Chikhi grenoble bioinfo_biodiv_juin_2011

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  • 1. Gntique des populations dans lespace et dans le temps: reconstruire lhistoire dmographique des populations Laboratoire Evolution et Diversit Biologique, CNRS, Toulouse Population and Conservation Genetics Group, IGC, Portugal Biodiversit et Informatique, Grenoble, 28 Juin 2011Photos: E. Qumr, F. Jan, B. Goossens
  • 2. POPULATION AND CONSERVATION GENETICS POPULATION GENETIC DATA Y chromosome mitochondrial DNA ---CAGTCAGTCAGT---CONSERVATION GENETICS HUMAN PAST DEMOGRAPHYHabitat Fragmentation Neolithic TransitionPopulation Decline Admixture in Human PopulationsAdmixture in Domesticates G T G G T T G G G G G NEW METHODS / SOFTWARE
  • 3. Problmatiques Impact de la fragmentation de lhabitat sur la diversit intra-spcifique : Diversit gntique et tailles des fragments Distance gographique entre fragments sur la diffrenciation gntique Barrires au flux gniques (routes, rivires, fleuves, villages, etc.) ? Dterminer, quantifier et dater dventuels vnements dmographiques (goulots dtranglements, expansions, mlanges) ayant influenc la diversit actuelle Importance relative de la fragmentation dorigine anthropique et des phnomnes naturels Importance de la structure spatiale, des expansions et contractions spatiales, de la structure sociale
  • 4. The Kinabatangan Sulu SeaFloodplain 1 cm = 5 km Agricultural lands (mostly oil palm plantations) Lower Kinabatangan Wildlife Sanctuary Virgin Jungle Reserves Kinabatangan River Main road (Sandakan Lahad Datu) Villages
  • 5. The Data 279 samples collected with 32 twice (hair + faeces) 247 individuals (176 nests and 71 faeces) extracted and amplified 200 individuals genotyped for 14 microsatellite loci divided into 9 samples (S1 to S9) 14*200 = 2800 genotypes (7 missing = 0.25%) 2 di and 12 tetra loci.
  • 6. Size Model of Beaumont 1999 and Storz et Beaumont, 2002 Linear Exponential N1 > N0 ? Parameters: N0 : current size N1 : ancestral size ta: nb of generations since the pop started to increase or decreaseN0 Reparameterize: r = N0/N1 tf = ta/ N0 = 2 N0 N1 < N0 ? Sampling ta (in generations) Past Present Time
  • 7. Model of Beaumont 1999 Microsatellite Data Storz and Beaumont, 2002Linear Exponential Microsatellite Data r = N0/N1 tf = ta/ N0 Exponential = 2 N0 N 0, N 1, t a,
  • 8. Population size change
  • 9. Time since the population size change FE: Forest exploitation F: Farmers HG: Hunter-gatherers thin line: S1 thick line : S2
  • 10. Conclusions (at the time)1. Strong signal for a bottleneck2. The signal is robust to the mutation model3. The signal is robust to a linear or exponential decrease (assuming a specific mutation model)4. The population decrease is very important5. The population decrease is very recent: recent anthropogenic changes
  • 11. Habitat Fragmentation (and loss) in Daraina 44 000 ha of fragmented forest Loky River Indian Ocean Manambato River Golden-crowned sifaka Propithecus tattersalli Erwan Qumr
  • 12. Habitat Fragmentation (and loss ?) in Daraina 44 000 ha of fragmented forest Ocan IndienPictures: E. Qumr
  • 13. Habitat Fragmentation (and loss) in Daraina Faeces from 230 individuals (105 social groups) 13 microsatellites Questions: 1. Role of the road as a barrier to gene flow 2. Role of savanna / grasslands 3. Role of the Manankolana river
  • 14. Habitat Fragmentation (and loss) in DarainaRle de la rivire Manakolana: * structure la diversit * ancienne barrire ? * lieu de peuplements humains ? * etc.
  • 15. Habitat fragmentation and loss time time
  • 16. GENETIC DIVERSITY Past NEW MUTATIONS POPULATION TIME SIZE (FINITE) LOSS OF MUTATIONS Present MUTATIONSGENETIC DIVERSITY GENETIC DRIFT
  • 17. GENETIC DIVERSITYPast Ne = 1000 Ne = 100PresentPresent Ne = 100 Ne = 1000 Ne = 500Present GENETIC DIVERSITY Different demographic histories can produce similar or counter-intuitive results
  • 18. GENETIC DIVERSITY EQUILIBRIUM (N1 pre-bottleneck) HETEROZYGOSITY: function(nA, freq.)NUMBER OF ALLELES EQUILIBRIUM (N0 post-bottleneck) TIME DIFFERENT TEMPORAL DYNAMICS OF THE TWO MEASURES
  • 19. GENETIC DIVERSITY Past Population size change : recognizable signatureTIME A B ... NPresent PROBLEM : STRUCTURED POPULATIONS GENERATE A SIMILAR SIGNATURE TRUE AND FALSE SIGNATURES: WHO SHOULD YOU BELIEVE?...
  • 20. Habitat fragmentation and loss time time
  • 21. Effect of population structure on bottleneck signals Models of population structure (100 demes in all simulations) Stepping-stone n-island model (100 islands) Stepping-stone (10 x 10) (toroidal) n-island Parameters used Stepwise mutation model assumed to simulate data FST values used { 0.01 ; 0.05 ; 0.1 ; 0.25 } Differentiation values used { 1; 10 } Number of loci { 5 ; 20 } Diversity 50 individuals sampled (100 genes) (mutation and pop size) Sampling schemes : n-islands model: samples from 1, 2, 10 and