Research Article: Clipperton Atoll as a model to study small marine populations: Endemism and the genomic consequences of small population size

Date Published: June 27, 2018

Publisher: Public Library of Science

Author(s): Nicole L. Crane, Juliette Tariel, Jennifer E. Caselle, Alan M. Friedlander, D. Ross Robertson, Giacomo Bernardi, Heather M. Patterson.


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.

Partial Text

Populations of marine organisms typically are very large, with population sizes (N) of 106 to 109 individuals being common [1]. Large populations in an open environment are predicted to show high levels of gene flow, resulting in low genetic population structure and speciation rates. An early paradox arose from the observation of elevated speciation rates and strong population structure in marine organisms, despite few physical barriers (i.e. preventing allopatric speciation), and large populations being the norm (i.e. countering neutral drift) [1].

In this study, we capitalized on the presence of endemic reef fishes at a small, extremely isolated atoll to address the evolutionary consequences of small population sizes in marine organisms. In this study, we confirmed that there is no evidence of gene flow between H. limbaughi and its sister species, nor between S. baldwini and its sister species, and that the system is effectively closed from a genetic standpoint, thus validating endemism in these two species.

The goal of this study was to empirically validate estimated Ne using genetic techniques, with visual census data for population size in small marine populations, and to investigate the consequences of small populations and closed systems on genetic diversity. We sought to capitalize on a unique system in the marine environment where endemic populations of reef fishes are exclusively found on a small remote island. The isolated Clipperton Atoll, at which we studied two of its seven endemic reef-fishes, H. limbaughi and S. baldwini, offered such an opportunity. Due in part to the limited spatial extent of habitat, and thus increased accuracy of diver surveys, the census data presented here were consistent across depths and years.




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