Semi-permeable species boundaries in the coral genus Madracis: Introgression in a brooding coral system P.R. Frade a,b,c,d,⇑ , M.C. Reyes-Nivia b,c , J. Faria b,e , J.A. Kaandorp f , P.C. Luttikhuizen b , R.P.M. Bak b,c a Unidad Académica de Sistemas Arrecifales, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Apdo. Postal 1152, Cancún, Quintana Roo 77500, Mexico b Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB Den Burg, The Netherlands c Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94766, 1090 GT Amsterdam, The Netherlands d Caribbean Research and Management of Biodiversity (CARMABI) Foundation, Piscaderabaai z/n, P.O. Box 2090, Willemstad, Curaçao, Netherlands Antilles e Department of Animal Biology, Faculty of Sciences, University of Lisbon, Campo Grande – Bloco C2, 1749-016 Lisboa, Portugal f Section Computational Science, Faculty of Science, University of Amsterdam, Kruislaan 403, 1098 SJ Amsterdam, The Netherlands article info Article history: Received 26 January 2010 Revised 5 July 2010 Accepted 15 September 2010 Available online 21 September 2010 Keywords: Hybridization Gene exchange Reticulate evolution Coalescent theory Disruptive selection Coral-symbiont associations abstract Introgressive hybridization is described in several phylogenetic studies of mass-spawning corals. How- ever, the prevalence of this process among brooding coral species is unclear. We used a mitochondrial (mtDNA: nad5) and two nuclear (nDNA: ATPSa and SRP54) intron markers to explore species barriers in the coral genus Madracis and address the role of hybridization in brooding systems. Specimens of six Caribbean Madracis morphospecies were collected from 5 to 60 m depth at Buoy One, Curaçao, sup- plemented by samples from Aruba, Trinidad & Tobago and Bermuda. Polymerase chain reaction and denaturing gradient gel electrophoresis were coupled to detect distinct alleles within single colonies. The recurrent nDNA phylogenetic non-monophyly among taxa is only challenged by Madracis senaria, the single monophyletic species within the genus. nDNA AMOVAs indicated overall statistical divergence (0.1% significance level) among species but pairwise comparisons of genetic differentiation revealed some gene exchange between Madracis taxa. mtDNA sequences clustered in two main groups representing typ- ical shallow and deep water Madracis species. Madracis pharensis shallow and deep colonies (with thresh- old at about 23–24 m) clustered in different mtDNA branches, together with their depth-sympatric congenerics. This divergence was repeated for the nDNA (ATPSa) suggestive of distinct M. pharensis depth populations. These matched the vertical distribution of the dinoflagellate symbionts hosted by M. phar- ensis, with Symbiodinium ITS2 type B7 in the shallows but type B15 in the deep habitats, suggesting sym- biont-related disruptive selection. Recurrent non-monophyly of Madracis taxa and high levels of shared polymorphism reflected in ambiguous phylogenetic networks indicate that hybridization is likely to have played a role in the evolution of the genus. Using coalescent forward-in-time simulations, lineage sorting alone was rejected as an explanation to the SRP54 genetic variation contained in Madracis mirabilis and Madracis decactis (species with an old fossil record), showing that introgressive hybridization has taken place between these species, either directly or through the gene pool of other Madracis taxa. Madracis widespread non-monophyly and the absence of statistical divergence between some species suggest that introgressive hybridization plays an important role in the evolution of the genus. Different reproductive traits and symbiont signatures of taxa forming distinct genetic clusters also point to the same conclusion. We suggest that Madracis morphospecies remain recognizable because introgressive hybridization is non-pervasive and/or because disruptive selection is in action. Ó 2010 Elsevier Inc. All rights reserved. 1. Introduction Scleractinian corals, the key tropical reef-building organisms, have high dispersal potential, large population sizes, ample distri- butions, overlapping generations and high fecundities (Hughes et al., 1992; Palumbi, 1994). These characteristics, enhanced by the absence of temporal barriers to interspecific breeding as a re- sult of synchronized spawning events, provide a great opportunity for introgression, the exchange of genes between hybridizing taxa 1055-7903/$ - see front matter Ó 2010 Elsevier Inc. All rights reserved. doi:10.1016/j.ympev.2010.09.010 ⇑ Corresponding author at: Unidad Académica de Sistemas Arrecifales, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Apdo. Postal 1152, Cancún, Quintana Roo 77500, Mexico. Fax: +52 998 871 0136. E-mail addresses: pfrade@cmarl.unam.mx (P.R. Frade), macatareyes@gmail.com (M.C. Reyes-Nivia), joaofariaos@gmail.com (J. Faria), j.a.kaandorp@uva.nl (J.A. Kaandorp), pieternella.luttikhuizen@nioz.nl (P.C. Luttikhuizen), rolf.bak@nioz.nl (R.P.M. Bak). Molecular Phylogenetics and Evolution 57 (2010) 1072–1090 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev