Data from: Host-specialist lineages dominate the adaptive radiation of reef coral endosymbionts

Bursts in species diversification are well documented among animals and plants, yet few studies have assessed recent adaptive radiations of eukaryotic microbes. Consequently, we examined the radiation of the most ecologically dominant group of endosymbiotic dinoflagellates found in reef-building corals, Symbiodinium Clade C, using nuclear ribosomal (ITS2), chloroplast (psbAncr), and multilocus microsatellite genotyping. Through a hierarchical analysis of high-resolution genetic data, we assessed whether ecologically distinct Symbiodinium, differentiated by seemingly equivocal rDNA sequence differences, are independent species lineages. We also considered the role of host specificity in Symbiodinium speciation and the correspondence between endosymbiont diversification and Caribbean paleo-history. According to phylogenetic, biological, and ecological species concepts, Symbiodinium Clade C comprises many distinct species. Although regional factors contributed to population-genetic structuring of these lineages, Symbiodinium diversification was mainly driven by host specialization. By combining patterns of the endosymbiont's host specificity, water depth distribution, and phylogeography with paleo-historical signals of climate change, we inferred that present-day species diversity on Atlantic coral reefs stemmed mostly from a post-Miocene adaptive radiation. Host-generalist progenitors spread, specialized, and diversified during the ensuing epochs of prolonged global cooling and change in reef-faunal assemblages. Our evolutionary reconstruction thus suggests that Symbiodinium undergoes “boom and bust” phases in diversification and extinction during major climate shifts.物种多样化的爆发事件在动植物类群中已有充分记录，但针对真核微生物近期适应辐射的研究却寥寥无几。为此，我们针对造礁珊瑚中生态占比最高的一类内共生甲藻——Symbiodinium C系群（Symbiodinium Clade C），借助核糖体核基因（ITS2）、叶绿体(psbAncr)以及多位点微卫星基因分型开展辐射演化分析。通过对高分辨率遗传数据进行层级化分析，我们验证了仅凭核糖体DNA序列差异难以区分的、具有生态分化的Symbiodinium是否属于独立的物种支系。我们同时探讨了宿主特异性在Symbiodinium物种形成中的作用，以及内共生体多样化与加勒比海古气候历史之间的关联。依据系统发育、生物学及生态学物种概念，Symbiodinium C系群包含多个独立物种。尽管区域因素对这些支系的群体遗传结构存在影响，但Symbiodinium的多样化主要由宿主特化所驱动。通过整合内共生体的宿主特异性、水深分布、系统地理学特征，以及气候变化的古历史信号，我们推断大西洋珊瑚礁现存的物种多样性主要源自中新世后的适应辐射事件。在随后长期全球降温以及珊瑚礁动物群组成发生改变的地质时期中，宿主泛化型祖先得以扩散、特化并发生多样化。因此，我们的演化重建结果表明，Symbiodinium在重大气候转变期间，会经历物种多样化与灭绝的“繁盛-衰亡”循环阶段。