Supplementary data for: From genomics to integrative taxonomy? The case study of Pocillopora corals

With the advent of genomics, sequencing thousands of loci from hundreds of individuals now appears feasible at reasonable costs, allowing complex phylogenies to be resolved. This is particularly relevant for cnidarians, for which insufficient data due to the small number of currently available markers, coupled with difficulties in inferring gene trees and morphological incongruences, encrypts species boundaries, thereby blurring the study and conservation of these organisms. Yet, can genomics alone be used to delimit species in an integrative taxonomic context? Here, focusing on the coral genus Pocillopora, which plays key roles in Indo-Pacific reef ecosystems but has challenged taxonomists for decades, we explored and discussed the usefulness of multiple criteria (genetics, morphology, biogeography and symbiosis ecology) to delimit species of this genus. Phylogenetic inferences, clustering approaches and species delimitation methods based on genome-wide single-nucleotide polymorphisms (SNPs) were first used to resolve Pocillopora phylogeny and propose genomic species hypotheses from 356 colonies sampled across the Indo-Pacific (western Indian Ocean, tropical southwestern Pacific and south-east Polynesia). These species hypotheses were then compared to previous genetic evidences, as well as to evidences based on morphology, biogeography and symbiosis. Genomics allowed to delimit 21 species hypotheses where only seven are currently recognised based on current taxonomy. Moreover, 13 species were strongly supported by all approaches, either confirming their currently recognised species status, or supporting the presence of new species that need to be formally described. Some of the other genomic species hypotheses were supported by biogeographic or symbiosis evidences, but additional investigations are needed to state on their species status. Altogether, our results support (1) the obsolescence of macromorphology (i.e., overall colony and branches shape) but the relevance of micromorphology (i.e., corallite structures) to refine Pocillopora species limits, (2) the need to identify molecularly species prior to their study, as morphology can blur species identification on the field, (3) the relevance of the mtORF (coupled with other markers in some cases) as a diagnostic marker of most species, and (4) the need for a taxonomical revision in the Pocillopora genus. These results give new insights into the usefulness of multiple criteria for resolving Pocillopora species limits and will ultimately provide helpful insights for the conservation of the species from this scleractinian genus.

随着基因组学技术的发展，如今以合理成本对数百个个体的数千个基因座开展测序已具备可行性，由此得以解析复杂的系统发育关系。这一点对于刺胞动物而言尤为关键：当前该类群可用的分子标记数量有限，加之基因树推断难度较大、形态特征存在不一致性，这些问题模糊了物种边界的界定，进而阻碍了这类生物的研究与保护工作。然而，在整合分类学的研究框架下，是否仅依靠基因组学技术即可完成物种界定呢？本研究聚焦于在印度洋-太平洋珊瑚礁生态系统中发挥关键作用、但数十年来一直困扰分类学界的杯形珊瑚属（Pocillopora），探讨了多套判定标准（遗传学、形态学、生物地理学以及共生生态学）在该属物种界定中的应用价值。研究团队首先基于在印度洋-太平洋区域（西印度洋、热带西南太平洋以及东南波利尼西亚）采集的356个珊瑚群体样本，利用全基因组单核苷酸多态性（SNPs）开展系统发育推断、聚类分析及物种界定方法研究，以解析杯形珊瑚属的系统发育关系，并提出基因组层面的物种假说。随后，我们将这些基因组物种假说与既往遗传学证据，以及基于形态学、生物地理学和共生关系的证据进行了对比分析。基因组学分析共提出了21个物种假说，而当前分类学仅认可其中7个物种。此外，有13个物种假说得到了所有分析方法的强力支持：这要么证实了它们当前的物种分类地位，要么表明存在亟待正式描述的新物种。其余部分基因组物种假说得到了生物地理学或共生关系证据的支持，但仍需开展额外研究方能明确其物种分类地位。综合来看，本研究结果支持以下四项结论：（1）大尺度形态学（即整体群体与分枝形态）已不再适用于该类群分类，但微尺度形态学（即珊瑚杯结构）在细化杯形珊瑚属的物种界限时仍具应用价值；（2）在开展物种研究前需先进行分子鉴定，因为野外仅凭形态特征难以准确识别物种；（3）线粒体开放阅读框（mtORF，部分场景下需结合其他标记）可作为多数物种的诊断标记；（4）杯形珊瑚属亟需开展分类学修订。本研究结果为评估多标准方法在解析杯形珊瑚属物种界限中的应用价值提供了新视角，最终也将为该石珊瑚类群的物种保护提供有益参考。