Data from: Demographic modelling with whole-genome data reveals parallel origin of similar Pundamilia cichlid species after hybridization

Modes and mechanisms of speciation are best studied in young species
pairs. In older taxa, it is increasingly difficult to distinguish what
happened during speciation from what happened after speciation. Lake
Victoria cichlids in the genus Pundamilia encompass a complex of young
species and polymorphic populations. One Pundamilia species pair, P.
pundamilia and P. nyererei, is particularly well suited to study
speciation because sympatric population pairs occur with different levels
of phenotypic differentiation and reproductive isolation at different
rocky islands within the lake. Genetic distances between allopatric island
populations of the same nominal species often exceed those between the
sympatric species. It thus remained unresolved whether speciation into P.
nyererei and P. pundamilia occurred once, followed by geographical range
expansion and interspecific gene flow in local sympatry, or if the species
pair arose repeatedly by parallel speciation. Here, we use genomic data
and demographic modelling to test these alternative evolutionary
scenarios. We demonstrate that gene flow plays a strong role in shaping
the observed patterns of genetic similarity, including both gene flow
between sympatric species and gene flow between allopatric populations, as
well as recent and early gene flow. The best supported model for the
origin of P. pundamilia and P. nyererei population pairs at two different
islands is one where speciation happened twice, whereby the second
speciation event follows shortly after introgression from an allopatric P.
nyererei population that arose earlier. Our findings support the
hypothesis that very similar species may arise repeatedly, potentially
facilitated by introgressed genetic variation.