Towards a rigorous species delimitation framework for scleractinian corals based on RAD sequencing: the case study of Leptastrea from the Indo-Pacific

Abstract

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 Please note that this is an author-produced PDF of an article accepted for publication following peer review. The definitive publisher-authenticated version is available on the publisher Web site.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.

High regional and intra-generic variation in susceptibility to mass bleaching in Indo-Pacific coral species

“…This result, and indeed our general findings, are consistent with recent genetics studies that indicate wide divergence within many species of Indian and Pacific Ocean reef corals, fishes and other reef fauna (summarized Richards et al, 2016). Several cryptic regional endemic species or subspecies have also been resolved within species previously considered pan Indo-Pacific (Richards et al, 2016;Arrigoni et al, 2020), suggesting regional divergence of reef faunas may be greater than currently recognised. Such cryptic regional endemics would account for some the regional variation documented here.…”

Morphological stasis masks ecologically divergent coral species on tropical reefs

“…One lineage represents the geographically separated Israel population (Gulf of Aqaba) and indicates the existence of a distinct species in the Red Sea region, corroborating a pattern observed in other corals [e.g. Stylophora pistillata ; (24, 40–41)]. The other three lineages occurred sympatrically on all of the sampled reefs in Australasia, hereafter arbitrarily referred to as “green”, “blue” and “red” lineage, with the assembled reference genome representing a genotype belonging to the “green” lineage.…”

Evolution and biogeography of the Zanclea-Scleractinia symbiosis

“…Scleractinian corals were identified at the genus or species level according to Veron et al (2016) and the most recent taxonomic classification (e.g. Wallace et al 2007;Benzoni et al 2010Benzoni et al , 2012Gittenberger et al 2011;Arrigoni et al 2014a, b;Huang et al 2014;Terraneo et al 2017Terraneo et al , 2019Arrigoni et al 2020). Zanclea polyps were identified at the genus or species level according to Boero et al (2000), Pantos and Bythell (2010), Hirose and Hirose (2011), and Montano et al (2015a).…”