Application of phylogenomic tools to unravel anthozoan evolution

Quek, Zheng Bin Randolph; Huang, Danwei

doi:10.1007/s00338-021-02072-3

Cited by 18 publications

(12 citation statements)

References 287 publications

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“…There is now a wealth of sequence data available from cnidarians ( Alama-Bermejo and Holzer 2021 ; Quek and Huang 2022 ; Santander et al 2022 ), but we chose to limit our main comparisons of voltage-gated K + channels to eight species with high-quality genomes and transcriptomes because estimates of ancestral channel sets depend on having a relatively complete picture of the channel genes present in each species. The species we chose are listed along with a consensus phylogeny of Cnidaria in figure 2 and represent key evolutionary nodes that enable several important comparisons.…”

Section: Resultsmentioning

confidence: 99%

Genome-Scale Analysis Reveals Extensive Diversification of Voltage-Gated K+ Channels in Stem Cnidarians

Lara

Simonson

Ryan

et al. 2023

Genome Biology and Evolution

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Ion channels are highly diverse in the cnidarian model organism Nematostella vectensis (Anthozoa), but little is known about the evolutionary origins of this channel diversity and its conservation across Cnidaria. Here we examined the evolution of voltage-gated K+ channels in Cnidaria by comparing genomes and transcriptomes of diverse cnidarian species from Anthozoa and Medusozoa. We found an average of over 40 voltage-gated K+ channel genes per species, and phylogenetic reconstruction of the Kv, KCNQ and EAG gene families identified 28 voltage-gated K+ channels present in the last common ancestor of Anthozoa and Medusozoa (23 Kv, 1 KCNQ and 4 EAG). Thus, much of the diversification of these channels took place in the stem cnidarian lineage prior to the emergence of modern cnidarian classes. In contrast, the stem bilaterian lineage, from which humans evolved, contained no more than 9 voltage-gated K+ channels. These results hint at a complexity to electrical signaling in all cnidarians that contrasts with the perceived anatomical simplicity of their neuromuscular systems. These data provide a foundation from which the function of these cnidarian channels can be investigated, which will undoubtedly provide important insights into cnidarian physiology.

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Section: Resultsmentioning

confidence: 99%

Genome-Scale Analysis Reveals Extensive Diversification of Voltage-Gated K+ Channels in Stem Cnidarians

Lara

Simonson

Ryan

et al. 2023

Genome Biology and Evolution

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“…Finally, cryptic diversity that went undetected in previous molecular and morphological studies validates the usefulness of phylotranscriptomics for resolving the evolutionary relationships of octocorals, and more generally of diverse lineages of marine taxa, including at shallow phylogenetic scales as examined here. Although phylotranscriptomics can be a reliable (and in some cases cheaper) alternative to several emerging approaches based on genome sequence data (e.g., Herrera & Shank, 2016 ; Quattrini et al, 2017 ; see discussion in Cheon et al, 2020 ), it remains largely underutilized in anthozoans (reviewed in Quek & Huang, 2022 ).…”

Section: Discussionmentioning

confidence: 99%

Not out of the Mediterranean: Atlantic populations of the gorgonian Paramuricea clavata are a separate sister species under further lineage diversification

Coelho

Pearson

Boavida

et al. 2023

Ecology and Evolution

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The accurate delimitation of species boundaries in nonbilaterian marine taxa is notoriously difficult, with consequences for many studies in ecology and evolution. Anthozoans are a diverse group of key structural organisms worldwide, but the lack of reliable morphological characters and informative genetic markers hampers our ability to understand species diversification. We investigated population differentiation and species limits in Atlantic (Iberian Peninsula) and Mediterranean lineages of the octocoral genus Paramuricea previously identified as P. clavata . We used a diverse set of molecular markers (microsatellites, RNA‐seq derived single‐copy orthologues [SCO] and mt‐mutS [mitochondrial barcode]) at 49 locations. Clear segregation of Atlantic and Mediterranean lineages was found with all markers. Species‐tree estimations based on SCO strongly supported these two clades as distinct, recently diverged sister species with incomplete lineage sorting, P. cf. grayi and P. clavata , respectively. Furthermore, a second putative (or ongoing) speciation event was detected in the Atlantic between two P. cf. grayi color morphotypes (yellow and purple) using SCO and supported by microsatellites. While segregating P. cf. grayi lineages showed considerable geographic structure, dominating circalittoral communities in southern (yellow) and western (purple) Portugal, their occurrence in sympatry at some localities suggests a degree of reproductive isolation. Overall, our results show that previous molecular and morphological studies have underestimated species diversity in Paramuricea occurring in the Iberian Peninsula, which has important implications for conservation planning. Finally, our findings validate the usefulness of phylotranscriptomics for resolving evolutionary relationships in octocorals.

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“…RAD‐seq is widely regarded as an effective method in molecular phylogenomics, and our study supports previous work showing its utility in resolving both deep and shallow phylogenetic relationships (Cariou et al, 2013; Hou et al, 2016; Eaton et al, 2017; Leaché & Oaks, 2017; Lecaudey et al, 2018; MacGuigan & Near, 2019; Du et al, 2020; Mu et al, 2020). One highly discussed shortcoming of RAD‐seq for deep phylogenetic resolution is that mutations in restriction sites within lineages under study lead to missing data, and the probability of mutation increases with time and evolutionary distance (Quek & Huang, 2021). Notably, the effects of missing data, or ADO, in RAD‐seq may be limited for relatively closely related taxa (e.g., with divergences up to ca.…”

Section: Discussionmentioning

confidence: 99%

Phylogenomics and biogeography of Torreya (Taxaceae)—Integrating data from three organelle genomes, morphology, and fossils and a practical method for reducing missing data from RAD‐seq

Zhou

Harris

Xiang

2022

J of Systematics Evolution

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Restriction site-associated DNA sequencing (RAD-seq) enables obtaining thousands of genetic markers for phylogenomic studies. However, RAD-seq data are subject to allele dropout (ADO) due to polymorphisms at enzyme cutting sites. We developed a new pipeline, RAD-seq Allele Dropout Remedy in our study of the gymnosperm genus, Torreya, to mitigate ADO in outgroups by recovering missing loci from previously published transcriptomes. By using RADADOR to supplement Rad-seq data in combination with plastome and mitochondrial gene sequences, morphology, and fossil records, we reconstructed the phylogenetic and biogeographic histories of the genus and tested hypotheses on anomalies of biodiversity of the eastern Asian-North American floristic disjunction. Our results showed that our pipeline recovered many loci missing from the outgroup, and the improved data yielded a more robust phylogeny for Torreya. Using the fossilized birth-death model and divergence-extinction-cladogenesis method, we resolved a detailed biogeographic history of Torreya that suggested a Jurassic origin spanning Laurasia and differential speciation and extinction among continents accounting for modern diversity, which is biased toward eastern Asia (EA). The biogeographic results also supported a vicariance origin of modern Torreya from a widespread ancestor in EA and North America (NA) in the mid-Eocene, and cross Beringian exchange in the early Paleogene before the vicariant isolation, in contrast to the "out of NA" pattern common to gymnosperms and to the "out of EA" hypothesis previously proposed for the genus. Furthermore, we observed phylogenetic discordance between the nuclear and plastid phylogenies for Torreya jackii, suggesting differential lineage sorting of plastid genomes among species of Torreya or plastid genome capture in T. jackii.

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Application of phylogenomic tools to unravel anthozoan evolution

Cited by 18 publications

References 287 publications

Genome-Scale Analysis Reveals Extensive Diversification of Voltage-Gated K+ Channels in Stem Cnidarians

Genome-Scale Analysis Reveals Extensive Diversification of Voltage-Gated K+ Channels in Stem Cnidarians

Not out of the Mediterranean: Atlantic populations of the gorgonian Paramuricea clavata are a separate sister species under further lineage diversification

Phylogenomics and biogeography of Torreya (Taxaceae)—Integrating data from three organelle genomes, morphology, and fossils and a practical method for reducing missing data from RAD‐seq

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