Fig. 1: The structured ancestry model used by cobraa.
From: A structured coalescent model reveals deep ancestral structure shared by all modern humans
a, Diagram of the structured model. Going forward in time, an ancestral population splits into two populations, A and B, at time T2. These remain in isolation until time T1 when there is an admixture event. b, We extend the SMC model to include the structure in a. We consider two sampled lineages from population A at t = 0. The consequences of ancestral recombination are partitioned into ten mutually exclusive cases, with an example from each illustrated. The gold lines indicate the two chromosomes sampled from the present at a particular locus, and the green line indicates the ‘floating’ lineage under the SMC model, which coalesces somewhere higher up on the tree in either population A or B.
