Accurate delimitation of species and their relationships is a fundamental issue in evolutionary biology and taxonomy and provides essential implications for conservation management. Scleractinian corals are difficult to identify because of their ecophenotypic and geographic variation and their morphological plasticity. Furthermore, phylogenies based on traditional loci are often unresolved at the species level because of uninformative loci. Here, we attempted to resolve these issues and proposed a consistent species definition method for corals by applying the genome-wide technique Restriction-site Associated DNA sequencing (RADseq) to investigate phylogenetic relationships and species delimitation within the genus Leptastrea. We collected 77 colonies from nine localities of the Indo-Pacific and subjected them to genomic analyses. Based on de novo clustering, we obtained 44,162 SNPs (3701 loci) from the holobiont dataset and 62,728 SNPs (9573 loci) from the reads that map to coral transcriptome to reconstruct a robust phylogenetic hypothesis of the genus. Moreover, nearly complete mitochondrial genomes and ribosomal DNA arrays were retrieved by reference mapping. We combined concatenation-based phylogenetic analyses with coalescent-based species tree and species delimitation methods. Phylogenies suggest the presence of six distinct species, three corresponding to known taxa, namely Leptastrea bottae, Leptastrea inaequalis, Leptastrea transversa, one characterized by a remarkable skeletal variability encompassing the typical morphologies of Leptastrea purpurea and Leptastrea pruinosa, and two distinct and currently undescribed species. Therefore, based on the combination of genomic, morphological, morphometric, and distributional data, we herein described Leptastrea gibbosa sp. n. from the Pacific Ocean and Leptastrea magaloni sp. n. from the southwestern Indian Ocean and formally considered L. pruinosa as a junior synonym of L. purpurea. Notably, mitogenomes and rDNA yielded a concordant yet less resolved phylogeny reconstruction compared to the ones based on SNPs. This aspect demonstrates the strength and utility of RADseq technology for disentangling species boundaries in closely related species and in a challenging group such as scleractinian corals.

中文翻译：

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基于 RAD 测序的石珊瑚的严格物种定界框架：来自印度-太平洋的 Leptastrea 的案例研究

物种及其关系的准确划定是进化生物学和分类学中的一个基本问题，对保护管理具有重要意义。由于它们的生态表型和地理变异以及它们的形态可塑性，石珊瑚很难被识别。此外，基于传统位点的系统发育通常由于无信息位点而无法在物种水平上得到解决。在这里，我们试图解决这些问题，并通过应用全基因组技术限制位点相关 DNA 测序 (RADseq) 来研究 Leptastrea 属内的系统发育关系和物种定界，提出了一种一致的珊瑚物种定义方法。我们从印太地区的 9 个地区收集了 77 个菌落，并对它们进行了基因组分析。基于从头聚类，我们从全息生物数据集中获得了 44,162 个 SNP（3701 个基因座），从映射到珊瑚转录组的读数中获得了 62,728 个 SNP（9573 个基因座），以重建该属的强大系统发育假设。此外，通过参考映射检索了几乎完整的线粒体基因组和核糖体 DNA 阵列。我们将基于串联的系统发育分析与基于聚结的物种树和物种定界方法相结合。系统发育表明存在六个不同的物种，三个对应于已知的分类群，即 Leptastrea bottae、Leptastrea inaequalis、Leptastrea transversa，一个以显着的骨骼变异为特征，包括 Leptastrea purpurea 和 Leptastrea pruinosa 的典型形态，以及两个不同且目前未描述的物种. 所以，基于基因组、形态学、形态计量学和分布数据的组合，我们在此描述了 Leptastrea gibbosa sp。n. 来自太平洋和 Leptastrea magaloni sp。n. 来自西南印度洋，并正式将 L. pruinosa 视为 L. purpurea 的初级同义词。值得注意的是，与基于 SNP 的系统发育相比，有丝分裂基因组和 rDNA 产生了一致但解析度较低的系统发育重建。这方面证明了 RADseq 技术在解开密切相关物种和具有挑战性的群体（如石珊瑚）中的物种边界方面的强度和实用性。pruinosa 作为 L. purpurea 的初级同义词。值得注意的是，与基于 SNP 的系统发育相比，有丝分裂基因组和 rDNA 产生了一致但解析度较低的系统发育重建。这方面证明了 RADseq 技术在解开密切相关物种和具有挑战性的群体（如石珊瑚）中的物种边界方面的强度和实用性。pruinosa 作为 L. purpurea 的初级同义词。值得注意的是，与基于 SNP 的系统发育相比，有丝分裂基因组和 rDNA 产生了一致但解析度较低的系统发育重建。这方面证明了 RADseq 技术在解开密切相关物种和具有挑战性的群体（如石珊瑚）中的物种边界方面的强度和实用性。