REPORT The distribution of intra-genomically variable dinoflagellate symbionts at Lord Howe Island, Australia Shaun P. Wilkinson 1 • Stefanie Pontasch 1 • Paul L. Fisher 1,2 • Simon K. Davy 1 Received: 9 May 2015 / Accepted: 22 September 2015 Ó Springer-Verlag Berlin Heidelberg 2015 Abstract The symbiotic dinoflagellates of corals and other marine invertebrates (Symbiodinium) are essential to the development of shallow-water coral reefs. This genus contains considerable genetic diversity and a correspond- ing range of physiological and ecological traits. Most genetic variation arises through the accumulation of somatic mutations that arise during asexual reproduction. Yet growing evidence suggests that occasional sexual reproductive events also occur within, and perhaps between, Symbiodinium lineages, further contributing to the pool of genetic variation available for evolutionary adaptation. Intra-genomic variation can therefore arise from both sexual and asexual reproductive processes, making it difficult to discern its underlying causes and consequences. We used quantitative PCR targeting the ITS2 locus to estimate proportions of genetically homo- geneous symbionts and intra-genomically variable Sym- biodinium (IGV Symbiodinium) in the reef-building coral Pocillopora damicornis at Lord Howe Island, Australia. We then sampled colonies through time and at a variety of spatial scales to find out whether the distribution of these symbionts followed patterns consistent with niche partitioning. Estimated ratios of homogeneous to IGV Symbiodinium varied between colonies within sites (metres to tens of metres) and between sites separated by hundreds to thousands of metres, but remained stable within colonies through time. Symbiont ratios followed a temperature gradient, with the local thermal maximum emerging as a negative predictor for the estimated proportional abun- dance of IGV Symbiodinium. While this pattern may result from fine-scale spatial population structure, it is consistent with an increased susceptibility to thermal stress, sug- gesting that the evolutionary processes that generate IGV (such as inter-lineage recombination and the accumulation of somatic mutations at the ITS2 locus) may have impor- tant implications for the fitness of the symbiont and that of the coral host. Keywords Coral Á Pocillopora damicornis Á Symbiodinium Á Intra-genomic variation Á ITS2 Introduction Corals are among the most ecologically important organ- isms in the ocean, yet are also among those most severely affected by rising temperatures. In particular, coral bleaching has caused catastrophic declines of reef areas in recent decades (Hughes et al. 2003; Hoegh-Guldberg et al. 2007; Pandolfi et al. 2011). Bleaching arises from the breakdown of the symbiosis between corals and their symbiotic dinoflagellate algae (genus Symbiodinium). Thermal stress and other environmental factors cause the host to expel or degrade its symbionts, causing starvation and death if the stressor persists, and the host is unable to regenerate residual algae or obtain symbionts de novo from the surrounding environment (Weis 2008). An important Communicated by Biology Editor Dr. Line K. Bay Electronic supplementary material The online version of this article (doi:10.1007/s00338-015-1357-0) contains supplementary material, which is available to authorized users. & Shaun P. Wilkinson shaunpwilkinson@gmail.com 1 School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Wellington 6012, New Zealand 2 Present Address: School of Civil Engineering, The University of Queensland, St Lucia, QLD 4072, Australia 123 Coral Reefs DOI 10.1007/s00338-015-1357-0