Aim This study examines the importance of geographic proximity, host life history and regional and local differences in environment (temperature and water clarity) in driving the ecological and evolutionary processes underpinning the global patterns of diversity and distribution of symbiotic dinoflagellates. By comparing and contrasting coral-algal symbioses from isolated regions with differing environmental conditions, we may assess the potential of coral communities to respond to significant changes in climate. Location Indian Ocean.Methods Community assemblages of obligate symbiotic invertebrates were sampled at numerous sites from two regions, the north-eastern Indian Ocean (Andaman Sea, western Thailand) and the western Indian Ocean (Zanzibar, Tanzania). Molecular genetic methods, including denaturing gradient gel electrophoresis analysis of the ribosomal internal transcribed spacers, DNA sequencing and microsatellite genotyping, were used to characterize the 'species' diversity and evolutionary relationships of symbiotic dinoflagellates (genus Symbiodinium). Host-symbiont specificity, geographic isolation and local and regional environmental factors were evaluated in terms of their importance in governing the distribution and prevalence of certain symbiont taxa.Results Host-generalist symbionts (C3u and D1-4, formerly D1a now designated Symbiodinium trenchi) frequently occurred alone and sometimes together in hosts with horizontal modes of symbiont acquisition. However, the majority of Symbiodinium diversity consisted of apparently host-specific 'species'. Clade C Symbiodinium were diverse and dominated host assemblages from sites sampled in the western Indian Ocean, a pattern analogous to symbiont communities on the Great Barrier Reef with similar environmental conditions. Clade D Symbiodinium were diverse and occurred frequently in hosts from the northeastern Indian Ocean, especially at inshore locations, where temperatures are warmer, water turbidity is high and large tidal exchanges commonly expose coral populations to aerial desiccation. Main conclusions Regional and local differences in cnidarian-algal combinations indicate that these symbioses are ecologically and evolutionarily responsive and can thrive under various environmental conditions. The high temperatures and turbid conditions of the north-eastern Indian Ocean partly

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West sides of the coral Coelastrea aspera, which had achieved thermo-tolerance after previous experience of high solar irradiance in the field, were rotated through 180o on a reef flat in Phuket, Thailand (7o50´N, 98o25.5´E), in 2000 in a manipulation experiment and secured in this position. In 2010, elevated sea temperatures caused extreme bleaching in these corals, with former west sides of colonies (now facing east) retaining four times higher symbiont densities than the east sides of control colonies, which had not been rotated and which had been subject to a lower irradiance environment than west sides throughout their lifetime. The reduced bleaching susceptibility of the former west sides in 2010, compared to handling controls, suggests that the rotated corals had retained a ‘memory’ of their previous high irradiance history despite living under lower irradiance for 10 years. Such long-term retention of an environmental ‘memory’ raises important questions about the acclimatisation potential of reef corals in a changing climate and the mechanisms by which it is achieved

Effects of combined rising sea temperature and increasing sea level on coral reefs, both factors associated with global warming, have rarely been addressed. In this ~40 y study of shallow reefs in the eastern Indian Ocean, we show that a rising relative sea level, currently estimated at ~11 mm y −1 , has not only promoted coral cover but also has potential to limit damaging effects of thermally-induced bleaching. In 2010 the region experienced the most severe bleaching on record with corals subject to sea temperatures of >31 °C for 7 weeks. While the reef flats studied have a common aspect and are dominated by a similar suite of coral species, there was considerable spatial variation in their bleaching response which corresponded with reef-flat depth. Greatest loss of coral cover and community structure disruption occurred on the shallowest reef flats. Damage was less severe on the deepest reef flat where corals were subject to less aerial exposure, rapid flushing and longer submergence in turbid waters. Recovery of the most damaged sites took only ~8 y. While future trajectories of these resilient reefs will depend on sea-level anomalies, and frequency of extreme bleaching the positive role of rising sea level should not be under-estimated.

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