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Cliona vermifera is one of the most abundant excavating sponges in Mexican coral reefs, and represents a potential threat to their health. It appears to have limited dispersal potential, but, paradoxically, it is widespread over much of the 2000 km of Mexican Pacific waters, suggesting mechanisms of long-distance dissemination. Despite its ecological importance, nothing is known about its patterns of genetic structure and connectivity in space and time. In this study, we assess levels of genetic structure and test the hypothesis of limited dispersal and isolation by distance among coral reef systems in the Mexican Pacific. Genetic diversity levels were consistently low in DNA sequences from two mitochondrial genes and one nuclear gene; however, they revealed strong and significant genetic differentiation throughout the study region. Patterns of genetic differentiation from the slow-evolving mitochondrial, but not the nuclear, genes were geographic scale dependent. We found higher mitochondrial genetic similarity among localities at 10-100s km than at larger scales (100-1000s km). However, all samples were genetically differentiated at the nuclear locus, which is inconsistent with frequent long-distance dispersal. Significant isolation by distance is consistent with life history traits shared by boring sponges: a short larval period and larval philopatric behavior. The patterns of genetic differentiation in C. vermifera concur with those found in other sympatric coral species, and suggest the influence of community-wide ecological and genetic mechanisms on the genetic makeup of coral reef species in the Mexican Pacific. Fixed genetic differences suggest that the southern population of Oaxaca may be experiencing incipient speciation. [ABSTRACT FROM AUTHOR]

Coral reefs are the most complex and diverse of aquatic ecosystems. Their vulnerability and deterioration in the face of anthropogenic disturbance require the adoption of conservation and restoration efforts to maintain their resilience, for which connectivity is of paramount importance. Dispersal of meroplanktonic larval stages drives the levels of connectivity among coral populations and is influenced by the local current regime, the synchronization of spawning events, and the capacity of larvae to reach recruitment sites. This research aims to quantify the levels of connectivity among Pavona gigantea populations in the Mexican Pacific, using two mitochondrial genes and a nuclear gene. Mitochondrial genes were insufficiently variable to test geographical heterogeneity, whereas the more variable ( h ≥ 0.86) nuclear rDNA indicated significant geographic differentiation ( Φ = 0.159, P < 0.001) among five locations along the Mexican Pacific, but no evidence of isolation by distance. Gene flow was limited among most sampled locales, and the largest estimate suggested moderate and unidirectional gene flow from Huatulco Bays to La Paz Bay and Marietas Islands. We found partial agreement between the patterns of connectivity among localities and the general pattern of superficial oceanographic circulation of the region, particularly in reference with the expected influence of the northward flowing West Mexican Current. These results suggest a limited demographic connectivity among Pavona gigantea populations along the Mexican Pacific, mediated by passive larval transport, and highlight the difficulty of predicting connectivity patterns on the basis of highly variable oceanographic regimes and reproductive events. The limited connectivity is of consequence for the viability and vulnerability of local populations and should be considered in the management and conservation strategies in the region. [ABSTRACT FROM AUTHOR]