In this study we estimated the timing of speciation events in a group of angelfishes using 1186 RADseq markers corresponding to 94,880 base pairs. The genus Holacanthus comprises seven species, including two clades of Panama trans-Isthmian geminates, which diverged approximately 3-3.5Mya. These clades diversified within the Tropical Eastern Pacific (TEP, three species) and Tropical Western Atlantic (TWA, two species) which our data suggest to have occurred within the past 1.5My in both ocean basins, but may have proceeded via different mechanisms. In the TEP, speciation is likely to have followed a peripatric pathway, while in the TWA, sister species are currently partially sympatric, thus raising the possibility of sympatric speciation. This study highlights the use of RADseq markers for estimating both divergence times and modes of speciation at a 1-3My timescale.

Estimating population sizes and genetic diversity are key factors to understand and predict population dynamics. Marine species have been a difficult challenge in that respect, due to the difficulty in assessing population sizes and the open nature of such populations. Small, isolated islands with endemic species offer an opportunity to groundtruth population size estimates with empirical data and investigate the genetic consequences of such small populations. Here we focus on two endemic species of reef fish, the Clipperton damselfish, Stegastes baldwini, and the Clipperton angelfish, Holacanthus limbaughi, on Clipperton Atoll, tropical eastern Pacific. Visual surveys, performed over almost two decades and four expeditions, and genetic surveys based on genomic RAD sequences, allowed us to estimate kinship and genetic diversity, as well as to compare population size estimates based on visual surveys with effective population sizes based on genetics. We found that genetic and visual estimates of population numbers were remarkably similar. S. baldwini and H. limbaughi had population sizes of approximately 800,000 and 60,000, respectively. Relatively small population sizes resulted in low genetic diversity and the presence of apparent kinship. This study emphasizes the importance of small isolated islands as models to study population dynamics of marine organisms.