REPORT Pervasive genetic structure at different geographic scales in the coral-excavating sponge Cliona vermifera (Hancock, 1867) in the Mexican Pacific M. G. Leo ´n-Pech 1 • J. A. Cruz-Barraza 2 • J. L. Carballo 2 • L. E. Calderon-Aguilera 3 • A. Rocha-Olivares 1 Received: 3 July 2014 / Accepted: 8 June 2015 / Published online: 21 June 2015 Ó Springer-Verlag Berlin Heidelberg 2015 Abstract 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, suggest- ing 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 dif- ferentiation 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. Keywords Excavating sponge Á Coral reefs Á Genetic structure Á Stepping stone Introduction Coral-excavating sponges are an essential component of coral reef ecosystems (Carballo et al. 2008a, b), and recent studies suggest a future increase in sponge bioerosion as an outcome of coral reef decline around the world (Nava and Carballo 2008; Scho ¨nberg and Ortiz 2008; Wisshak et al. 2012; Carballo et al. 2013b). Despite their ecological importance, the population dynamics of coral-excavating sponges, including how populations are genetically struc- tured and connected in space and time, remain largely unknown. This is of great relevance given their sessile nature and the spatial patchiness of their habitat consisting mainly of coral calcareous structures. Available population genetics studies of Porifera refer mostly to non-excavating species (Duran et al. 2004a, b, c; Bentlage and Wo ¨rheide 2007; Wo ¨rheide et al. 2008; Lo ´pez-Legentil and Pawlik 2009; DeBiasse et al. 2010), whereas those focused on coral-excavating sponges deal mostly with their molecular Communicated by Biology Editor Dr. Ruth Gates & A. Rocha-Olivares arocha@cicese.mx 1 Molecular Ecology Laboratory, Biological Oceanography Department, CICESE, Carretera Ensenada Tijuana No. 3918, C.P. 22860 Ensenada, Baja California, Mexico 2 Institute of Marine Sciences and Limnology, Universidad Nacional Auto ´noma de Me ´xico (Unidad Acade ´mica Mazatlan), Avenida Joel Montes Camarena s/n, PO Box 811, 82040 Mazatla ´n, SIN, Mexico 3 Fisheries and Coastal Ecology Laboratory, Marine Ecology Department, CICESE, Carretera Ensenada Tijuana No. 3918, 22860 Ensenada, Baja California, Mexico 123 Coral Reefs (2015) 34:887–897 DOI 10.1007/s00338-015-1316-9