A hybrid-capture approach to reconstruct the phylogeny of Scleractinia (Cnidaria: Hexacorallia)

Quek, Z.B. Randolph; Jain, Sudhanshi S.; Richards, Zoe T.; Arrigoni, Roberto; Benzoni, Francesca; Hoeksema, Bert W.; Carvajal, Jose I.; Wilson, Nerida G.; Baird, Andrew H.; Kitahara, Marcelo V.; Seiblitz, Isabela G. L.; Vaga, Claudia F.; Huang, Danwei

doi:10.1016/j.ympev.2023.107867

Cited by 20 publications

(3 citation statements)

References 152 publications

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“…Moreover, across Singaporean reefs, phylogenetic analyses of Porites could not resolve morphologically identified species, forming a complex that included P. australiensis, P. lobata and P. lutea (Quek et al, 2023;Quek & Huang, 2019). Further highlighting the taxonomic incongruencies among massive Porites, colonies matching the morphology of P. lutea were identified in three distinct genetic clades of Porites across the Pacific, and two in P. lobata (Forsman et al, 2009).…”

Section: Some Cryptic Lineages May Represent Widespread Speciesmentioning

confidence: 98%

Distinct modes of holobiont specialization among cryptic coral lineages

Grupstra,

Meyer-Kaiser,

Bennett

et al. 2024

Preprint

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As ocean warming threatens reefs worldwide, identifying corals with adaptations to higher temperatures is critical for conservation. Genetically distinct but morphologically similar (i.e.,cryptic) coral populations can be specialized to extreme habitats and thrive under stressful conditions. These corals often associate with locally beneficial microbiota (Symbiodiniaceae photobionts and bacteria), clouding interpretation of the drivers of thermal tolerance. Here, we leverage a holobiont (massivePorites) with high host-partner fidelity to investigate adaptive variation across classic (“typical” conditions) and extreme reefs characterized by higher temperatures and light attenuation. We uncovered three cryptic lineages that exhibit limited micro-morphological variation; one lineage dominated classic reefs (L1), one had more even distributions (L2), and a third was restricted to extreme reefs (L3). Two lineages were more closely related to populations ∼4300 km away, suggesting that these lineages are widespread. All corals harboredCladocopiumC15 photobionts, but strain-level compositions differed among lineages and reef types. L1 associated with distinct photobionts and bacteria in each reef type, whereas L2 had relatively stable associations. L3 hosted unique photobiont strains, signaling high host-photobiont fidelity. Analysis of light harvesting capacity and thermal tolerance revealed key adaptive variation underpinning survival in distinct habitats. L1 had the highest light absorption efficiency and lowest thermal tolerance, suggesting it is a classic reef specialist. L3 had the lowest light absorption efficiency and the highest thermal tolerance, showing that it is an extreme reef specialist. L2 had intermediate light absorption efficiency and thermal tolerance, signaling habitat generalism, potentially explaining how it survives well in both habitat types. These findings reveal diverging holobiont strategies to cope with extreme conditions. Resolving coral lineages is key to understanding variation in thermal tolerance among coral populations; uncovering thermally-tolerant holobionts can strengthen our understanding of coral evolution and symbiosis, and support global conservation and restoration efforts.

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Section: Some Cryptic Lineages May Represent Widespread Speciesmentioning

confidence: 98%

Distinct modes of holobiont specialization among cryptic coral lineages

Grupstra,

Meyer-Kaiser,

Bennett

et al. 2024

Preprint

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“… Paragoniastrea is characterized by encrusting or massive colony morphology, plocoid, cerioid or meandroid in corallite arrangements, and developed paliform lobes. These characteristics are similar to those of Favites and Goniastrea , but Paragoniastrea is distinguished from these genera by its distinct phylogenetic affinities ( Huang et al 2014 ; Quek et al 2023 ) and several morphological differences in corallite characteristics, such as the height of calice relief, septa (number, tooth height, and spacing), and theca structure ( Huang et al 2014 ).…”

Section: Introductionmentioning

confidence: 94%

Paragoniastrea variabilis Kishi, Nomura & Fukami, sp. nov. (Cnidaria, Anthozoa, Scleractinia), a new coral species previously considered as a variant of Paragoniastrea deformis, from Japan and northern Taiwan

Kishi,

Nomura,

Nozawa

et al. 2024

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A new zooxanthellate scleractinian coral, Paragoniastrea variabilis Kishi, Nomura & Fukami, sp. nov. (Scleractinia, Merulinidae), is described from non-coral reef regions of Japan and northern Taiwan. This new species was previously recognized as a morphological variant of Paragoniastrea deformis (Veron, 1990) and can be morphologically distinguished from that species by lacking groove-and-tube structures on corallite wall joints, and by having larger calices, numerous septa, and up to three corallites in one valley. The new species also formed an independent clade from its congeners, P. australensis (Milne Edwards & Haime, 1857), P. deformis and P. russelli (Wells, 1954), in the molecular phylogeny based on the mitochondrial intergenic region and nuclear ribosomal internal transcribed spacers.

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“…Historically assigned to the family Caryophylliidae, both genera have been recovered from previous studies as sister taxa occupying an early divergent position in the vacatinan clade (Kitahara et al, 2016;Quek et al, 2023;Stolarski et al, 2011 [only Stephanocyathus included]; but see Campoy et al, 2020). Kitahara and Cairns (2021) proposed 'Clade B', which is composed of a lineage of early diverging genera-that is Aulocyathus, Conotrochus, Faustinotrochus, Lochmaeotrochus, Stephanocyathus and Vaughanella-within vacatinan scleractinians previously assigned to the family Caryophylliidae.…”

Section: Introductionmentioning

confidence: 99%

Untangling deep‐sea corals systematics: Description of a new family, Stephanocyathidae (Anthozoa, Scleractinia), through a genomic approach

Vaga,

Seiblitz,

Capel

et al. 2024

Zoologica Scripta

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Once considered the most speciose mostly azooxanthellate scleractinian group, the family Caryophylliidae is found to be highly polyphyletic based on molecular data and is undergoing a process of systematic revision. High‐throughput sequencing methods coupled with morphological analyses have facilitated revision of several scleractinian lineages, including the aforementioned family. In previous studies that relied on few mitochondrial and nuclear markers, the caryophylliid genera Stephanocyathus and Vaughanella were phylogenetically recovered in separate clades from the lineage that includes the type genus of the family, Caryophyllia, which is considered the ‘true’ Caryophylliidae. To help untangle the relationship among taxa of this family, here a new deep‐sea scleractinian family (Stephanocyathidae Vaga, Cairns & Kitahara fam. nov.) is proposed based on phylogenomic reconstructions coupled with molecular features, specifically gene order, of the complete mitochondrial genome. Evolutionary reconstructions were based on both mitochondrial and nuclear ultraconserved elements (UCEs) and exon loci data sets and confirmed the divergent position of the genera Stephanocyathus and Vaughanella. The new family shows a specific gene transposition in the mitochondrial genome, not present in the ‘true’ caryophylliid lineage, but instead already observed for the species Paraconotrochus antarcticus, recovered as sister taxon of the here proposed new family. Although its phylogenetic position is unknown, the genus Ericiocyathus is also added to the new family, based on macromorphological similarities. This study represents a step forward in our understanding of deep‐sea corals relationships and provide further information (e.g., mitochondrial gene order) that will aid in future efforts of assessing the systematic of caryophylliid lineages.

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A hybrid-capture approach to reconstruct the phylogeny of Scleractinia (Cnidaria: Hexacorallia)

Cited by 20 publications

References 152 publications

Distinct modes of holobiont specialization among cryptic coral lineages

Distinct modes of holobiont specialization among cryptic coral lineages

Paragoniastrea variabilis Kishi, Nomura & Fukami, sp. nov. (Cnidaria, Anthozoa, Scleractinia), a new coral species previously considered as a variant of Paragoniastrea deformis, from Japan and northern Taiwan

Untangling deep‐sea corals systematics: Description of a new family, Stephanocyathidae (Anthozoa, Scleractinia), through a genomic approach

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A hybrid-capture approach to reconstruct the phylogeny of Scleractinia (Cnidaria: Hexacorallia)

Cited by 20 publications

References 152 publications

Distinct modes of holobiont specialization among cryptic coral lineages

Distinct modes of holobiont specialization among cryptic coral lineages

Paragoniastrea variabilis Kishi, Nomura &amp; Fukami, sp. nov. (Cnidaria, Anthozoa, Scleractinia), a new coral species previously considered as a variant of Paragoniastrea deformis, from Japan and northern Taiwan

Untangling deep‐sea corals systematics: Description of a new family, Stephanocyathidae (Anthozoa, Scleractinia), through a genomic approach

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Paragoniastrea variabilis Kishi, Nomura & Fukami, sp. nov. (Cnidaria, Anthozoa, Scleractinia), a new coral species previously considered as a variant of Paragoniastrea deformis, from Japan and northern Taiwan