how to calculate F stats and what they mean
A) genotype freq: #/total pop
allele freq:
(2p + pq)/ (2total)
(2q +pq)/(2total)
Hi = observed # of pq
Hsi = 2pq
B) average out allele freq, Hi, and Hsi between both pops
C) total expected (avg pq values from B)
= 2pq
Fis = (Hs -Hi)/Hs
- (inbreeding coefficient)
- 0-random mating (hetero)
- 1 - inbred (homo)
Fst = (Ht - Hs)/Ht
- genetic difference between two pops at allele freq lvl
- 0-0.25 (higher=more diff)
Fit= (Ht - Hi)/Ht
- shows genentic homozygosity compared across both pop
- 0 heterozygous easy gene flow
- 0.45 considered high and limited regionally structured, adaptive locally, limited mating and movement across pops
what types of outlier tests are used to identify loci under selection and what does it reveal
FST Outlier Tests
- Detect loci whose FST different to neutral expectations.
- Higher FST:different alleles/location
- Lower FST: same across pop
Environmental Correlation Tests
- correlation between allele frequencies and environmental variables
- sig. relation = environmental selection
- need to use both
- Loci that are both FST outliers and environmentally correlated = strong evidence for local adaptation.
What is the difference between IBD and IBE, and how can we distinguish between them using genetic data?
Isolation by Distance (IBD):
- differentiation increases with distance.
- Caused by limited dispersal → gene flow stronger nearby
- Expected under neutral processes
- Mantel test between genetic/ distance
- Pattern: Gradual
Isolation by Environment (IBE):
-differentiation correlates with environment
- local adaptation: even across short distances.
- Tests: EAA, redundancy analysis (RDA), or partial Mantel controlling for distance.
- Pattern: Sharp allele frequency shifts at environmental boundaries.
