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Variation:

Variation:. Variation is present within individuals among individuals within populations among populations. Populations that are spatially isolated will tend to diverge genetically genetic drift natural selection and local adaptation. p = .8 q = .2. p = .5 q = .5. p = .7 q = .3.

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Variation:

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  1. Variation: Variation is present • within individuals • among individuals within populations • among populations

  2. Populations that are spatially isolated will tend to diverge genetically • genetic drift • natural selection and local adaptation p = .8 q = .2 p = .5 q = .5 p = .7 q = .3 p = .55 q = .45 p = .5 q = .5

  3. Populations that are spatially isolated will tend to diverge genetically • each population is representative of the species, but may not contain all of the species’ variation • many populations may disappear before the species is endangered

  4. Population models - metapopulations - networks of populations that have some degree of gene flow among geographically separate populations - regular extinction and recolonization events endangered Glanville fritillary butterfly (Finland) – occupies meadows 1600 meadows, of which 320-524 were occupied in 1993-96 approx 200 extinctions and 114 colonizations per year Alan Barnes

  5. Populations that are spatially isolated will tend to diverge genetically • how many subpopulations can we afford to lose? • which ones do we choose to save? how many? • how many do we have habitat for? • how different is different enough to warrant isolation/preservation?

  6. Populations that are spatially isolated will tend to diverge genetically • how many subpopulations can we afford to lose? • which ones do we choose to save? how many? • how many do we have habitat for? • how different is different enough to warrant isolation/preservation?

  7. Populations that are spatially isolated will tend to diverge genetically • how many subpopulations can we afford to lose? • which ones do we choose to save? how many? • how many do we have habitat for? • how different is different enough to warrant isolation/preservation? how well can we describe differences among populations?

  8. Measurement of genetic differentiation among populations: genetic distance (D) • Quantitative measure of genetic divergence between two sequences, individuals, or taxa • Relative estimate of the time that has past since two populations existed as a single, panmictic population

  9. Three most commonly used distance measures • Nei’s genetic distance (Nei, 1972) • Cavalli-Sforza chord measure (Cavalli-Sforza and Edwards, 1967) • Reynolds, Weir, and Cockerham’s genetic distance (1983) • Nei’s assumes that differences arise due to mutation and genetic drift, C-S and RWC assume genetic drift only

  10. Nei’s Genetic Distance Assumes: • All loci have same rate of neutral mutation • Mutation-genetic drift equilibrium • Stable effective population size

  11. Genetic distance Nei’s genetic distance surveyed over wide variety of taxa: geographic populations 0.024 + 0.003 subspecies 0.171 + 0.004 species 0.626 + 0.028 genera 1.340 + 0.064 Avise and Smith 1977, Davis 1983

  12. Genetic distance Fixed alleles – single allele at freq. = 1.0 Rare alleles - < 0.05% Private alleles – unique to one population

  13. Genetic distance (D) Dendrogram of genetic distances: (clustered using UPGMA, Unweighted Pair-Group Method with Arithmetic Mean: each new unit has a distance to the cluster = average of the distance from unit to each species in the cluster)

  14. Lampsilis cardium (pocketbook mussel) Lampsilis ovata (pocketbook mussel)

  15. Lampsilis cardium (pocketbook mussel) Lampsilis ovata (pocketbook mussel)

  16. Lampsilis cardium (pocketbook mussel) WV L. ovata IL L. cardium WV L. cardium VT L. “ovata” MO L. cardium WV L. fasciola 0.00 0.01 0.02 0.03 0.04 0.9 Nei’s genetic distance Lampsilis ovata (pocketbook mussel)

  17. Genetic distance (D)

  18. Genetic distance (D)

  19. Quantifying the distribution of variation T = total population S = subpopulations I = individuals

  20. Quantifying the distribution of variation Fis - inbreeding coefficient of individual relative to its sub- population FIS = HS – HI HS where: HS is average expected heterozygosity in each subpopulation HI is average observed heterozygosity

  21. Quantifying the distribution of variation Fis - inbreeding coefficient of individual relative to its sub- population FIS = HS – HI HS used to detect departures from Hardy-Weinberg equilibrium in "good" single populations positive value = heterozygote deficiency (Wahlund effect) zero value = all sub-populations in Hardy-Weinberg equilibrium (random mating within subpopulations) negative value = heterozygote excess

  22. Quantifying the distribution of variation Fst - inbreeding coefficient of sub-population relative to the whole population = fixation index FST = HT – HS HT HT = average expected heterozygosity in the pooled populations

  23. Quantifying the distribution of variation Fst - inbreeding coefficient of sub-population relative to the whole population = fixation index FST = HT – HS HT measures degree of population differentiation within species always positive 0.00 = sub-popns have same allele frequencies 0.05-0.15 = moderate differentiation 0.15-0.25 = great differentiation >0.25 = extremely different 1.0 = popns fixed for different alleles

  24. Quantifying the distribution of variation Fit - inbreeding coefficient of individuals relative to whole population FIT = HT – HI HT

  25. Quantifying the distribution of variation Fit - inbreeding coefficient of individuals relative to whole population FIT = HT – HI HT seldom used; any departure from single panmictic population will lead to significant value used to detect departures from Hardy-Weinberg equilibrium in the total population

  26. populations are gradually going extinct – but more than one species (Daugherty et al. 1990) Tuatara – New Zealand

  27. Tuatara – New Zealand little genetic differentiation between subpopulations black rhino www.southafrica.net

  28. Genetic diversity among populations Increases due to isolation, genetic drift Decreases due to gene flow (migration)

  29. Population models - metapopulations - networks of populations that have some degree of gene flow among geographically separate populations - regular extinction and recolonization events

  30. Population models - metapopulations - source-sink populations SINK SOURCE

  31. Population models - metapopulations - source-sink populations - isolation by distance

  32. Clegg, S.M., S.M. Degnan, J. Kikkawa, et al. 2002. Genetic consequences of sequential founder events by an island-colonizing bird. PNAS 99:8127-8132 silvereye (Zosterops lateralis)

  33. Gene flow among populations as migrants move between populations, they homogenize allele frequencies among populations

  34. Gene flow among populations as migrants move between populations, they homogenize allele frequencies among populations - Is this good or bad? consider invasions, stocked species…

  35. Gene flow among populations Δp = m(p1 – p2) change in allele frequency is a function of the migration rate and the difference in allele frequencies between the original populations

  36. Gene flow among populations gene flow (migration) • larger populations diverge slowly through drift – few migrants needed to counteract • small populations diverge rapidly through drift – more migrants needed to counteract

  37. Issues with genetic diversity among populations outbreeding depression/hybridization • local adaptation

  38. Issues with genetic diversity among populations outbreeding depression/hybridization • local adaptation example: ibex extirpated from Czechoslovakia (Capra ibex ibex) - transplanted from Austria successfully (Capra ibex ibex) - then added bezoars (C. i. aegagrus) and Nubian ibex (C. i. nubiana) - fertile hybrids rutted in early fall instead of winter (as natives did) - kids of hybrids born in February, coldest month of year, entire population went extinct David Hall

  39. Issues with genetic diversity among populations outbreeding depression/hybridization • local adaptation • co-adapted gene complexes

  40. inbreeding depression outbreeding depression Reproductive success inbreeding random mating inter-breeding

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