As most coral reef organisms with a pelagic larval phase are presumed to be readily dispersed between distant populations, sea-surface current patterns should be crucial for predicting ecological and genetic connections among threatened reef populations1. Here we investigate this idea by examining variations in the genetic structuring of populations of the mantis shrimp Haptosquilla pulchella taken from 11 reef systems in Indonesia, in which a series of 36 protected areas2 are presumed to be connected by strong ocean currents. Our results reveal instead that there is a strong regional genetic differentiation that mirrors the separation of ocean basins during the Pleistocene low-sea-level stands, indicating that ecological connections are rare across distances as short as 300–400 km and that biogeographic history also influences contemporary connectivity between reef ecosystems.
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