Since Darwin first proposed that new species could arise without geographic separation, biologists have debated whether or not divergence occurs in the presence of gene exchange. Today we understand that new species can diverge while exchanging genes, depending on the strength of disruptive natural selection and the factors that affect the linkage relationships of genes under disruptive selection. This mode of diversification—divergence with gene flow—includes sympatric speciation, in which gene exchange occurs since onset of divergence, and secondary contact following a period of geographic isolation, as well as all sorts of situations in which gene flow happens intermittently. In recent years, statistical tools have been developed that can reveal the action of gene flow during divergence. Isolation-with-migration (IM) models include parameters for population size, time of population separation, and gene exchange, and they have been used extensively to estimate levels of gene exchange. A survey of studies that have used these models shows that a plurality find little evidence of gene flow; however, many report nonzero gene exchange.


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