1 3 Mar Biol (2015) 162:81–98 DOI 10.1007/s00227-014-2560-1 ORIGINAL PAPER Population structure of the corals Orbicella faveolata and Acropora palmata in the Mesoamerican Barrier Reef System with comparisons over Caribbean basin-wide spatial scale I. Porto-Hannes · A. L. Zubillaga · T. L. Shearer · C. Bastidas · C. Salazar · M. A. Coffroth · A. M. Szmant Received: 19 February 2014 / Accepted: 23 October 2014 / Published online: 6 November 2014 © Springer-Verlag Berlin Heidelberg 2014 Calabash (Belize) and A. palmata from Puerto Morelos (Mexico) showed some genetic differentiation from the rest of the MBRS populations, and (3) A. palmata from MBRS, Panama, Puerto Rico and Venezuela were grouped into four subregions that could be considered as management units. A more spatially detailed sampling program and the inclu- sion of recruits will be necessary to get a comprehensive understanding of coral population structure and current gene flow patterns in these two species. Introduction Coral reefs have been declining dramatically world-wide due to multiple stressors including habitat loss, overfishing, pollution, tourism (Jackson et al. 2001; Kramer and Kramer 2002), the increasing prevalence of diseases (Harvell et al. 1999; Garzón-Ferreira et al. 2001; Cróquer and Weil 2009) and bleaching (Hoegh-Guldberg et al. 2007; Carilli et al. 2009). The combination of the devastating effects of these factors has challenged coral reef resilience, particularly in the Caribbean, where extensive degradation of reef habi- tats has been reported (Hughes 1994; Hughes and Tanner Abstract Studies of genetic diversity and population genetic structure in marine organisms are relevant to under- standing populations’ variability, and therefore their ability to withstand environmental perturbations, their potential for resistance to local extinction and their natural rate of recovery. Population structure and genetic diversity were assessed at a regional spatial scale (i.e., Mesoamerican Bar- rier Reef System, MBRS) in two major reef building coral species Orbicella (formerly Montastraea) faveolata and Acropora palmata, and at a larger spatial scale (i.e., Car- ibbean-wide; MBRS, Panama, Venezuela and Puerto Rico) for A. palmata only. The most significant findings were as follows: (1) high genetic diversity and low clonality were found for both species, which is expected for O. faveolata but not for A. palmata, (2) both species showed low-to- moderate, yet significant population structure among popu- lations along the MBRS; in particular, O. faveolata and A. palmata from Ambergris (Belize) and O. faveolata from Communicated by C. Riginos. Electronic supplementary material The online version of this article (doi:10.1007/s00227-014-2560-1) contains supplementary material, which is available to authorized users. I. Porto-Hannes (*) · M. A. Coffroth Graduate Program in Evolution, Ecology and Behavior, State University of New York at Buffalo, 411 Cooke Hall, Buffalo, NY 14260, USA e-mail: isabelha@buffalo.edu A. L. Zubillaga · C. Bastidas Departamento de Biología de Organismos, Universidad Simón Bolívar, Caracas 1080, Venezuela T. L. Shearer School of Biology, Georgia Institute of Technology, 310 Ferst Dr., Atlanta, GA 30332, USA C. Salazar Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Carrera 24 No 63C-69, Bogotá, D.C. 111221, Colombia M. A. Coffroth Department of Geology, State University of New York at Buffalo, 411 Cooke Hall, Buffalo, NY 14260, USA A. M. Szmant Center for Marine Science, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC 28409, USA