References
Akey JM
(2009) Constructing genomic maps of positive selection in humans: where do we go from here? Genome Research 19: 711–722.
Akey JM
,
Zhang G
,
Zhang K
,
Jin L
and
Shriver MD
(2002) Interrogating a high‐density SNP map for signatures of natural selection. Genome Research 12: 1805–1814.
Andersen KG
,
Shylakhter I
,
Tabrizi S
et al. (2012) Genome‐wide scans provide evidence for positive selection of genes implicated in Lassa fever. Philosophical Transactions of the Royal Society of London Series B: Biological Sciences 367: 868–877.
Andres AM
,
Soldevila M
,
Navarro A
et al. (2004) Positive selection in MAOA gene is human exclusive: determination of the putative amino acid change selected in the human lineage. Human Genetics 115: 377–386.
Aoki K
(2002) Sexual selection as a cause of human skin colour variation: Darwin's hypothesis revisited. Annals of Human Biology 29: 589–608.
Barreiro LB
and
Quintana‐Murci L
(2010) From evolutionary genetics to human immunology: how selection shapes host defence genes. Nature Reviews Genetics 11: 17–30.
Bersaglieri T
,
Sabeti PC
,
Patterson N
et al. (2004) Genetic signatures of strong recent positive selection at the lactase gene. American Journal of Human Genetics 74: 1111–1120.
Bigham A
,
Bauchet M
,
Pinto D
et al. (2010) Identifying signatures of natural selection in Tibetan and Andean populations using dense genome scan data. PLoS Genetics 6: e1001116.
Bird CP
,
Stranger BE
,
Liu M
et al. (2007) Fast‐evolving noncoding sequences in the human genome. Genome Biology 8: R118.
Bustamante CD
,
Fledel‐Alon A
,
Williamson S
et al. (2005) Natural selection on protein‐coding genes in the human genome. Nature 437: 1153–1157.
Carlson CS
,
Thomas DJ
,
Eberle MA
et al. (2005) Genomic regions exhibiting positive selection identified from dense genotype data. Genome Research 15: 1553–1565.
Clark AG
,
Glanowski S
,
Nielsen R
et al. (2003) Inferring nonneutral evolution from human‐chimp‐mouse orthologous gene trios. Science 302: 1960–1963.
Currat M
,
Trabuchet G
,
Rees D
et al. (2002) Molecular analysis of the beta‐globin gene cluster in the Niokholo Mandenka population reveals a recent origin of the beta(S) Senegal mutation. American Journal of Human Genetics 70: 207–223.
Ding YC
,
Chi HC
,
Grady DL
et al. (2002) Evidence of positive selection acting at the human dopamine receptor D4 gene locus. Proceedings of the National Academy of Sciences of the USA 99: 309–314.
Enard W
,
Przeworski M
,
Fisher SE
et al. (2002) Molecular evolution of FOXP2, a gene involved in speech and language. Nature 418: 869–872.
Enattah NS
,
Sahi T
,
Savilahti E
et al. (2002) Identification of a variant associated with adult‐type hypolactasia. Nature Genetics 30: 233–237.
Fay JC
and
Wu CI
(2000) Hitchhiking under positive Darwinian selection. Genetics 155: 1405–1413.
Fujimoto A
,
Kimura R
,
Ohashi J
et al. (2008). A scan for genetic determinants of human hair morphology: EDAR is associated with Asian hair thickness. Human Molecular Genetics 17: 835–843.
Fullerton SM
,
Bartoszewicz A
,
Ybazeta G
et al. (2002) Geographic and haplotype structure of candidate type 2 diabetes susceptibility variants at the calpain‐10 locus. American Journal of Human Genetics 70: 1096–1106.
Fumagalli M
,
Sironi M
,
Pozzoli U
et al. (2011) Signatures of environmental genetic adaptation pinpoint pathogens as the main selective pressure through human evolution. PLoS Genetics 7: e1002355.
Gilad Y
,
Rosenberg S
,
Przeworski M
,
Lancet D
and
Skorecki K
(2002) Evidence for positive selection and population structure at the human MAO‐A gene. Proceedings of the National Academy of Sciences of the USA 99: 862–867.
Goldman D
and
Enoch MA
(1990) Genetic epidemiology of ethanol metabolic enzymes: a role for selection. World Review of Nutrition and Dietetics 63: 143–160.
Green RE
,
Krause J
,
Briggs AW
et al. (2010) A draft sequence of the Neandertal genome. Science 328: 710–722.
Grossman SR
,
Andersen KG
,
Shlyakhter I
et al. (2013) Identifying recent adaptations in large‐scale genomic data. Cell 152: 703–713.
Grossman SR
,
Shlyakhter I
,
Karlsson EK
et al. (2010) A composite of multiple signals distinguishes causal variants in regions of positive selection. Science 327: 883–886.
Hamblin MT
and
Di Rienzo A
(2000) Detection of the signature of natural selection in humans: evidence from the Duffy blood group locus. American Journal of Human Genetics 66: 1669–1679.
Hamblin MT
,
Thompson EE
and
Di Rienzo A
(2002) Complex signatures of natural selection at the Duffy blood group locus. American Journal of Human Genetics 70: 369–383.
Han Y
,
Gu S
,
Oota H
et al. (2007) Evidence of positive selection on a class I ADH locus. American Journal of Human Genetics 80: 441–456.
Hancock AM
,
Witonsky DB
,
Alkorta‐Aranburu G
et al. (2011) Adaptations to climate‐mediated selective pressures in humans. PLoS Genetics 7: e1001375.
Hancock AM
,
Witonsky DB
,
Gordon AS
et al. (2008) Adaptations to climate in candidate genes for common metabolic disorders. PLoS Genetics 4: e32.
Hedrick PW
,
Whittam TS
and
Parham P
(1991) Heterozygosity at individual amino acid sites: extremely high levels for HLA‐A and ‐B genes. Proceedings of the National Academy of Sciences of the USA 88: 5897–5901.
Hermisson J
and
Pennings PS
(2005) Soft sweeps: molecular population genetics of adaptation from standing genetic variation. Genetics 169: 2335–2352.
Hernandez RD
,
Kelley JL
,
Elyashiv E
et al. (2011) Classic selective sweeps were rare in recent human evolution. Science 331: 920–924.
Hollox EJ
,
Poulter M
,
Zvarik M
et al. (2001) Lactase haplotype diversity in the Old World. American Journal of Human Genetics 68: 160–172.
Hughes AL
and
Nei M
(1988) Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature 335: 167–170.
Jablonski NG
and
Chaplin G
(2000) The evolution of human skin coloration. Journal of Human Evolution 39: 57–106.
Kamberov YG
,
Wang S
,
Tan J
et al. (2013) Modeling recent human evolution in mice by expression of a selected EDAR variant. Cell 152: 691–702.
Katzmarzyk PT
and
Leonard WR
(1998) Climatic influences on human body size and proportions: ecological adaptations and secular trends. American Journal of Physical Anthropology 106: 483–503.
Kelley JL
,
Madeoy J
,
Calhoun JC
,
Swanson W
and
Akey JM
(2006) Genomic signatures of positive selection in humans and the limits of outlier approaches. Genome Research 16: 980–989.
Kim Y
and
Stephan W
(2002) Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics 160: 765–777.
Kimura M
(1968) Evolutionary rate at the molecular level. Nature 217: 624–626.
Kimura R
,
Fujimoto A
,
Tokunaga K
and
Ohashi J
(2007) A practical genome scan for population‐specific strong selective sweeps that have reached fixation. PLoS ONE 2: e286.
Kimura R
,
Ohashi J
,
Matsumura Y
et al. (2008) Gene flow and natural selection in oceanic human populations inferred from genome‐wide SNP typing. Molecular Biology and Evolution 25: 1750–1761.
Kimura R
,
Yamaguchi T
,
Takeda M
et al. (2009) A common variation in EDAR is a genetic determinant of shovel‐shaped incisors. American Journal of Human Genetics 85: 528–535.
Lachance J
,
Vernot B
,
Elbers CC
et al. (2012) Evolutionary history and adaptation from high‐coverage whole‐genome sequences of diverse African hunter–gatherers. Cell 150: 457–469.
Lamason RL
,
Mohideen MA
,
Mest JR
et al. (2005) SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans. Science 310: 1782–1786.
Lao O
,
de Gruijter JM
,
van Duijn K
,
Navarro A
and
Kayser M
(2007) Signatures of positive selection in genes associated with human skin pigmentation as revealed from analyses of single nucleotide polymorphisms. Annals of Human Genetics 71: 354–369.
Li J
,
Liu Y
,
Xin X
et al. (2012) Evidence for positive selection on a number of MicroRNA regulatory interactions during recent human evolution. PLoS Genetics 8: e1002578.
Lopez Herraez D
,
Bauchet M
,
Tang K
et al. (2009) Genetic variation and recent positive selection in worldwide human populations: evidence from nearly 1 million SNPs. PLoS One 4: e7888.
Makova KD
,
Ramsay M
,
Jenkins T
and
Li WH
(2001) Human DNA sequence variation in a 6.6‐kb region containing the melanocortin 1 receptor promoter. Genetics 158: 1253–1268.
Maynard‐Smith J
and
Haigh J
(1974) The hitch‐hiking effect of a favourable gene. Genetical Research 23: 23–35.
McDonald JH
and
Kreitman M
(1991) Adaptive protein evolution at the Adh locus in Drosophila
. Nature 351: 652–654.
McLean CY
,
Reno PL
,
Pollen AA
et al. (2011) Human‐specific loss of regulatory DNA and the evolution of human‐specific traits. Nature 471: 216–219.
Meyer M
,
Kircher M
,
Gansauge MT
et al. (2012) A high‐coverage genome sequence from an archaic Denisovan individual. Science 338: 222–226.
Miura K
,
Yoshiura K
,
Miura S
et al. (2007) A strong association between human earwax‐type and apocrine colostrum secretion from the mammary gland. Human Genetics 121: 631–633.
Miyata T
and
Yasunaga T
(1980) Molecular evolution of mRNA: a method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its application. Journal of Molecular Evolution 16: 23–36.
Nakajima T
,
Wooding S
,
Sakagami T
et al. (2004) Natural selection and population history in the human angiotensinogen gene (AGT): 736 complete AGT sequences in chromosomes from around the world. American Journal of Human Genetics 74: 898–916.
Nakajima T
,
Wooding S
,
Satta Y
et al. (2005) Evidence for natural selection in the HAVCR1 gene: high degree of amino‐acid variability in the mucin domain of human HAVCR1 protein. Genes and Immunity 6: 398–406.
Nakano M
,
Miwa N
,
Hirano A
,
Yoshiura K
and
Niikawa N
(2009) A strong association of axillary osmidrosis with the wet earwax type determined by genotyping of the ABCC11 gene. BMC Genetics 10: 42.
Nei M
and
Gojobori T
(1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Molecular Biology and Evolution 3: 418–426.
Nielsen R
,
Bustamante C
,
Clark AG
et al. (2005a) A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biology 3: e170.
Nielsen R
,
Williamson S
,
Kim Y
et al. (2005b) Genomic scans for selective sweeps using SNP data. Genome Research 15: 1566–1575.
Norton HL
,
Kittles RA
,
Parra E
et al. (2007) Genetic evidence for the convergent evolution of light skin in Europeans and East Asians. Molecular Biology and Evolution 24: 710–722.
Ohashi J
,
Naka I
,
Patarapotikul J
et al. (2004) Extended linkage disequilibrium surrounding the hemoglobin E variant due to malarial selection. American Journal of Human Genetics 74: 1198–1208.
Ohashi J
,
Naka I
and
Tsuchiya N
(2011) The impact of natural selection on an ABCC11 SNP determining earwax type. Molecular Biology and Evolution 28: 849–857.
Oota H
,
Pakstis AJ
,
Bonne‐Tamir B
et al. (2004) The evolution and population genetics of the ALDH2 locus: random genetic drift, selection, and low levels of recombination. Annals of Human Genetics 68: 93–109.
Osier MV
,
Pakstis AJ
,
Soodyall H
et al. (2002) A global perspective on genetic variation at the ADH genes reveals unusual patterns of linkage disequilibrium and diversity. American Journal of Human Genetics 71: 84–99.
Park JH
,
Yamaguchi T
,
Watanabe C
et al. (2012) Effects of an Asian‐specific nonsynonymous EDAR variant on multiple dental traits. Journal of Human Genetics 57: 508–514.
Peng GS
and
Yin SJ
(2009) Effect of the allelic variants of aldehyde dehydrogenase ALDH2*2 and alcohol dehydrogenase ADH1B*2 on blood acetaldehyde concentrations. Human Genomics 3: 121–127.
Perler F
,
Efstratiadis A
,
Lomedico P
et al. (1980) The evolution of genes: the chicken preproinsulin gene. Cell 20: 555–566.
Perry GH
,
Dominy NJ
,
Claw KG
et al. (2007) Diet and the evolution of human amylase gene copy number variation. Nature Genetics 39: 1256–1260.
Pickrell JK
,
Coop G
,
Novembre J
et al. (2009) Signals of recent positive selection in a worldwide sample of human populations. Genome Research 19: 826–837.
Pollard KS
,
Salama SR
,
King B
et al. (2006) Forces shaping the fastest evolving regions in the human genome. PLoS Genetics 2: e168.
Prabhakar S
,
Noonan JP
,
Paabo S
and
Rubin EM
(2006) Accelerated evolution of conserved noncoding sequences in humans. Science 314: 786.
Prabhakar S
,
Visel A
,
Akiyama JA
et al. (2008) Human‐specific gain of function in a developmental enhancer. Science 321: 1346–1350.
Pritchard JK
and
Di Rienzo A
(2010) Adaptation ‐ not by sweeps alone. Nature Reviews Genetics 11: 665–667.
Pritchard JK
,
Pickrell JK
and
Coop G
(2010) The genetics of human adaptation: hard sweeps, soft sweeps, and polygenic adaptation. Current Biology 20: R208–R215.
Prugnolle F
,
Manica A
,
Charpentier M
et al. (2005) Pathogen‐driven selection and worldwide HLA class I diversity. Current Biology 15: 1022–1027.
Przeworski M
,
Coop G
and
Wall JD
(2005) The signature of positive selection on standing genetic variation. Evolution 59: 2312–2323.
Rees JL
(2003) Genetics of hair and skin color. Annual Review of Genetics 37: 67–90.
Reich D
,
Green RE
,
Kircher M
et al. (2010) Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468: 1053–1060.
Roberts DF
(1953) Body weight, race and climate. American Journal of Physical Anthropology 11: 533–558.
Rockman MV
,
Hahn MW
,
Soranzo N
,
Goldstein DB
and
Wray GA
(2003) Positive selection on a human‐specific transcription factor binding site regulating IL4 expression. Current Biology 13: 2118–2123.
Sabeti PC
,
Reich DE
,
Higgins JM
et al. (2002) Detecting recent positive selection in the human genome from haplotype structure. Nature 419: 832–837.
Sabeti PC
,
Varilly P
,
Fry B
et al. (2007) Genome‐wide detection and characterization of positive selection in human populations. Nature 449: 913–918.
Sabeti PC
,
Walsh E
,
Schaffner SF
et al. (2005) The case for selection at CCR5‐Delta32. PLoS Biology 3: e378.
Schaffner SF
,
Foo C
,
Gabriel S
et al. (2005) Calibrating a coalescent simulation of human genome sequence variation. Genome Research 15: 1576–1583.
Schlebusch CM
,
Skoglund P
,
Sjodin P
et al. (2012) Genomic variation in seven Khoe‐San groups reveals adaptation and complex African history. Science 338: 374–379.
Soejima M
,
Tachida H
,
Ishida T
,
Sano A
and
Koda Y
(2006) Evidence for recent positive selection at the human AIM1 locus in a European population. Molecular Biology and Evolution 23: 179–188.
Somel M
,
Liu X
and
Khaitovich P
(2013) Human brain evolution: transcripts, metabolites and their regulators. Nature Reviews Neuroscience 14: 112–127.
Stedman HH
,
Kozyak BW
,
Nelson A
et al. (2004) Myosin gene mutation correlates with anatomical changes in the human lineage. Nature 428: 415–418.
Stephens JC
,
Reich DE
,
Goldstein DB
et al. (1998) Dating the origin of the CCR5‐Delta32 AIDS‐resistance allele by the coalescence of haplotypes. American Journal of Human Genetics 62: 1507–1515.
Storz JF
,
Payseur BA
and
Nachman MW
(2004) Genome scans of DNA variability in humans reveal evidence for selective sweeps outside of Africa. Molecular Biology and Evolution 21: 1800–1811.
Tajima F
(1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585–595.
Takahata N
,
Satta Y
and
Klein J
(1992) Polymorphism and balancing selection at major histocompatibility complex loci. Genetics 130: 925–938.
Tang K
,
Thornton KR
and
Stoneking M
(2007) A new approach for using genome scans to detect recent positive selection in the human genome. PLoS Biology 5: e171.
Tang K
,
Wong LP
,
Lee EJ
,
Chong SS
and
Lee CG
(2004) Genomic evidence for recent positive selection at the human MDR1 gene locus. Human Molecular Genetics 13: 783–797.
Teshima KM
,
Coop G
and
Przeworski M
(2006) How reliable are empirical genomic scans for selective sweeps? Genome Research 16: 702–712.
The Chimpanzee Sequencing and Analysis Consortium (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69–87.
The 1000 Genomes Project Consortium (2010) A map of human genome variation from population‐scale sequencing. Nature 467: 1061–1073.
The International HapMap Consortium (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449: 851–861.
Thompson EE
,
Kuttab‐Boulos H
,
Witonsky D
et al. (2004) CYP3A variation and the evolution of salt‐sensitivity variants. American Journal of Human Genetics 75: 1059–1069.
Tishkoff SA
,
Varkonyi R
,
Cahinhinan N
et al. (2001) Haplotype diversity and linkage disequilibrium at human G6PD: recent origin of alleles that confer malarial resistance. Science 293: 455–462.
Vander Molen J
,
Frisse LM
,
Fullerton SM
et al. (2005) Population genetics of CAPN10 and GPR35: implications for the evolution of type 2 diabetes variants. American Journal of Human Genetics 76: 548–560.
Verrelli BC
,
McDonald JH
,
Argyropoulos G
et al. (2002) Evidence for balancing selection from nucleotide sequence analyses of human G6PD. American Journal of Human Genetics 71: 1112–1128.
Voight BF
,
Kudaravalli S
,
Wen X
and
Pritchard JK
(2006) A map of recent positive selection in the human genome. PLoS Biology 4: e72.
Wang E
,
Ding YC
,
Flodman P
et al. (2004) The genetic architecture of selection at the human dopamine receptor D4 (DRD4) gene locus. American Journal of Human Genetics 74: 931–944.
Wang ET
,
Kodama G
,
Baldi P
and
Moyzis RK
(2006) Global landscape of recent inferred Darwinian selection for Homo sapiens
. Proceedings of the National Academy of Sciences of the USA 103: 135–140.
Williamson SH
,
Hubisz MJ
,
Clark AG
et al. (2007) Localizing recent adaptive evolution in the human genome. PLoS Genetics 3: e90.
Yi X
,
Liang Y
,
Huerta‐Sanchez E
et al. (2010) Sequencing of 50 human exomes reveals adaptation to high altitude. Science 329: 75–78.
Yoshiura K
,
Kinoshita A
,
Ishida T
et al. (2006) A SNP in the ABCC11 gene is the determinant of human earwax type. Nature Genetics 38: 324–330.
Zhou G
,
Zhai Y
,
Dong X
et al. (2004) Haplotype structure and evidence for positive selection at the human IL13 locus. Molecular Biology and Evolution 21: 29–35.
Zimmerman PA
,
Woolley I
,
Masinde GL
et al. (1999) Emergence of FY*A(null) in a Plasmodium vivax‐endemic region of Papua New Guinea. Proceedings of the National Academy of Sciences of the USA 96: 13973–13977.
Further Reading
Biswas S
and
Akey JM
(2006) Genomic insights into positive selection. Trends in Genetics 22: 437–446.
Nielsen R
,
Hellmann I
,
Hubisz M
,
Bustamante C
and
Clark AG
(2007) Recent and ongoing selection in the human genome Nature Reviews Genetics 8: 857–868.
Sabeti PC
,
Schaffner SF
,
Fry B
et al. (2006) Positive natural selection in the human lineage. Science 312: 1614–1620.