Data from: Species divergence and maintenance of species cohesion of three closely related Primula species in the Qinghai-Tibet Plateau

Aim: Understanding the relative roles of geography and ecology in driving
speciation, population divergence and maintenance of species cohesion is
of great interest to molecular ecology. Closely related species that are
parapatrically distributed in mountainous areas provide an ideal model to
evaluate these key issues, especially when genomic data are analyzed
within a spatially and ecologically explicit context. Here we used three
closely related species of Primula that occur in the Himalayas, the
Hengduan Mountains and Northeast Qinghai-Tibet Plateau (QTP) to examine
spatial and ecological effects on interspecific divergence and maintenance
of species cohesion. Location: Himalayas, the Hengduan Mountains and
Northeast QTP Methods: We used genomic data for 770 samples of the three
species using double-digest restriction site-associated DNA (ddRAD)
sequencing and combined approximate Bayesian computation (ABC) modeling,
generalized linear mixed modeling (GLMM) and niche-based species
distribution modeling (SDM). Results: The three species are clearly
delimited by the RADseq data. Further ABC modeling indicates that P.
tibetica diverged first followed by a later divergence between P. nutans
and P. fasciculata. The time frames of the divergences among the three
species coincide with the uplifts of the Hengduan Mountains and the
northern QTP during the late Miocene and Pliocene followed by a long
period of founder events. SDMs indicate that the three species might have
survived in different refugia during glaciations and came into secondary
contact during the postglacial expansions but with no significant
introgression. Finally, GLMM suggests that both the geographical and
ecological factors play roles in population differentiation in P.
fasciculata and P. tibetica, while for P. nutans, geography is the major
driver of genomic variation. The different roles played by geographical
and ecological factors in the three species may have affected the
maintenance of species cohesion. Main conclusion: Our results provide
insights of unprecedented details into the start and maintenance of
interspecific divergence in the context of changing environments in
mountains. Our findings highlight the significance of combining population
genomics with environmental data when evaluating the effects of geography
and ecology on interspecific divergence and maintenance of closely related
species.