Phylogenomics of Porites from the Arabian Peninsula

The advent of high throughput sequencing technologies provides an opportunity to resolve phylogenetic relationships among closely related species. By incorporating hundreds to thousands of unlinked loci and single nucleotide polymorphisms (SNPs), phylogenomic analyses have a far greater potential to resolve species boundaries than approaches that rely on only a few markers. Scleractinian taxa have proved challenging to identify using traditional morphological approaches and many groups lack an adequate set of molecular markers to investigate their phylogenies. Here, we examine the potential of Restriction-site Associated DNA sequencing (RADseq) to investigate phylogenetic relationships and species limits within the coral genus Porites. A total of 137 colonies were collected from 16 localities in the seas surrounding the Arabian Peninsula and ascribed to 13 nominal and one undescribed species based on their morphology. Reference mapping was used to retrieve and compare nearly complete mitochondrial genomes, ribosomal DNA, and histone loci. De novo assembly and reference mapping to the P. lobata coral transcriptome were used to obtain loci and SNPs from the holobiont and coral datasets, respectively. A suite of species discovery methods (phylogenetic, ordination, and clustering analyses) and species delimitation approaches (coalescent-based, species tree, and Bayesian Factor delimitation) suggested the presence of eight molecular lineages, one of which included six morphospecies. The time-calibrated phylogeny suggested that this species complex originated recently, 500 Ka, while the Arabian endemic lineages diverged during the Miocene, a value consistent with the hypothesis of a coral centre of origin in the northern Indian Ocean during this period. Our phylogenomic approach provided a fully supported phylogeny of Porites from the Arabian Peninsula, suggesting the power of RADseq data to solve the species delineation problem in this speciose coral genus.

TERRANEO Tullia Isotta;  BENZONI Francesca;  ARRIGONI Roberto;  BAIRD Andrew;  MARIAPPAN Kiruthiga;  FORSMAN Zac;  WOOSTER Michael;  BOUWMEESTER Jessica;  MARSHELL Alyssa;  BERUMEN Michael; 

2022-08-24

ACADEMIC PRESS INC ELSEVIER SCIENCE

JRC118490

1055-7903 (online),   

https://www.sciencedirect.com/science/article/pii/S1055790321001068,    https://publications.jrc.ec.europa.eu/repository/handle/JRC118490,   

10.1016/j.ympev.2021.107173 (online),