Data from: Contrasting signatures of genomic divergence during sympatric speciation

The transition from “well-marked varieties” into “well-defined species”
has puzzled evolutionary biologists ever since Darwin —
especially when extensive gene flow between incipient species is possible
due to the lack of physical barriers (sympatric speciation). Gene flow
counteracts the build-up of genome-wide differentiation, which is both a
hallmark of speciation and forms the underlying basis of irreversible
reproductive barriers (incompatibilities) that ultimately complete the
speciation process. Theory predicts that the genetic architecture of
divergently selected traits can influence whether sympatric speciation
occurs. However, empirical data to test this prediction remain rare and
are often difficult to synthesize across animal taxa due to idiosyncrasies
in their biology and evolutionary histories. Here, within a young species
complex of Neotropical cichlid fish (Amphilophus spp.), we analyzed
genomic divergence among populations and species, and the genetic
architecture of traits that have been suggested to be important for this
divergence, by generating a new genome assembly and re-sequencing 453
genomes. We found that species differing in mono/oligogenic traits
affecting ecological performance and/or mate choice show remarkably
localized genomic differentiation. In contrast, differentiation between
species that diverged in polygenic traits is widespread and much higher
overall, consistent with the evolution of effective and stable genome-wide
barriers to gene flow. Thus, we conclude that simple trait architectures
are not always as conducive to speciation-with-gene-flow as previously
suggested, whereas, unexpectedly, polygenic architectures can promote
rapid and stable speciation in sympatry.