Molecular Ecology (2007) 16, 3721–3733 doi: 10.1111/j.1365-294X.2007.03403.x © 2007 The Authors Journal compilation © 2007 Blackwell Publishing Ltd Blackwell Publishing Ltd Niche partitioning of closely related symbiotic dinoflagellates EUGENIA M. SAMPAYO,* LORENZO FRANCESCHINIS,*† OVE HOEGH-GULDBERG,* SOPHIE DOVE * *Centre for Marine Studies, The University of Queensland, St Lucia, Qld 4072, Australia, †Department of Marine Biology, University of Bremen, Bremen, Germany Abstract Reef-building corals are fundamental to the most diverse marine ecosystems, yet a detailed understanding of the processes involved in the establishment, persistence and ecology of the coral–dinoflagellate association remains largely unknown. This study explores symbiont diversity in relation to habitat by employing a broad-scale sampling regime using ITS2 and denaturing gradient gel electrophoresis. Samples from Pocillopora damicornis, Stylophora pistillata and Seriatopora hystrix all harboured host-specific clade C symbiont types at Heron Island (Great Barrier Reef, Australia). While Ser. hystrix associated with a single symbiont profile along its entire depth distribution, both P. damicornis and Sty. pistillata associated with multiple symbiont profiles that showed a strong zonation with depth. It is shown that, with an increased sampling effort, previously identified ‘rare’ symbiont types within this group of host species are in fact environmental specialists. A multivariate approach was used to expand on the common distinction of symbionts by a single genetic identity. It shows merit in its capacity not only to include all the variability present within the marker region but also to reliably represent ecological diversification of symbionts. Furthermore, the cohesive species concept is explored to explain how niche partitioning may drive diversification of closely related symbiont lineages. This study provides thus evidence that closely related symbionts are ecologically distinct and fulfil their own niche within the ecosystem provided by the host and external environment. Keywords: ecology, Pocillopora, Seriatopora, Stylophora, Symbiodinium-ITS2, zonation Received 9 December 2006; revision accepted 27 April 2007 Introduction Reef-building corals form a mutualistic relationship with unicellular dinoflagellates (genus Symbiodinium) and this symbiosis underpins the success of tropical reef building systems worldwide. Despite the persistence of coral reef systems over geological time, there has been a dramatic and unprecedented decline of coral community composition and diversity over the last 30 years. Approximately 30% of reefs have already been damaged and a further 60% of coral reefs are predicted to be lost within the next 30 years (Hughes et al. 2003). A detailed understanding, however, of the processes involved in the establishment, persistence, and ecology of the coral–dinoflagellate association remains largely unknown. Initially, reef-building corals were thought to associate with a single symbiont, Symbiodinium microadriaticum (Freudenthal 1962) but additional species were later described based on differences in morphological ultra- structure (Blank & Trench 1985; Trench & Blank 1987), cell size (LaJeunesse 2001), isozyme profiles (Schoenberg & Trench 1980), and photosynthetic efficiency (Chang et al. 1983; Iglesias-Prieto & Trench 1994, 1997a). However, the description of Symbiodinium species is complex due to the lack of clear morphological features, but the introduction of molecular techniques has assisted the differentiation of Symbiodinium types, with thus far eight major clades have been identified. Their phylogeny is supported by various molecular markers, e.g. 18S rDNA (Rowan & Powers 1991), 28S rDNA (Loh et al. 2001), 23S chloroplast large subunit (Santos et al. 2002) and mitochondrial DNA (Takabayashi et al. 2004). Different clades have been shown to exhibit distinct geographical distributions at Correspondence: Eugenia Sampayo, Fax: +61 (0)733654755, e.sampayo@cms.uq.edu.au