Lecture 13:
Chapter 6:
6.4 testing for selection from polymorphism and divergence data:
Recap:
- The rate of divergence can be estimated by the number of differences between two species,
if the speciation time is known.
- Molecular clock to estimate divergence times.
- Rate of coalescence depends on:
o Ne which can vary between different parts of the genome (mtDNA = Y-chromosome <
X < autosome)
o Selection
- Slow coalescence can lead to incomplete lineage sorting (ILS)
- For ancient splits, to calculate the number of replacements, we must correct for multiple hits
and reversals
- The mutation rate differs between synonymous and non-synonymous sites
- Rate of neutral molecular evolution (rate of substitution) λ = u
- Ka / Ks can be used to infer different kinds of selection
Rate of molecular evolution between species
- If T2 << T1 polymorphisms in ancestral population will contribute little to overall divergence
between species. Then T ~ T1 and overall sequence divergence between species is 2T 1u / Tg
- For closely related species T2 cannot be ignored.
- So we have to add to the divergence during T 1 (2T1u /tg), ancestral polymorphism: expected
divergence between two alleles within a population
,-
,Probability that gene tree = species tree depends on:
- Time between speciation events
,
Chapter 6:
6.4 testing for selection from polymorphism and divergence data:
Recap:
- The rate of divergence can be estimated by the number of differences between two species,
if the speciation time is known.
- Molecular clock to estimate divergence times.
- Rate of coalescence depends on:
o Ne which can vary between different parts of the genome (mtDNA = Y-chromosome <
X < autosome)
o Selection
- Slow coalescence can lead to incomplete lineage sorting (ILS)
- For ancient splits, to calculate the number of replacements, we must correct for multiple hits
and reversals
- The mutation rate differs between synonymous and non-synonymous sites
- Rate of neutral molecular evolution (rate of substitution) λ = u
- Ka / Ks can be used to infer different kinds of selection
Rate of molecular evolution between species
- If T2 << T1 polymorphisms in ancestral population will contribute little to overall divergence
between species. Then T ~ T1 and overall sequence divergence between species is 2T 1u / Tg
- For closely related species T2 cannot be ignored.
- So we have to add to the divergence during T 1 (2T1u /tg), ancestral polymorphism: expected
divergence between two alleles within a population
,-
,Probability that gene tree = species tree depends on:
- Time between speciation events
,
