):290-4
13115700
Genet Res. 1997 Oct;70(2):155-74
9449192
Nat Genet. 2008 Mar;40(3):340-5
18246066
PLoS Genet. 2009 Jun;5(6):e1000500
19503611
FEBS J. 2007 Nov;274(22):6011-23
17961181
Nature. 2009 Oct 8;461(7265):747-53
19812666
J Lipid Res. 2002 Dec;43(12):2007-16
12454260
Proc Biol Sci. 2009 Oct 7;276(1672):3447-55
19586946
Biochem J. 2001 Jun 15;356(Pt 3):907-10
11389701
PLoS Genet. 2008 Feb;4(2):e32
18282109
Am J Hum Genet. 2004 Jun;74(6):1111-20
15114531
Proc Natl Acad Sci U S A. 2006 Jan 3;103(1):135-40
16371466
PLoS One. 2008 Sep 05;3(9):e3136
18773084
PLoS Genet. 2005 Dec;1(6):e82
16429165
Nat Genet. 2007 Sep;39(9):1140-4
17694055
Genome Res. 2009 May;19(5):826-37
19307593
Nat Genet. 2007 Oct;39(10):1256-60
17828263
Science. 2008 Feb 22;319(5866):1100-4
18292342
Comp Biochem Physiol B Biochem Mol Biol. 2008 May;150(1):1-9
18328758
Biochemistry. 2004 Aug 10;43(31):10138-48
15287741
Am J Hum Genet. 2004 Dec;75(6):1059-69
15492926
Nat Genet. 2007 Jan;39(1):31-40
17159977
Am J Cardiol. 1995 May 1;75(14):956-9
7733014
PLoS Genet. 2007 Jun;3(6):e90
17542651
Genetics. 2005 Apr;169(4):2335-52
15716498
Nature. 2003 Jun 12;423(6941):742-7
12802332
Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50
16199517
BMC Med Genet. 2009 Jun 03;10:49
19493349
Philos Trans R Soc Lond B Biol Sci. 2010 Aug 27;365(1552):2459-68
20643735
Curr Biol. 2010 Feb 23;20(4):R208-15
20178769
Am J Hum Genet. 2008 Jan;82(1):57-72
18179885
Genome Res. 2005 Nov;15(11):1553-65
16251465
J Nutr. 2003 Nov;133(11 Suppl 2):3893S-3897S
14672287
Evolution. 1984 Nov;38(6):1358-1370
28563791
Nature. 2008 Feb 21;451(7181):998-1003
18288195