Genetic diversity, population structure, and demographic history of exploited sea urchin populations (Tripneustes gratilla) in the Philippines

The sea urchin, Tripneustes gratilla is ecologically and economically important in the Indo-Pacific region. We use population genetic methods to investigate the population structure and historical demography of exploited populations in the Philippines. Sea urchins were collected from 6 localities in western Luzon and 4 outgroup sites. Samples were sequenced for mitochondrial cytochrome oxidase-1 gene (n = 282) and genotyped for seven microsatellite loci (n = 277). No significant genetic structure was found for either class of markers, indicating either extensive gene flow across the archipelago, or that populations have high genetic diversity and have not yet attained equilibrium between genetic drift and migration following large changes in demography. Interestingly, demographic inferences from the two types of markers were discordant. Mitochondrial lineages showed demographic expansion during the Pleistocene while microsatellite data indicated population decline. Estimates for the date of each event suggest that a Pleistocene expansion could have preceded a more recent population decline, but we also discuss other hypotheses for the discordant inferences. The high genetic diversity and broad distribution of haplotypes in populations that recently recovered from fishery collapse indicate that this species is very resilient over evolutionary timescales.