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FIGURE 1-6 The two stages of ecological speciation-with-gene-flow. (A) The duration of Stage 1 is noted by the light gray, Stage 2 by the darker arrow. Events during each stage are as described in the text. (B) Cartoon of gene trees within a species tree for ecological speciation-with-gene-flow. Each gene is polymorphic in the original population, with a frequency (p) as noted on the axis at the left of the drawing. As time goes on, some loci quickly diverge at about the same time under divergent selection. Solid triangles denote selected QTL, open triangles are divergence hitchhikers. This divergence is mostly complete by the end of Stage 1. During Stage 2, a handful of additional loci diverge under selection, and loci that were unaffected by divergent selection diverge by independent responses to uniform or balancing selection, or by drift (solid rectangles). (C) Gene trees in a species tree under allopatry, symbols are as in (B) . If an allopatric population enters a new environment, there may be a period of rapid response to divergent selection similar to Stage 1 in (A) . Otherwise, genes diverge over a long time period under any combination of divergent selection, independent responses to uniform or balancing selection, or drift, eventually all coming into concordance to produce the branching pattern of the new species.

FIGURE 1-6 The two stages of ecological speciation-with-gene-flow. (A) The duration of Stage 1 is noted by the light gray, Stage 2 by the darker arrow. Events during each stage are as described in the text. (B) Cartoon of gene trees within a species tree for ecological speciation-with-gene-flow. Each gene is polymorphic in the original population, with a frequency (p) as noted on the axis at the left of the drawing. As time goes on, some loci quickly diverge at about the same time under divergent selection. Solid triangles denote selected QTL, open triangles are divergence hitchhikers. This divergence is mostly complete by the end of Stage 1. During Stage 2, a handful of additional loci diverge under selection, and loci that were unaffected by divergent selection diverge by independent responses to uniform or balancing selection, or by drift (solid rectangles). (C) Gene trees in a species tree under allopatry, symbols are as in (B) . If an allopatric population enters a new environment, there may be a period of rapid response to divergent selection similar to Stage 1 in (A) . Otherwise, genes diverge over a long time period under any combination of divergent selection, independent responses to uniform or balancing selection, or drift, eventually all coming into concordance to produce the branching pattern of the new species.

to distinguish the eventual species, and genetic divergence at the major QTL for these traits defines the branches of what will ultimately become the species tree. Because selection accelerates progression to reciprocal monophyly (Avise, 2000), loci within these genomic regions are expected to become reciprocally monophyletic long before the rest of the genome, on approximately the same timescale as the divergence of the quantitative traits that these genes affect. During this phase, few other genetic differences are expected between the incipient species. This restriction of genetic



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