quantifying the distribution of variation
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Quantifying the distribution of variation. Variation within individuals within subpopulations among subpopulations (in total population). Quantifying the distribution of variation. Variation within individuals within subpopulations among subpopulations (in total population). - PowerPoint PPT PresentationTRANSCRIPT
Quantifying the distribution of variation
Variationwithin individuals within subpopulations among subpopulations (in total population)
Quantifying the distribution of variation
Variationwithin individuals within subpopulations among subpopulations (in total population)
Quantifying the distribution of variation I = individuals S = subpopulations T = total population
H is observed heterozygosity (# heterozygotes/N) in a populationHI is observed heterozygosity (# heterozygotes/N) averaged over individuals in all subpopulationsHS is expected heterozygosity in each subpopulation if it was in H-W equilibrium, averaged across subpopulationsHT is expected heterozygosity if subpopulations are combined as one population
Quantifying the distribution of variation I = individuals S = subpopulations T = total population
H is observed heterozygosity (# heterozygotes/N) in a populationHI is observed heterozygosity (# heterozygotes/N) averaged over individuals in all subpopulationsHS is expected heterozygosity in each subpopulation if it was in H-W equilibrium, averaged across subpopulationsHT is expected heterozygosity if subpopulations are combined as one population
HS
HS
HS
HT
Quantifying the distribution of variation
HI observed heterozygosity averaged over individuals in all subpopulationsHS expected heterozygosity in each subpopulation (if it was in H-W equilib.) averaged across subpopulationsHT expected heterozygosity if subpopulations are combined as one population
AA AA Aa aa aa Aa Aa Aa Aa AAp 0.5 0.6
H 1/5 = 0.2 4/5 = 0.8
Quantifying the distribution of variation
HI observed heterozygosity averaged over individuals in all subpopulationsHS expected heterozygosity in each subpopulation (if it was in H-W equilib.) averaged across subpopulationsHT expected heterozygosity if subpopulations are combined as one population
AA AA Aa aa aa Aa Aa Aa Aa AAp 0.5 0.6
H 1/5 = 0.2 4/5 = 0.8
HI (0.2 + 0.8)/2 = 0.5
Quantifying the distribution of variation
HI observed heterozygosity averaged over individuals in all subpopulationsHS expected heterozygosity in each subpopulation (if it was in H-W equilib.) averaged across subpopulationsHT expected heterozygosity if subpopulations are combined as one population
AA AA Aa aa aa Aa Aa Aa Aa AAp 0.5 0.6
H 1/5 = 0.2 4/5 = 0.8
HI (0.2 + 0.8)/2 = 0.5
HS (av. of 2pq) 2 x 0.5 x 0.5 = 0.5 2 x 0.6 x 0.4 = 0.48 (0.5 + 0.48)/2 = 0.49
If all subpopulations were in H-W equilibrium, HI would = HS
Quantifying the distribution of variation
HI observed heterozygosity averaged over individuals in all subpopulationsHS expected heterozygosity in each subpopulation (if it was in H-W equilib.) averaged across subpopulationsHT expected heterozygosity if subpopulations are combined as one population
AA AA Aa aa aa Aa Aa Aa Aa AAp 0.5 0.6
H 1/5 = 0.2 4/5 = 0.8
HI (0.2 + 0.8)/2 = 0.5
HS (av. of 2pq) 2 x 0.5 x 0.5 = 0.5 2 x 0.6 x 0.4 = 0.48 (0.5 + 0.48)/2 = 0.49
HT (2 x pav x qav) 2 x 0.55 x 0.45 = 0.495
Quantifying the distribution of variation
HI observed heterozygosity averaged over individuals in all subpopulationsHS expected heterozygosity in each subpopulation (if it was in H-W equilib.) averaged across subpopulationsHT expected heterozygosity if subpopulations are combined as one population
AA AA Aa aa aa Aa Aa Aa Aa AAp 0.5 0.6
H 1/5 = 0.2 4/5 = 0.8
HI (0.2 + 0.8)/2 = 0.5
HS (av. of 2pq) 2 x 0.5 x 0.5 = 0.5 2 x 0.6 x 0.4 = 0.48 (0.5 + 0.48)/2 = 0.49
HT (2 x pav x qav) 2 x 0.55 x 0.45 = 0.495
If all subpopulations were the same, HS would = HT
FIT – reduction in heterozygosity of individuals relative to whole population
FIT = HT – HI
HT
HI observed heterozygosity averaged over individuals in all subpopulationsHS expected heterozygosity in each subpopulation averaged across subpopulationsHT expected heterozygosity if subpopulations are combined as one population
FIT – reduction in heterozygosity of individuals relative to whole population
FIT = HT – HI
HT
- any departure from single panmictic population will lead to significant value- used to detect departures from Hardy-Weinberg equilibrium in total population
HI observed heterozygosity averaged over individuals in all subpopulationsHS expected heterozygosity in each subpopulation averaged across subpopulationsHT expected heterozygosity if subpopulations are combined as one population
FIS - inbreeding coefficient of individual relative to its sub-population (change in H due to non-random mating)
FIS = HS – HI
HS
HI observed heterozygosity averaged over individuals in all subpopulationsHS expected heterozygosity in each subpopulation averaged across subpopulationsHT expected heterozygosity if subpopulations are combined as one population
FIS - inbreeding coefficient of individual relative to its sub-population
FIS = HS – HI
HS
used to detect departures from Hardy-Weinberg equilibrium in "good" populations
positive value = heterozygote deficiency (Wahlund effect) zero value = all sub-populations in Hardy-Weinberg equilibrium
(random mating within subpopulations)negative value = heterozygote excess
HI observed heterozygosity averaged over individuals in all subpopulationsHS expected heterozygosity in each subpopulation averaged across subpopulationsHT expected heterozygosity if subpopulations are combined as one population
FST - inbreeding coefficient of sub-population relative to the whole population = fixation index
FST = HT – HS
HT
HI observed heterozygosity averaged over individuals in all subpopulationsHS expected heterozygosity in each subpopulation averaged across subpopulationsHT expected heterozygosity if subpopulations are combined as one population
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 frequencies0.05-0.15 = moderate differentiation0.15-0.25 = great differentiation>0.25 = extremely different 1.0 = popns fixed for different alleles
HI observed heterozygosity averaged over individuals in all subpopulationsHS expected heterozygosity in each subpopulation averaged across subpopulationsHT expected heterozygosity if subpopulations are combined as one population
Taxa (# species) FstAmphibians (33) 0.32Reptiles (22) 0.26Mammals (57) 0.24Fish (79) 0.14Insects (46) 0.10Birds (23) 0.05
Plants – animal poll. 0.22Plants – wind poll. 0.10
Dispersal and gene flow
Quantifying the distribution of variation
HI HS HT
AA, AA, AA , AA BB, BB, BB, BB 0 0 0.5
AA, AB, AB, BB AA, AB,AB, BB 0.5 0.5 0.5
AB, AB, AB, AB AB, AB, AB, AB 1 0.5 0.5
AA, BB, BB, BB AB, AB, AA, BB 0.25 0.44 0.47
HI observed heterozygosity averaged over individuals in all subpopulations (# heterozygotes/ total N)
HS expected heterozygosity in each subpopulation (if it was in H-W equilib.) averaged across subpopulations (# heterozygotes/total N)
HT expected heterozygosity if subpopulations are combined as one population
FIS - inbreeding coefficient of individual relative to its sub-population
FIS = HS – HI
HS
Quantifying the distribution of variation
positive value = heterozygote deficiency zero value = all sub-populations in Hardy-Weinberg equilibriumnegative value = heterozygote excess
HI HS HT FIS
AA, AA, AA , AA BB, BB, BB, BB 0 0 0.5 0
AA, AB, AB, BB AA, AB,AB, BB 0.5 0.5 0.5 0
AB, AB, AB, AB AB, AB, AB, AB 1 0.5 0.5 -1
AA, BB, BB, BB AB, AB, AA, BB 0.25 0.44 0.47 0.43
Pacific yew (Taxus brevifolia)
9 populations examined at 21 loci
FIS = 0.49
high level of inbreeding?dioecious – so likely due to clustering of relatives
FIT - reduction in heterozygosity of individuals relative to whole population
FIT = HT – HI
HT
Quantifying the distribution of variation
HI HS HT FIT
AA, AA, AA , AA BB, BB, BB, BB 0 0 0.5 1
AA, AB, AB, BB AA, AB,AB, BB 0.5 0.5 0.5 0
AB, AB, AB, AB AB, AB, AB, AB 1 0.5 0.5 -1
AA, BB, BB, BB AB, AB, AA, BB 0.25 0.44 0.47 0.46
used to detect departures from Hardy-Weinberg equilibrium in total population
FST - inbreeding coefficient of sub-population relative to the whole population
FST = HT – HS
HT
Quantifying the distribution of variation
HI HS HT FST
AA, AA, AA , AA BB, BB, BB, BB 0 0 0.5 1
AA, AB, AB, BB AA, AB,AB, BB 0.5 0.5 0.5 0
AB, AB, AB, AB AB, AB, AB, AB 1 0.5 0.5 0
AA, BB, BB, BB AB, AB, AA, BB 0.25 0.44 0.47 0.07
measures degree of population differentiation within species (always positive)
Pacific yew (Taxus brevifolia)
9 populations examined at 21 loci
FST = 0.078
Low to moderate level of population differentiation