Data from: Historical demography of four gecko species specializing in boulder cave habitat – its implications in the evolutionary dead end hypothesis and conservation

Specialization in narrow ecological niches might not only help species to
survive in competitive or unique environments but also contribute to their
extermination over evolutionary time. Although the “evolutionary dead end”
hypothesis has long been debated, empirical evidence from species with
detailed information on niche specialization and evolutionary history is
still rare. Here we used a group of four closely related Cnemaspis gecko
species that highly depend on granite boulder caves in the Mekong Delta to
illuminate the potential impact of ecological specialization on their
evolution and population dynamics. Isolated by the unsuitable habitat of a
flood plain, these boulder-dwelling geckos are among the most narrowly
distributed Squamata species in the world. We applied several
coalescence-based approaches combined with the RAD-seq technique to
estimate their divergence times, gene flow and demographic fluctuations
during the speciation and population differentiation processes. Our
results showed long-term population shrinkage in the four geckos and
limited gene flow during their divergence. The results suggest that the
erosion and fragmentation of the granite boulder hills have had great
impacts on these populations’ divergences and population declines. We
argue that the specialist gecko’s habitat specialization has facilitated
the fine-scaled speciation in these granite rocky hills; in contrast,
specialization might also have pushed these species toward the edge of
extinction. Our study also emphasizes the conservation urgency of these
vulnerable, cave-dependent geckos.