Geographic differences in vertical connectivity in the Caribbean coral Montastraea cavernosa despite high levels of horizontal connectivity at shallow depths X. SERRANO,* 1 I. B. BAUMS, † K. O’ REILLY,* T. B. SMITH, ‡ R. J. JONES, § T. L. SHEARER, ¶ F. L. D. NUNES** †† and A. C. BAKER* *Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA, †Department of Biology, The Pennsylvania State University, 208 Mueller Laboratory, University Park, PA 16802, USA, ‡Center for Marine and Environmental Studies, University of the Virgin Islands, #2 John Brewer’s Bay, St. Thomas, USVI 00802-9990, USA, §Australian Institute of Marine Science, The UWA Oceans Institute, 35 Stirling Highway, Crawley, WA 6009, Australia, ¶School of Biology, Georgia Institute of Technology, 310 Ferst Dr., Atlanta, GA 30332, USA, **Laboratory of Artificial and Natural Evolution, Department of Genetics & Evolution, University of Geneva, Sciences III, 30 quai Ernest Ansermet, 1211 Geneva 4, Switzerland, ††Laboratoire des Sciences de l’Environnement Marin, Institut Universitaire Europ  een de la Mer, Universit  e de Bretagne Occidentale, Technopole Brest Iroise, 29280 Plouzan e, France Abstract The deep reef refugia hypothesis proposes that deep reefs can act as local recruitment sources for shallow reefs following disturbance. To test this hypothesis, nine polymor- phic DNA microsatellite loci were developed and used to assess vertical connectivity in 583 coral colonies of the Caribbean depth-generalist coral Montastraea cavernosa. Samples were collected from three depth zones (≤10, 15–20 and ≥25 m) at sites in Flor- ida (within the Upper Keys, Lower Keys and Dry Tortugas), Bermuda, and the U.S. Virgin Islands. Migration rates were estimated to determine the probability of coral larval migration from shallow to deep and from deep to shallow. Finally, algal symbi- ont (Symbiodinium spp.) diversity and distribution were assessed in a subset of corals to test whether symbiont depth zonation might indicate limited vertical connectivity. Overall, analyses revealed significant genetic differentiation by depth in Florida, but not in Bermuda or the U.S. Virgin Islands, despite high levels of horizontal connectiv- ity between these geographic locations at shallow depths. Within Florida, greater verti- cal connectivity was observed in the Dry Tortugas compared to the Lower or Upper Keys. However, at all sites, and regardless of the extent of vertical connectivity, migra- tion occurred asymmetrically, with greater likelihood of migration from shallow to intermediate/deep habitats. Finally, most colonies hosted a single Symbiodinium type (C3), ruling out symbiont depth zonation of the dominant symbiont type as a structur- ing factor. Together, these findings suggest that the potential for shallow reefs to recover from deep-water refugia in M. cavernosa is location-specific, varying among and within geographic locations likely as a consequence of local hydrology. Keywords: climate change, cnidarians, conservation genetics, deep reef refugia hypothesis, great star coral, mesophotic, population genetics—empirical Received 26 August 2013; revision received 4 July 2014; accepted 11 July 2014 Correspondence: Xaymara M. Serrano, Fax: +1 305 421 4600; E-mail: xserrano@rsmas.miami.edu 1 Present address: National Oceanic and Atmospheric Adminis- tration, Atlantic Oceanographic and Meteorological Laboratory, 4301 Rickenbacker Causeway, Miami, FL 33149, USA. © 2014 John Wiley & Sons Ltd Molecular Ecology (2014) doi: 10.1111/mec.12861