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Genetic Structure of Chimpanzee Populations

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Genetic Structure of Chimpanzee Populations OurOur endangeredendangered cousinscousins thethe greatgreat apesapes CelineCeline BecquetBecquet Dept. Human Genetics Molly Przeworski’’s Lab Feb 2008 Marcelo Nobrega Aaron Turkewitz OutlineOutline ReviewReview onon conservationconservation geneticsgenetics IntroductionIntroduction toto ourour endangeredendangered cousinscousins NotionNotion ofof species,species, subspecies/populationsubspecies/population InvestigatingInvestigating thethe geneticsgenetics structurestructure ofof commoncommon chimpanzeechimpanzee HowHow badbad isis it?it? Conservation Genetics Conservation biology studies populations affected by habitat loss, exploitation, and/or environmental change. Used to be address from a mathematical, evolutionary, or taxonomic point of view Maximizes the number of individuals in the population AND ensures that they have the capacity for continued adaptation to a changing environment. This capacity is brought about by genetic diversity and it is essential that this is maintained. z “effective” population size is positively correlated with the genetic diversity possessed by the population as a whole. The loss of genetic variation decreases a species’ ability to evolve to deal with change in the environment Event kill 80% non-blue Inbreeding reduces population fitness % Hatch % deformed % change for a Measure of fitness Egg Mass Survival weight Random genetic drift becomes the main evolutionary process, instead of natural selection N=10 Simulations of genetic drift for 20 alleles with initial frequency 0.5. In general, alleles drift to fixation (frequency of 0 or 1) significantly faster in smaller populations. Thus even harmful mutations can accumulate N= 100 Conservation Genetics GeneticsGenetics studiesstudies thethe inheritanceinheritance andand investigatesinvestigates thethe genesgenes responsibleresponsible forfor inheritedinherited traits.traits. Provides new insights into the extent of diversity among the individuals in a population Without using genetics, we could focus our efforts on the wrong population or waste valuable resources on a population that isn't as endangered… TheThe greatgreat apesapes ~15 My Our closest living relatives. 95-99% of DNA shared between human and chimpanzees. Living models to understand the evolution of biology and culture of humans. Endangered environments and species. ~8 My ~6-7 My ~.8 My Notion of species and subspecies or population A species is a group of organisms capable of interbreeding and producing fertile offspring Notion of species and subspecies or population Notion of species and subspecies or population A species is a group of organisms capable of interbreeding and producing fertile offspring Gorilla, orangutans and chimpanzee are clearly different species. What about bonobo and chimpanzees? Some hybrids reported, but none in the wild (don’’t overlap in their current ranges). Notion of species and subspecies or population A species is a group of organisms capable of interbreeding and producing fertile offspring Gorilla, orangutans and chimpanzee are clearly different species. What about bonobo and chimpanzees? Some hybrids reported, but non in the wild. (don’’t overlap in their current ranges). What is a subspecies? GeographicalGeographical rangesranges ofof thethe greatgreat apeape populationspopulations andand speciesspecies Western Sumatran Central Eastern Bornean bonobos Western Eastern GeographicalGeographical rangerange ofof OrangutansOrangutans Bornean Sumatran VAN SCHAIK et al. 2003 GeographicalGeographical rangerange ofof GorillasGorillas Western Eastern Thalmann et al. 2006 GeographicalGeographical rangerange ofof chimpanzeeschimpanzees eastern western bonobo central Won & Hey 2005 GeneticGenetic StructureStructure ofof ChimpanzeeChimpanzee PopulationsPopulations Celine Becquet, Nick Patterson, Anne Stone, Molly Przeworski and David Reich 2007, PloS Genetics 3:e66. GeneticGenetic StructureStructure ofof ChimpanzeeChimpanzee PopulationsPopulations GoalsGoals ofof thethe studystudy Do the subspecies labels correspond to well- defined genetic populations? Is there evidence of migration between them? How many genetic markers do we need to assign individuals? What about the individuals of unknown origins? DataData -- SamplesSamples 66 labelslabels –– 8484 individualsindividuals 16 Central 7 Eastern 41 Western (1 w/ “Nigerian mtDNA”) 11 Unknown chimpanzee subspecies (1 w/ “Nigerian mtDNA”) 3 Hybrid (1 w/ “Nigerian mtDNA”) 6 Bonobos DataData –– 5151 WildWild SamplesSamples 66 labelslabels –– 8484 individualsindividuals 16 Central (12 wild) z Gabon / province of Gabon 7 Eastern (6 wild) z Country of origin 41 Western (33 wild - 1 w/ “Nigerian mtDNA”) z Sierra-Leone or unknown origin 11 Unknown chimpanzee subspecies (1 w/ “Nigerian mtDNA”) 3 Hybrid (1 w/ “Nigerian mtDNA”) 6 Bonobos OriginOrigin ofof wildwild chimpanzeechimpanzee samplessamples eastern western bonobo central Won & Hey 2005 IdealIdeal samplingsampling eastern western bonobo central Won & Hey 2005 ChimpChimp nestnest ChimpChimp nestnest ChimpChimp nestnest BonoboBonobo nestnest OrangutanOrangutan nestnest OrangutanOrangutan nestnest OrangutanOrangutan nestnest SamplingSampling inin thethe fieldfield GorillaGorilla nestnest DataData –– GeneticGenetic MarkersMarkers 310310 MicrosatellitesMicrosatellites GoodGood qualityquality (estimated(estimated basedbased onon duplicates:duplicates: averageaverage ofof twotwo erroneouserroneous genotypegenotype callscalls perper individual)individual) 295295 autosomalautosomal markersmarkers 221221 tetratetra--,, 6262 tritri--,, 1111 didi--nucleotidesnucleotides WhyWhy microsatellitesmicrosatellites?? WhyWhy microsatellitesmicrosatellites?? You genotype Marker 1 From mum From dad Marker 2 Marker 3 WhyWhy microsatellitesmicrosatellites?? You genotype Marker 1 From mum From dad Marker 2 Marker 3 UsefulUseful becausebecause HighlyHighly variablevariable (usually(usually twotwo differentdifferent allelesalleles withinwithin anan individual)individual) FingerprintsFingerprints areare usedused inin forensicforensic andand paternity/parentagepaternity/parentage teststests ProgramProgram STRUCTURESTRUCTURE 1. There are 4 populations each of which is characterized by a set of allele frequencies at each marker. Pop1 Pop2 Pop3 Pop4 50% 75% 1% 50% Marker 4 25% 25% 75% 50% 25% 24% Pritchard et al. 2000 ProgramProgram STRUCTURESTRUCTURE 1. There are 4 populations each of which is characterized by a set of allele frequencies at each marker. Pop1 Pop2 Pop3 Pop4 50% 75% 1% 50% Marker 4 25% 25% 75% 50% 25% 24% 2. Individuals in the sample are assigned to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Marker 4 for Population of individual 1 individual 1 Marker 4 for Population of individual 2 individual 2 Pritchard et al. 2000 ProgramProgram STRUCTURESTRUCTURE 1. There are 4 populations each of which is characterized by a set of allele frequencies at each marker. Pop1 Pop2 Pop3 Pop4 50% 75% 1% 50% Marker 4 25% 25% 75% 50% 25% 24% 2. Individuals in the sample are assigned to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Marker 4 for Population of individual 1 individual 1 Marker 4 for Population of individual 2 individual 2 3. Loop on 1 and 2 until it fits the data Pritchard et al. 2000 OutputOutput ofof thethe ProgramProgram STRUCTURESTRUCTURE The 2 alleles at the 310 markers for this individuals pop1 pop2 pop3 Pritchard et al. 2000 STRUCTURESTRUCTURE withwith fourfour clustersclusters Wild-caught hybrids Central Eastern Western Bonobos Unknown Hybrids Nigerian mtDNA Pritchard et al. 2000 ConceptConcept ofof InformativenessInformativeness Different alleles 60% Marker 1 100% 40% Marker 2 50% 10% 50% 50% 40% Marker 3 100% 5% 95% Marker 4 10% 90% 50% 50% Pop1 Pop2 ConceptConcept ofof InformativenessInformativeness Different alleles 60% Marker 1 100% 40% Marker 2 50% 10% 50% 50% 40% Marker 3 100% 5% 95% Marker 4 10% 90% 50% 50% Pop1 Pop2 ConceptConcept ofof InformativenessInformativeness Calculated the informativeness of the markers (Rosenberg et al. 2002) Run STRUCTURE for different set of most informative markers Found: 30 most informative markers = minimum set to find four clusters. 71/75 samples assigned to same cluster. Identified 6/9 hybrids. PopulationPopulation differentiation:differentiation: FFST Total genetic variation Totvar −Withinvar Within-population FST = Genetic variation Totvar Central Eastern F = 0.05 STC ,E PopulationPopulation differentiation:differentiation: FFST Total genetic variation Within-population Genetic variation Central Eastern F = 0.05 STC ,E Central Western Eastern Western F = 0.25 F = 0.31 STC ,W STE ,W F = 0.51− 0.68 STBonobo−chimpanzee TellsTells usus aboutabout thethe historyhistory ofof thesethese populationspopulations andand speciesspecies Central Eastern Western Bonobos DivergenceDivergence timetime estimatesestimates fromfrom anotheranother studystudy ~785-920ky ~280-440ky ~220ky Central Eastern Western Bonobos ConclusionsConclusions ofof thethe studystudy The subspecies labels correspond to genetically defined populations. Little evidence of migration in the wild (at least with these samples). Central and Eastern chimpanzee are more closely related than they are to Western chimpanzee. Propose 30 markers which provide excellent power for classification HowHow badbad isis it?it? The chimpanzee, gorilla, bonobo and orangutan are listed as endangered species AllAll thethe greatgreat apeape
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