Lecture 7- Coalescent theory Flashcards
what does coalescent theory refer to
the modelling of how alleles may have been derived from a common ancestor
limitations of this method
can only be used when positive selection is weak- assumption that all alleles are equally likely to be passed on
application
anthropology, epidemiology, association mapping (variation vs human disease), cancer bio
‘null model’ conditions
haploid population (N)
no strong selection
generations are non-overlapping
population size is constant
wright-fisher model
model of genetic drift
how does the wright-fisher model work (roughly)
traces the mutation through- e.g. looking at the probability it will become fixed/going extinct, can be used from the past or from the present to trace ancestry
what is a coalescent event
a point where there is shared ancestry
equation for probability of coalescence
(1/N) * i(i-1)/2
i = no of sampled lineages
represents probability that 2 lineages share a parent * number of possible pairs of sampled lineages
i(i-1)/2N
how can you work out time to MRCA from N and i
(2N(i-1))/i generations
how do you account for time
to look at r at a specific time, plug in the population size at the time r(t)=(i(i-1))/2N(t)
relationship of coalescent events and pop size
smaller pop = more events
sequence diversity relationship to mutation rate
sequence diversity = 2N*mutation rate
how does pop size impact sequence diversity
larger pop size = higher diversity because more time for mutations to emerge
methods of estimating population sizes from phylogenies
Tajima’s D, skyline plots
Tajima’s D
measures what kind of mutations are occurring- high/med/low frequency, etc- which can be used to infer the structure of a population, e.g. less low-frequency mutations at bottlenecks
