Classical Skyline Plot

Kingman’s coalescent u9 u7 u5 u3 u8 u6 u4 u2 Random collision of lineages as go back in time (sans recombination) Collision is faster the smaller the effective population size Average time for n Average time for copies to coalesce to 4N k(k−1) k−1 = In a diploid population of effective population size N, copies to coalesce = 4N (1 − 1n ( generations k Average time for two copies to coalesce = 2N generations Week 9: Coalescents – p.17/60 Coalescence is faster in small populations Change of population size and coalescents Ne time the changes in population size will produce waves of coalescence time Coalescence events time the tree The parameters of the growth curve for Ne can be inferred by likelihood methods as they affect the prior probabilities of those trees that fit the data. Week 9: Coalescents – p.24/60 “Skyline ” and “Skyride ” plots in BEAS