Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore; Yale-NUS College, National University of Singapore, Singapore 138527, Singapore.
Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore.
Mol Phylogenet Evol. 2023 Sep;186:107867. doi: 10.1016/j.ympev.2023.107867. Epub 2023 Jun 20.
A well-supported evolutionary tree representing most major lineages of scleractinian corals is in sight with the development and application of phylogenomic approaches. Specifically, hybrid-capture techniques are shedding light on the evolution and systematics of corals. Here, we reconstructed a broad phylogeny of Scleractinia to test previous phylogenetic hypotheses inferred from a few molecular markers, in particular, the relationships among major scleractinian families and genera, and to identify clades that require further research. We analysed 449 nuclear loci from 422 corals, comprising 266 species spanning 26 families, combining data across whole genomes, transcriptomes, hybrid capture and low-coverage sequencing to reconstruct the largest phylogenomic tree of scleractinians to date. Due to the large number of loci and data completeness (less than 38% missing data), node supports were high across shallow and deep nodes with incongruences observed in only a few shallow nodes. The "Robust" and "Complex" clades were recovered unequivocally, and our analyses confirmed that Micrabaciidae Vaughan, 1905 is sister to the "Robust" clade, transforming our understanding of the "Basal" clade. Several families remain polyphyletic in our phylogeny, including Deltocyathiidae Kitahara, Cairns, Stolarski & Miller, 2012, Caryophylliidae Dana, 1846, and Coscinaraeidae Benzoni, Arrigoni, Stefani & Stolarski, 2012, and we hereby formally proposed the family name Pachyseridae Benzoni & Hoeksema to accommodate Pachyseris Milne Edwards & Haime, 1849, which is phylogenetically distinct from Agariciidae Gray, 1847. Results also revealed species misidentifications and inconsistencies within morphologically complex clades, such as Acropora Oken, 1815 and Platygyra Ehrenberg, 1834, underscoring the need for reference skeletal material and topotypes, as well as the importance of detailed taxonomic work. The approach and findings here provide much promise for further stabilising the topology of the scleractinian tree of life and advancing our understanding of coral evolution.
随着系统发育基因组学方法的发展和应用，能够代表石珊瑚主要谱系的可靠进化树已经在望。具体来说，杂交捕获技术正在揭示珊瑚的进化和系统发育。在这里，我们重建了石珊瑚的广泛系统发育，以检验以前从少数分子标记推断出的系统发育假设，特别是主要石珊瑚科和属之间的关系，并确定需要进一步研究的进化枝。我们分析了来自 422 种珊瑚的 449 个核基因座，其中包括 266 个种，跨越 26 个科，综合了整个基因组、转录组、杂交捕获和低覆盖度测序的数据，以构建迄今为止最大的石珊瑚系统发育树。由于基因座数量多且数据完整性高（缺失数据不到 38%），在浅部和深部节点上的节点支持度都很高，只有少数浅部节点存在不一致。“Robust”和“Complex”进化枝被明确地重建，我们的分析还证实了 Micrabaciidae Vaughan, 1905 与“Robust”进化枝是姐妹关系，这改变了我们对“Basal”进化枝的理解。在我们的系统发育中，有几个科仍然是多系的，包括 Deltocyathiidae Kitahara, Cairns, Stolarski & Miller, 2012、 Caryophylliidae Dana, 1846 和 Coscinaraeidae Benzoni, Arrigoni, Stefani & Stolarski, 2012，我们在此正式提出 Pachyseridae 科来容纳 Pachyseris Milne Edwards & Haime, 1849，它在系统发育上与 Agariciidae Gray, 1847 不同。研究结果还揭示了物种鉴定错误和形态复杂进化枝内的不一致性，例如 Acropora Oken, 1815 和 Platygyra Ehrenberg, 1834，这强调了需要参考骨骼材料和模式标本，以及详细的分类工作的重要性。这里的方法和发现为进一步稳定石珊瑚生命树的拓扑结构和推进我们对珊瑚进化的理解提供了很大的希望。
