Data from: Adaptation to reef habitats through selection on the coral animal and its associated microbiome

Spatially adjacent habitats on coral reefs can represent highly distinct environments, often harbouring different coral communities. Yet, certain coral species thrive across divergent environments. It is unknown whether the forces of selection are sufficiently strong to overcome the counteracting effects of the typically high gene flow over short distances, and for local adaptation to occur. We screened the coral genome (using restriction-site-associated sequencing [RAD-seq]), and characterized both the dinoflagellate photosymbiont and tissue-associated prokaryote microbiomes (using metabarcoding) of a reef flat and slope population of the reef-building coral, Pocillopora damicornis, at two locations on Heron Island in the southern Great Barrier Reef. Reef flat and slope populations were separated by <100 m horizontally and ~5 m vertically and the two study locations were separated by ~1 km. For the coral host, genetic divergence between habitats was much greater than between locations, suggesting limited gene flow between the flat and slope populations. Consistent with environmental selection, outlier loci primarily belonged to the conserved, minimal cellular stress response, likely reflecting adaptation to the different temperature and irradiance regimes on the reef flat and slope. Similarly, the prokaryote community differed across both habitat and, to a lesser extent, location, whereas the dinoflagellate photosymbionts differed by habitat but not location. The observed intra-specific diversity associated with divergent habitats supports that environmental adaptation involves multiple members of the coral holobiont. Adaptive alleles or microbial associations present in coral populations from the environmentally-variable reef flat may provide a source of adaptive variation for assisted evolution approaches, through assisted gene flow, artificial cross-breeding or probiotic inoculations, with the aim to increase climate resilience in the slope populations.

珊瑚礁上空间毗邻的生境往往构成差异显著的环境，通常栖息着截然不同的珊瑚群落。然而，部分珊瑚物种却能在迥异的生境中茁壮成长。目前尚不明确，选择压力是否足够强劲，足以克服短距离范围内普遍存在的强基因流所带来的拮抗效应，从而使本地适应得以发生。本研究以大堡礁南部赫伦岛两处采样点的造礁珊瑚（reef-building coral）鹿角杯形珊瑚（Pocillopora damicornis）的礁坪与礁坡种群为研究对象，采用限制性酶切位点相关DNA测序（restriction-site-associated sequencing, RAD-seq）对珊瑚宿主基因组进行筛查，并通过宏条形码（metabarcoding）技术对其体内的鞭毛藻光合共生体（dinoflagellate photosymbiont）与组织相关原核生物微生物组进行表征。礁坪与礁坡种群的水平间距不足100米，垂直高差约5米，而两处采样点间距约1千米。针对珊瑚宿主，不同生境间的遗传分化程度远高于不同采样点间的分化，这表明礁坪与礁坡种群间的基因流有限。与环境选择假说一致的是，筛选出的异常位点主要隶属于保守的基础细胞应激反应通路，这很可能反映了珊瑚对礁坪与礁坡间不同温度与光照强度环境的适应。类似地，原核生物群落同时存在生境与采样点层面的差异（其中采样点的差异相对较弱），而鞭毛藻光合共生体群落仅存在生境层面的差异，不受采样地点的影响。本研究观测到的与迥异生境相关的种内多样性，证实环境适应涉及珊瑚共生功能体（coral holobiont）的多个组成成员。来自环境异质性较强的礁坪珊瑚种群所携带的适应性等位基因或微生物共生关联，可通过辅助基因流、人工杂交或益生菌接种等辅助进化手段，为提升礁坡种群的气候韧性提供适应性变异来源。