Divergence with Gene Flow: Models and Data

Abstract

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.

A separate lowstand lake at the northern edge of Lake Tanganyika? Evidence from phylogeographic patterns in the cichlid genus Tropheus

“…However, Electronic supplementary material The online version of this article (doi:10.1007/s10750-016-2939-8) contains supplementary material, which is available to authorized users. such pathways rarely proceed in a linear fashion by divergence alone, as repeated intermezzos of gene flow perturbate gene pools and set the stage for selection, drift, and speciation (King & Lawson, 1995;Rossiter, 1995;Pinho & Hey, 2010;. On the long run, secondary admixis can either render population distinctness or produce novel and distinct hybrid entities, which can evolve to novel species (Seehausen, 2004;Nolte & Tautz, 2010).…”

Hybrid fitness, adaptation and evolutionary diversification: lessons learned from Louisiana Irises

“…Their meta-analysis included studies that used the isolation-with-migration (or IM) models as the basis for estimating population parameters, including gene flow. Although many of the 200+ studies inferred a lack of gene flow, over half of the cases examined detected 2NM estimates of 40.1 (Pinho and Hey, 2010); this result is not consistent with an hypothesis of purely allopatric divergence with no introgression.…”

“…For example, Pinho and Hey (2010) used a meta-analysis to estimate the frequency of related lineages that experienced introgressive hybridization during their divergence. Their meta-analysis included studies that used the isolation-with-migration (or IM) models as the basis for estimating population parameters, including gene flow.…”

“…These include: (1) hybrid genotypes with high relative fitness are produced more often than previously assumed (Arnold and Hodges, 1995); (2) even hybrids with low relative fitness may act as a conduit for genetic exchange, given that they have some level of fertility (Arnold and Hodges, 1995;Arnold, 1997Arnold, , 2006; and (3) for many taxonomic groups, allopatric divergence is not as frequent as divergence accompanied by some level of at least intermittent gene flow (that is, parapatric or sympatric divergence; Pinho and Hey (2010)). Numerous authors including Darwin himself-see above quote-contributed to the formulation of the first hypothesis (relating to the production of relatively fit hybrid genotypes).…”

“…The third hypothesis derives from the recognition that a majority of plant lineages have allopolyploid ancestry (that is, polyploid lineages formed through hybridization; Arnold (1997Arnold ( , 2006), as well as from the proliferation of studies (mainly involving animal complexes) that have detected past gene flow during speciation through the application of various algorithms (Wakeley and Hey, 1997;Templeton, 2001;Geneva and Garrigan, 2010;Wang and Hey, 2010) to genomic data sets (Salzburger et al, 2002;Seehausen, 2004;Won and Hey, 2005;Anderson et al, 2009;Green et al, 2010;Pinho and Hey, 2010; see also Arnold (2006Arnold ( , 2008 for a review of additional examples). Less frequently referred to are the literally thousands of studies documenting genetic exchange within groups of organisms as diverse as viruses, prokaryotes, plants and animals (see Grant and Grant (1992); Arnold (1997Arnold ( , 2006Arnold ( , 2008; Rieseberg (1997) and Seehausen (2004) for references to some of these studies).…”