Can genomic data alone tell us whether speciation happened with gene flow?

Abstract

The allopatric model, which requires a period of geographical isolation for speciation to complete, has been the standard model in the modern era. Recently, "speciation with gene flow" has been widely discussed in relation to the model of "strict allopatry" and the level of DNA divergence across genomic regions. We wish to caution that genomic data by themselves may only permit the rejection of the simplest form of allopatry. Even a slightly more complex and realistic model that starts with subdivided populations would be impossible to reject by the genomic data alone. To resolve this central issue of speciation, other forms of observations such as the sequencing of reproductive isolation genes or the identification of geographical barrier(s) will be necessary.

Ecological speciation in sympatric palms: 4. Demographic analyses support speciation of Howea in the face of high gene flow

“…Unlike recent genomic reanalyses of classic cases of speciation in sympatry, our results support the proposition that Howea palms must have diverged with continuous gene flow. We note, however, that genomic data by themselves may only permit the rejection of the simplest form of allopatry (Yang et al ). In this sense, our demographic analyses should be seen in concert with other lines of evidence such as the geological history of LHI, lack of population structure on LHI, and the finding of candidate reproductive isolation genes (Dunning et al ).…”

Speciation as a sieve for ancestral polymorphism

“…Such an observation could be interpreted as evidence of a period of differential gene flow following an initial split (cf. Yang, He, Shi, & Wu, ). This latter case highlights the fact that sieved polymorphism can mimic the signature of other evolutionary processes, and distinguishing among these may be challenging without additional pieces of evidence (see below).…”

In the absence of reproductive isolation – Extensive gene flow after speciation

“…Assuming that the current evidence for "speciation with gene flow" 30,31 is convincing, (but see ref. 32,33 ), we ask what it takes to corroborate the genic concept of species. It requires answering the following questions: i) the proportion of the genome that is non-introgressable, ii) the number and size distribution of such non-introgressable segments and, in particular, iii) the genic content within these segments.…”

“…Based on this conjecture, genomic islands have been identified either by the relative level of divergence or by the absolute divergence 12,13,15,[17][18][19][20][21][22][23] . The former procedure has been questioned 24 and the absolute divergence has also been cast in doubt 25 . In general, if the ancestral species is geographically structured before speciation, the level of divergence would be highly variable across the genome and the highly divergent genomic islands may be merely a stochastic consequence 25 .…”

“…The former procedure has been questioned 24 and the absolute divergence has also been cast in doubt 25 . In general, if the ancestral species is geographically structured before speciation, the level of divergence would be highly variable across the genome and the highly divergent genomic islands may be merely a stochastic consequence 25 .…”