Phylogenomics of Porites from the Arabian Peninsula

Terraneo, Tullia Isotta; Benzoni, Francesca; Arrigoni, Roberto; Baird, Andrew H.; Mariappan, Kadarkaraisamy; Forsman, Zac H.; Wooster, Michael K.; Bouwmeester, Jessica; Marshell, Alyssa; Berumen, Michael L.

doi:10.1016/j.ympev.2021.107173

Cited by 21 publications

(42 citation statements)

References 104 publications

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“…RADseq approaches have several advantages, including relatively low sequencing costs facilitating the generation of population-level data sets, and applicability to species without prior genomic knowledge. Hence, our data confirm RADseq as a promising as tool for accurate inference of evolutionary history and species limits in poorly known taxa, as observed in numerous recent studies (e.g., Razkin et al 2016;Rodríguez et al 2017;Paetzold et al 2019;Rancilhac et al 2019;Appelhans et al 2020;Arrigoni et al 2020;Dufresnes et al 2020aDufresnes et al , 2020bTerraneo et al 2021).…”

Section: Discussionsupporting

confidence: 89%

Exploring the impact of read clustering thresholds on RADseq-based systematics: an empirical example from European amphibians

Rancilhac

Sylvestre

Hutter

et al. 2023

Preprint

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Restriction site-Associated DNA sequencing (RADseq) has great potential for genome-wide systematics studies of non-model organisms. However, accurately assembling RADseq reads into orthologous loci remains a major challenge in the absence of a reference genome. Traditional assembly pipelines cluster putative orthologous sequences based on a user-defined clustering threshold. Because improper clustering of orthologs is expected to affect results in downstream analyses, it is crucial to design pipelines for empirically optimizing the clustering threshold. While this issue has been largely discussed from a population genomics perspective, it remains understudied in the context of phylogenomics and coalescent species delimitation. To address this issue, we generated RADseq assemblies of representatives of the amphibian genera Discoglossus, Rana, Lissotriton and Triturus using a wide range of clustering thresholds. Particularly, we studied the effects of the intra-sample Clustering Threshold (iCT) and between-sample Clustering Threshold (bCT) separately, as both are expected to differ in multi-species data sets. The obtained assemblies were used for downstream inference of concatenation-based phylogenies, and multi-species coalescent species trees and species delimitation. The results were evaluated in the light of a reference genome-wide phylogeny calculated from newly generated Hybrid-Enrichment markers, as well as extensive background knowledge on the species' systematics. Overall, our analyses show that the inferred topologies and their resolution are resilient to changes of the iCT and bCT, regardless of the analytical method employed. Except for some extreme clustering thresholds, all assemblies yielded identical, well-supported inter-species relationships that were mostly congruent with those inferred from the reference Hybrid-Enrichment data set. Similarly, coalescent species delimitation was consistent among similarity threshold values. However, we identified a strong effect of the bCT on the branch lengths of concatenation and species trees, with higher bCTs yielding trees with shorter branches, which might be a pitfall for downstream inferences of evolutionary rates. Our results suggest that the choice of assembly parameters for RADseq data in the context of shallow phylogenomics might be less challenging than previously thought. Finally, we propose a pipeline for empirical optimization of the iCT and bCT, implemented in optiRADCT, a series of scripts readily usable for future RADseq studies.

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Section: Discussionsupporting

confidence: 89%

Exploring the impact of read clustering thresholds on RADseq-based systematics: an empirical example from European amphibians

Rancilhac

Sylvestre

Hutter

et al. 2023

Preprint

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“…Leveraging host sequences in the ITS2 metabarcoding dataset, we were able to expand lineage assignment beyond those colonies that were sequenced with 2b-RAD (n = 67). As expected, all Porites ITS2 sequences belonged to one of the 8 previously described Porites lineages (clade V or the Porites lobata/lutea clade ( 49 ); Fig S4). However, examining colonies that were sequenced using both ITS2 and 2b-RAD (n = 64 with successful host sequences), we found that ITS2 sequences were consistently dissimilar across cryptic Porites lineages.…”

Section: Resultssupporting

confidence: 84%

“…We leveraged this extreme climatic event as a natural experiment to directly test whether coral bleaching susceptibility or survivorship could be predicted by the genetic structure of the affected colonies and/or their associated algal symbionts, and further assessed changes in the relative abundance of host and symbiont genotypes by comparing a larger sampling of colonies from before, during and after the heatwave. Recent molecular studies have determined that the genus Porites comprises at least eight clades, some characterized by complex genetic structure ( 41, 49 ), possibly reflecting cryptic or pseudo-cryptic lineages within each clade. Our study focused on one of these clades (Clade V from ref 49 ; also known as the Porites lobata/lutea clade )) facilitating a deeper look into the functional differences between finer-scale cryptic lineages than has previously been achieved in this group.…”

Section: Introductionmentioning

confidence: 99%

Marine heatwaves threaten cryptic coral diversity and erode associations amongst coevolving partners

Starko

Fifer

Claar

et al. 2023

Preprint

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Climate change-amplified heatwaves are known to drive extensive mortality in marine foundation species. However, a paucity of longitudinal genomic datasets has impeded understanding of how these rapid selection events alter species genetic structure. Impacts of these events may be exacerbated in species with obligate symbioses, where the genetics of multiple co-evolving species may be affected. Here, we tracked the symbiotic associations and fate of reef-building corals for six years through a prolonged heatwave. Coral genetics strongly predicted survival of the common coral Porites through the event, with strong differential survival (15 to 64%) apparent across morphologically identical -but genetically distinct- lineages. The event also disrupted strong associations between coral lineages and their symbiotic partners, homogenizing symbiotic assemblages across lineages and reducing the specificity of coral-algal symbioses. These results highlight that marine heatwaves threaten cryptic genetic diversity of foundation species and have the potential to decouple tight relationships between co-evolving host-symbiont pairs.

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“…While in this study we focused only on molecular and morphological data, Luzon et al (2017Luzon et al ( , 2018 showed that additional source of information useful for exploring the systematics of Euphylliidae may be represented by reproductive data. Luzon et al (2017Luzon et al ( , 2018 found that the distinction between Euphyllia and Fimbriaphyllia was also supported by their sexuality and reproductive mode since E. glabrescens is a hermaphroditic brooder while species of Fimbriaphyllia are gonochoric broadcast spawners (Baird et al, 2009(Baird et al, , 2021. In our study, we found a sister relationship between Gyrosmilia interrupta, which is known to be a gonochoric spawner (Bouwmeester al., 2016), and Ctenella chagius.…”

Section: Discussionsupporting

confidence: 70%

Phylogenetics and taxonomy of the scleractinian coral family Euphylliidae

et al. 2023

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The family Euphylliidae consists of reef-building zooxanthellate scleractinian corals distributed across the Indo-Pacific. Seven extant genera comprising a total of 22 valid species are currently recognised. Recent studies have re-organised the taxonomy of the family at the genus level based on molecular and morphological data, including a comprehensive revision of Euphyllia and the resurrection of Fimbriaphyllia. Here, three mitochondrial loci (coi, 12S rRNA, and 16S rRNA) were sequenced and morphological examinations were conducted at three scales (macro/micromorphology and microstructure of the skeleton, and polyp morphology) to study the phylogeny and taxonomy of Euphylliidae. We analysed a total of 11 valid species collected from seven Indo-Pacific localities. The monotypic genus Coeloseris, currently in Agariciidae, was also investigated since previous molecular data suggested a close relationship with the Euphylliidae. Molecular and morphological phylogenetic trees were broadly concordant in the definition of genus-level clades. All analysed genera, i.e., Ctenella, Euphyllia, Fimbriaphyllia, Galaxea, and Gyrosmilia, were reciprocally monophyletic based on molecular results. Coeloseris was nested within the family and, therefore, is formally moved into Euphylliidae. Updated morphological diagnoses are provided for each investigated genus. This study further demonstrated that a phylogenetic classification of scleractinian corals can be achieved by applying a combined morpho-molecular approach. Finally, we encourage phylogenetic and taxonomic studies of the euphylliid taxa not yet analysed molecularly, such as the monotypic genera Montigyra and Simplastrea.

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Phylogenomics of Porites from the Arabian Peninsula

Cited by 21 publications

References 104 publications

Exploring the impact of read clustering thresholds on RADseq-based systematics: an empirical example from European amphibians

Exploring the impact of read clustering thresholds on RADseq-based systematics: an empirical example from European amphibians

Marine heatwaves threaten cryptic coral diversity and erode associations amongst coevolving partners

Phylogenetics and taxonomy of the scleractinian coral family Euphylliidae

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