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Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs
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نویسنده
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freedman a.h. ,schweizer r.m. ,ortega-del vecchyo d. ,han e. ,davis b.w. ,gronau i. ,silva p.m. ,galaverni m. ,fan z. ,marx p. ,lorente-galdos b. ,ramirez o. ,hormozdiari f. ,alkan c. ,vilà c. ,squire k. ,geffen e. ,kusak j. ,boyko a.r. ,parker h.g. ,lee c. ,tadigotla v. ,siepel a. ,bustamante c.d. ,harkins t.t. ,nelson s.f. ,marques-bonet t. ,ostrander e.a. ,wayne r.k. ,novembre j.
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منبع
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plos genetics - 2016 - دوره : 12 - شماره : 3
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چکیده
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Controlling for background demographic effects is important for accurately identifying loci that have recently undergone positive selection. to date,the effects of demography have not yet been explicitly considered when identifying loci under selection during dog domestication. to investigate positive selection on the dog lineage early in the domestication,we examined patterns of polymorphism in six canid genomes that were previously used to infer a demographic model of dog domestication. using an inferred demographic model,we computed false discovery rates (fdr) and identified 349 outlier regions consistent with positive selection at a low fdr. the signals in the top 100 regions were frequently centered on candidate genes related to brain function and behavior,including lhfpl3,cadm2,grik3,sh3gl2,mbp,pde7b,ntan1,and glra1. these regions contained significant enrichments in behavioral ontology categories. the 3rdtop hit,ccrn4l,plays a major role in lipid metabolism,that is supported by additional metabolism related candidates revealed in our scan,including scp2d1 and pdxc1. comparing our method to an empirical outlier approach that does not directly account for demography,we found only modest overlaps between the two methods,with 60% of empirical outliers having no overlap with our demography-based outlier detection approach. demography-aware approaches have lower-rates of false discovery. our top candidates for selection,in addition to expanding the set of neurobehavioral candidate genes,include genes related to lipid metabolism,suggesting a dietary target of selection that was important during the period when proto-dogs hunted and fed alongside hunter-gatherers. © 2016,public library of science. all rights reserved.
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آدرس
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department of ecology and evolutionary biology,university of california,los angeles,los angeles,ca, United States, department of ecology and evolutionary biology,university of california,los angeles,los angeles,ca, United States, department of ecology and evolutionary biology,university of california,los angeles,los angeles,ca, United States, department of ecology and evolutionary biology,university of california,los angeles,los angeles,ca, United States, national human genome research institute,national institutes of health,bethesda,md, United States, department of biological statistics and computational biology,cornell university,ithaca,ny, United States, cibio-up,university of porto,vairão, Portugal, ispra,ozzano dell’emilia, Italy, key laboratory of bioresources and ecoenvironment,sichuan university,chengdu, China, department of measurement and information systems,budapest university of technology and economics,budapest, Hungary, icrea at institut de biologia evolutiva (csic-universitat pompeu fabra),barcelona, Spain, icrea at institut de biologia evolutiva (csic-universitat pompeu fabra),barcelona, Spain, department of computer science,university of california,los angeles,los angeles,ca, United States, bilkent university,ankara, Turkey, estación biológia de doñana ebd-csic,sevilla, Spain, department of human genetics,university of california,los angeles,los angeles,ca, United States, department of zoology,tel aviv university,tel aviv, Israel, department of biology,university of zagreb,zagreb, Croatia, department of biomedical sciences,cornell university,ithaca,ny, United States, icrea at institut de biologia evolutiva (csic-universitat pompeu fabra),barcelona, Spain, life technologies,foster city,ca, United States, life technologies,foster city,ca, United States, simons center for quantitative biology,cold spring harbor laboratory,cold spring harbor,ny, United States, stanford school of medicine,stanford,ca, United States, life technologies,foster city,ca, United States, department of human genetics,university of california,los angeles,los angeles,ca, United States, icrea at institut de biologia evolutiva (csic-universitat pompeu fabra),barcelona,spain,centro nacional de analisis genomico (cnag/pcb),baldiri reixach 4–8,barcelona, Spain, national human genome research institute,national institutes of health,bethesda,md, United States, department of ecology and evolutionary biology,university of california,los angeles,los angeles,ca, United States, department of ecology and evolutionary biology,university of california,los angeles,los angeles,ca,united states,department of human genetics,university of chicago,chicago,il, United States
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Authors
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