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Popula'onGenomicsofHumanAdapta'on,Part2
Tes'ngForAdap'veEvolu'on
1) Ka/Ks>12) Ka/Ks>Pa/Ps
Tes'ngForAdap'veEvolu'on
1) Ka/Ks>12) Ka/Ks>Pa/Ps
-BOTH METHODS REQUIRE RECURRENT ADAPTIVE EVOLUTION
Tes'ngForAdap'veEvolu'on
1) Ka/Ks>12) Ka/Ks>Pa/Ps
-BOTH METHODS REQUIRE RECURRENT ADAPTIVE EVOLUTION -PICK UP GENES SUBJECT TO RECURRENT ADAPTATION, E.G. IMMUNITY AND REPRODUCTIVE GENES
Tes'ngForAdap'veEvolu'on
1) Ka/Ks>12) Ka/Ks>Pa/Ps
-BOTH METHODS REQUIRE RECURRENT ADAPTIVE EVOLUTION -PICK UP GENES SUBJECT TO RECURRENT ADAPTATION, E.G. IMMUNITY AND REPRODUCTIVE GENES -WHAT ABOUT UNIQUE EVENTS OF ADAPTIVE EVOLUTION?
Tes'ngForAdap'veEvolu'on
1) Ka/Ks>12) Ka/Ks>Pa/Ps
-BOTH METHODS REQUIRE RECURRENT ADAPTIVE EVOLUTION -PICK UP GENES SUBJECT TO RECURRENT ADAPTATION, E.G. IMMUNITY AND REPRODUCTIVE GENES -WHAT ABOUT UNIQUE EVENTS OF ADAPTIVE EVOLUTION? -WHAT ABOUT RECENT POSITIVE SELECTION ACTING WITHIN HUMAN POPULATIONS (local adaptation)?
Tes'ngForAdap'veEvolu'on
1) Ka/Ks>12) Ka/Ks>Pa/Ps3) NEUTRALPOLYMORPHISM!
EffectofPosi'veSelec'ononNEUTRALPOLYMORPHISM
EffectofPosi'veSelec'ononNEUTRALPOLYMORPHISM
Neutral variation is reduced with positive selection
EffectsofPosi'veSelec'ononNeutralPolymorphism
increase in linkage disequilibrium
EffectsofPosi'veSelec'ononNeutralPolymorphism
shift in SNP frequencies
EffectsofPosi'veSelec'ononNeutralPolymorphism
Increased differentiation among populations
Posi'veselec'oneffects
1) Reduceddiversity2) shiPsinSNPfrequencies(excesslow
frequency)3) Increaseinlinkagedisequilibrium4) increaseinpopula'ondifferen'a'on
Dis'nguishingNaturalSelec'onvs.Demographichistory:Genome-widepa\ernsofdiversity
• demographiceffectsshouldactgenome-wide,inaconsistentmanner
Dis'nguishingNaturalSelec'onvs.Demographichistory:Genome-widepa\ernsofdiversity
• demographiceffectsshouldactgenomewide,inaconsistentmanner
• naturalselec'oncausesinconsistenciesamonggenesintheirpa\ernsofdiversity
Dis'nguishingNaturalSelec'onvs.Demographichistory:Genome-widepa\ernsofdiversity
• demographiceffectsshouldactgenomewide,inaconsistentmanner
• naturalselec'oncausesinconsistenciesamonggenesintheirpa\ernsofdiversity
• challenge:howcanweusethisprincipletounderstandtheroleofselec'onvs.demographyonpa\ernsofdiversity?
Dis'nguishingNaturalSelec'onvs.Demographichistory:Genome-widepa\ernsofdiversity
• demographiceffectsshouldactgenomewide,inaconsistentmanner
• naturalselec'oncausesinconsistenciesamonggenesintheirpa\ernsofdiversity
• challenge:howcanweusethisprincipletounderstandtheroleofselec'onvs.demographyonpa\ernsofdiversity?
characterizegenomicdistribu'onofpa\ernsofgene'c
diversity
Dis'nguishingDemographyandSelec'on
• Inagenomiccontext,cantheresultsbeexplainedbyasinglehistoricalmodel,orarethereinconsistenciesacrossgenesintheirhistory?
SignalofPosi'veSelec'on:ExampleofFOXP2
• muta'onsingenewithinhumansknowntoconferspecificaffectsonlanguageaquisi'on/grammarabili'es
• firstgenepossiblyimplicatedindevelopmentofhumanlanguageability
• twoaminoaciddifferencesfromchimpanzees,onepossiblyfunc'onal
Enard et al Nature 418, 869-872(22 August 2002)
Pa\ernsofDiversityatFOXP2
• unusualexcessoflow-frequencypolymorphisms(only1in315referencegenesshowedsuchanextremeexcess)
• modelingtheselec'vesweepconsistentwithselec'onhappeninginthelast200,000years
Enard et al Nature 418, 869-872(22 August 2002)
Evolu'onofSkinPigmenta'on:LocalAdapta'onAssociatedWithUVradia'on
Evolu'onofSkinPigmenta'on:LocalAdapta'onAssociatedWithUVradia'on
Annual Mean UVB Intensity
Jablonski and Chaplin PNAS May 11, 2010 vol. 107 no. Supplement 2 8962-8968
Tradeoffsassociatedwithlightanddarkpigmenta'on
Jablonski and Chaplin PNAS May 11, 2010 vol. 107 no. Supplement 2 8962-8968
TradeoffsassociatedwithSkinpigmenta'on
• HighUVradia'on:interfereswithfolate,selectsforincreasedpigmenta'on
• lowUVradia'on:reducesvitaminDsynthesis,selectsforreducedpigmenta'on
Posi'veSelec'ononSkinPigmenta'on
-SLC24A5 one of approx. 10 genes implicated in pigmentation -reduction in polymorphism in European population -includes one of only two fixed differences between European and East Asian population samples
Lamason et al Science 16 December 2005: Vol. 310 no. 5755 pp. 1782-1786
Scanning the Genome For Positive Selection/Adaptive Fixations
Rasmus Nielsen, UC Berkeley
-CLR statistic: compares probability that a region has its own SNP frequency distribution compared with the probability that it’s part of the genome-wide distribution
Williamson et al (PLoS Genet. 2007 Jun;3(6):e90. Epub 2007 Apr 20)
Evidence for Adaptive Evolution in Pigmentation Genes
Scanning the Genome For Positive Selection/Adaptive Fixations
-Williamson et al (PLoS Genet. 2007 Jun;3(6):e90. Epub 2007 Apr 20) Identified 101 regions showing strong signature of selection -genes under positive selection included pigmentation genes, immunity genes, olfactory receptors -as much as 10% of genome linked to regions subject to selective sweeps??
Whataboutincompletesweeps?
• veryrecentposi'veselec'onandlocaladapta'onmayoPenNOTshowfixa'onevents
• scansforallelesathighfrequencywithlowdiversity
EffectsofPosi'veSelec'ononNeutralPolymorphism
increase in linkage disequilibrium
SignalsofongoingPosi'veSelec'on
Advantageous allele at high frequency, found on only one genomic background
Mutations, Phenotype, and fitness: e.g. of G6PD
Mutations, Phenotype, and fitness: e.g. of G6PD
DNA B GTG AAT CTA TGTA A- ATG GAT CTG TGTG
protein (allozymes)
B A-
phenotype B ‘wild type’ A- reduced enzyme activity/resistance to malaria
+
-
Val Asn Leu Met Asp Leu
negative
neutral
RecentPosi'veSelec'onatG6PDlocus
LactasePersistence:Gene/CultureCoevolu'on
• Lactasegenetypicallydown-regulatedinadults• pastoralculturesshowlactosetoleranceintoadulthood
SignalsofPosi'veSelec'ononLactasePersistence
Bersaglieri et al, American Journal of Human Genetics Volume 74, Issue 6, June 2004, Pages 1111-1120
• independentevolu'onoflactosetoleranceinAfricaandEurasia
ConvergentEvolu'onofLactasePersistence
Tishkoff et al Nature Genetics 39, 31 - 40 (2006)
SignatureofPosi'veSelec'ononLactasePersistenceinbothAfrica
andEurasia
-persistence allele shows very low diversity despite being common =high linkage disequilibrium -diversity patterns consistent with selective sweep in past 7000 years
Tishkoff et al Nature Genetics 39, 31 - 40 (2006)
Genome-WideScanforRecentPosi'veSelec'on
Jonathan Pritchard, University of Chicago
Genome-WideScansforPosi'veSelec'on
Voight et al PLoS Biol. 2006 March; 4(3): e72.
WhatGenesShowEvidenceforposi'veselec'on?
• reproduc'on:Spermmo'lity,spermandeggviability,femaleimmuneresponsetosperm
• skinpigmenta'on-fourgenesshowevidenceforrecentposi'veselec'oninEuropeanpopula'ons
• diet:carbohydratemetabolism,processingoffa\yacids
YietalScience2July2010:Vol.329no.5987pp.75-78
Fig. 1 Two-dimensional unfolded site frequency spectrum for SNPs in Tibetan (x axis) and Han (y axis) population samples.
X Yi et al. Science 2010;329:75-78
Published by AAAS
Fig. 2 Population-specific allele frequency change.
X Yi et al. Science 2010;329:75-78
Published by AAAS
GenesSubjecttoAdapta'ontoHighEleva'on
-EPAS1: transcription factor involved in hypoxia response -associated with lower hemoglobin and lower erythrocyte counts at high elevation