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Figure 1 | BMC Evolutionary Biology

Figure 1

From: Distinguishing migration from isolation using genes with intragenic recombination: detecting introgression in the Drosophila simulans species complex

Figure 1

Ancestral recombination graph, genealogies and polymorphisms for samples taken from two populations exchanging migrants. Colors represent the different sections defined by recombination events. A. Ancestral recombination graph (lines in black) of six gene copies (1–6) sampled from two populations (represented by background blue shade). Present is represented at the top and past at the bottom (the time is not scaled). Each gene copy is represented by a four-colour bar; within which, dotted sections represent the length of the gene that will not leave descendants in the sample. B. Genealogies of the six gene copies (1–6) for each of the segments (represented by different colours) delimited by the recombination events. Mutation events are represented on the branches together with their position in the alignment. C. DNA sequence alignment of the six gene copies (1–6) plus an outgroup (OUT) sequence used to inferr the ancestral state of mutations. An introgression block (or migrant tract) is marked with a grey rectangle. D. Categories of polymorphic sites [30] found in the alignment (fixed differences, F, exclusive polymorphisms of each population, X1 and X2, and shared polymorphisms, S). The randomness of the order of categories is assessed with two statistics based on the number of runs (R, see main text for more details). E. Categories of polymorphic sites taking into account the direction of mutation [in practice, by means of an outgroup [38] and whether the derived state is fixed in population 1 (f1, f1x2) or in population 2 (f2, f2x1). The spatial clustering of polymorphic site categories along the alignment is assessed with the W statistic (see main text for details).

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