MS 366 Population Genetics

10 April 2019

The Coalescent: Population genetic inference using genealogies

The Coalescent (Kingman, 1982)

 Retrospective model of gene divergence in a genealogy
 Looking backward in time to ‘coalescence’ of lineages: most common ancestor (MRCA)
 Looking from present going backward in time and searching for where the lineages coalesce
 Contain information about historical demography and processes that shape diversity
 Genealogies contain information about historical demography and processes that shape diversity)
 tmRCA influenced by; factors that influence coalescence of lineages
o Population size
o Migration rates
o Changes in population size
 Framework for estimating population genetic parameters in natural populations:
o Population size
o Migration rate
o Recombination rate
 Framework that allows simultaneous calculation of population size, migration rate, and
demography
 Derived from population genetic models (Wright-Fisher model)

Wright-Fisher Population model

 Each individual releases many gametes, new individuals are drawn randomly from the gamete
pool (RANDOM SAMPLING WITH REPLACEMENT)
 Population size is CONSTANT
 Not all alleles are transmitted to the next generation
 Probability that an allele in G2 has a parent in G1 = 1
 Probability that a randomly-selected allele in G2 has the same parent in G1 = 1/2N
 If we sample 2 extant gene copies
o P(Coalesces 1 generation ago), t1 = 1/2N
o P(Coalesces 2 generations ago), t2 = (1-1/2N) * 1/2N
o Probability of coalescence in generation t = (1-(1/2N)) t-1 (1/2N)
o Exact probability of coalescing at or before generation t = 1-e -1/2N * t
 If we sample k gene copies
o P (Coalescence) = k(k-1)/2/2N
o Average time to coalescence = 1/Probability of coalescence = 2N/k(k-1)/2 = 4N/k(k-1)
o Increasing sample size, increases number of generations, increases coalescence

Time to coalescence
 As k becomes smaller, Time to coalescence increases
o T(Coalescence) = 4N/k(k-1)
 Fewer lineages sampled, Time to coalescence becomes longer
o Each successive most recent ancestor, the time to coalescence increases
o More recent, less coalescent time

Kingman’s coalescent
 P (Coalescence) = k(k-1)/2 * 1/2N
MS 366 Population Genetics
10 April 2019

 TMRCA = 4N(1-(1/k))
 What is the effect of larger population sizes to the coalescence time?
o Larger population sizes, greater coalescence time
 What is the effect of number of lineages sampled to the coalescence time?
o Time to coalescence is longer as you approach the most recent ancestor; more lineages,
longer coalescence time

The Coalescent: Implications of the theory

 Time to ancestry is related to the effective population size (Ne) and number of lineages (k)
o More lineages  longer time to MRCA
o Larger N  longer time to tMRCA

Using the coalescent

 Inference of and statistical analysis of population parameters based on molecular data (Rosenberg
& Nordborg 2002)
o Mutation rate
o Time to most recent common ancestor
o Recombination rate
o Ancestral population size (demographic history, theta = 4N emU)
o Migration rate
 Mathematical modelling, hypothesis testing
 Some widely-used software: (estimating population parameters, statistical testing)
o Migrate-n (Beerli)
o LAMARC (Beerli & Felsenstein)
o IM (Hey)
o Genetree (Bahlo & Griffith)
o Geodis (Posada)

Data Input
 SNPs
 Microsatellite data