BackgroundCoral reefs are hotspots of biodiversity, yet processes of diversification in these ecosystems are poorly understood. The environmental heterogeneity of coral reef environments could be an important contributor to diversification, however, evidence supporting ecological speciation in corals is sparse. Here, we present data from a widespread coral species that reveals a strong association of host and symbiont lineages with specific habitats, consistent with distinct, sympatric gene pools that are maintained through ecologically-based selection.Methodology/Principal FindingsPopulations of a common brooding coral, Seriatopora hystrix, were sampled from three adjacent reef habitats (spanning a ∼30 m depth range) at three locations on the Great Barrier Reef (n = 336). The populations were assessed for genetic structure using a combination of mitochondrial (putative control region) and nuclear (three microsatellites) markers for the coral host, and the ITS2 region of the ribosomal DNA for the algal symbionts (Symbiodinium). Our results show concordant genetic partitioning of both the coral host and its symbionts across the different habitats, independent of sampling location.Conclusions/SignificanceThis study demonstrates that coral populations and their associated symbionts can be highly structured across habitats on a single reef. Coral populations from adjacent habitats were found to be genetically isolated from each other, whereas genetic similarity was maintained across similar habitat types at different locations. The most parsimonious explanation for the observed genetic partitioning across habitats is that adaptation to the local environment has caused ecological divergence of distinct genetic groups within S. hystrix.

Symbiotic algae in coral species distributed over a large depth range are confronted with major differences in light conditions. We studied the genetic variation of Symbiodinium in the coral genus Madracis over depth (5-40 m) and at two different colony surface positions. Using polymerase chain reaction-denaturing gradient gel electrophoresis ITS2 nuclear ribosomal DNA analyses, we consistently identified three symbiont genotypes with distributions that reveal patterns of host specificity and depth-based zonation. ITS2 type B7 Symbiodinium is the generalist type, occurring in all zooxanthellate Madracis corals and at all depths. Type B13 is restricted to the shallow water specialist Madracis mirabilis. Type B15 is typical of deep reef environments and replaces B7 in the depth generalist Madracis pharensis. Contrasting with variation over depth, we found strong functional within-colony uniformity in symbiont diversity. Relating symbiont distributions to measured physical factors (irradiance, light spectral distribution, temperature), suggests depth-based ecological function and host specificity for Symbiodinium ITS2 types, even among closely related coral species.

Despite a growing interest in mesophotic coral ecosystems (MCEs), information on the photosynthetic endosymbionts (genus Symbiodinium) associated with scleractinian corals inhabiting deep reef ecosystems is sparse. Here, the deep-water Symbiodinium diversity is assessed from 10 different coral genera at a depth range of 45 to 70 m on the Great Barrier Reef (GBR), Australia. Symbiodinium identity was established using denaturing gradient gel electrophoresis (DGGE) fingerprinting of the internal transcribed spacer region 2 (ITS2) of the ribosomal DNA. Except for the novel Symbiodinium type C131 (found in Porites), all Symbiodinium types have previously been identified in shallow reef corals across the Pacific. Specimens of Seriatopora, Montipora, and Porites harboured similar symbionts as reported in shallow water (e.g. C3n, C3n-hh, C15, and C17), thus adhering to patterns of host-specificity across a wide depth range. However, several other Symbiodinium types were found to transcend previously established patterns of host-specificity at mesophotic depths. For example, 'host-specialist' types C3i and C3k (previously only reported in Acropora spp.) were found here to associate with a range of different genera (Leptoseris, Pachyseris, Fungia, and Echinophyllia). Although limited in sample size, this preliminary survey indicates that mesophotic habitats on the GBR may not represent an isolated community in terms of Symbiodinium diversity, which has significant relevance to their potential to act as refugia. Moreover, the present study identifies the need to examine symbiont diversity across broad environmental ranges (including MCEs) in order to gain an accurate understanding of symbiosis specificity and distribution range of specific coral-Symbiodinium associations. KEY WORDS: Symbiodinium · Mesophotic · Deep reefs · Coral · ITS2 · DGGE · Great Barrier ReefResale or republication not permitted without written consent of the publisher Mar Ecol Prog Ser 439: 117-126, 2011 118 zation of Symbiodinium into cladal (e.g. Rowan & Powers 1991, Baker & Rowan 1997 and subcladal types (e.g. van Oppen et al. 2001, LaJeunesse 2002 has greatly enhanced our understanding of the symbiosis. Studies of Symbiodinium diversity on broad latitudinal or longitudinal gradients have shown distinct biogeographical patterns (e.g. LaJeunesse et al. 2003, Silverstein et al. 2011), whereas more local or species-specific studies have highlighted ecological zonation, physiological diversification, and host-specificity of distinct symbionts (e.g. Rowan & Knowlton 1995, LaJeunesse et al. 2003, 2004, Iglesias-Prieto et al. 2004, Sampayo et al. 2007, Frade et al. 2008a.Community-wide shifts in symbiont diversity occur with increasing depth (LaJeunesse 2002, LaJeunesse et al. 2003, 2004, but this observation is likely to be, in part, the result of host community composition changes over depth. Nonetheless, studies focusing on single coral species show a similar pattern, and depth zonation of symbionts has been shown to occur on a cladal...