7 - measuring genetic diversity

intra-population

within the same population or species

inter-population

between different populations or species

how to calculate allelic richness

sum of all alleles found across all loci, divided by number of loci

how to calculate polymorphic loci

count of polymorphic (2 or more alleles) loci divided by total number of loci

how to calculate effective number of alleles (Ae)

1/expected homozygosity

how to calculate expected homozygosity (Ho)

allelic frequency squared and added together

f(150) = 0.6

f(154) = 0.4

expected homozygosity = (0.6²) + (0.4²)

how to calculate expected heterozygosity (He)

1 - expected homozygosity

steps to solve for F-statistics

1. find the frequencies of each alleles (pi and qi)

2. find the expected heterozygosity in each population (2 pi qi)

3. find the average of each allele frequency (po and qo)

4. solve for HT = 2 po qo

5. solve for HI = average heterozygous counts

6. solve for HS = average of (2 pi qi)

how can you test if inbreeding depression is likely to occur?

• AMOVA (analysis of molecular variation)

• uncorrected p - number of differences divided by length

• K2P transition and transversion models

• GTR (generalize time-reversible) models

FIS means?

deficiency or excess of heterozygotes in each population

FIT means?

deficiency or excess of heterozygotes in group of populations

FST means?

degree of gene differentiation among populations in terms of allele frequencies