Universal target‐enrichment baits for anthozoan (Cnidaria) phylogenomics: New approaches to long‐standing problems

Abstract

Anthozoans (e.g., corals, anemones) are an ecologically important and diverse group of marine metazoans that occur from shallow to deep waters worldwide. However, our understanding of the evolutionary relationships among the ~7,500 species within this class is hindered by the lack of phylogenetically informative markers that can be reliably sequenced across a diversity of taxa. We designed and tested 16,306 RNA baits to capture 720 ultraconserved element loci and 1,071 exon loci. Library preparation and target enrichment were performed on 33 taxa from all orders within the class Anthozoa. Following Illumina sequencing and Trinity assembly, we recovered 1,774 of 1,791 targeted loci. The mean number of loci recovered from each species was 638 ± 222, with more loci recovered from octocorals (783 ± 138 loci) than hexacorals (475 ± 187 loci). Parsimony informative sites ranged from 26 to 49% for alignments at differing hierarchical taxonomic levels (e.g., Anthozoa, Octocorallia, Hexacorallia). The per cent of variable sites within each of three genera (Acropora, Alcyonium, and Sinularia) for which multiple species were sequenced ranged from 4.7% to 30%. Maximum-likelihood analyses recovered highly resolved trees with topologies matching those supported by other studies, including the monophyly of the order Scleractinia. Our results demonstrate the utility of this target-enrichment approach to resolve phylogenetic relationships from relatively old to recent divergences. Redesigning the baits with improved affinities to capture loci within each subclass will provide a valuable toolset to address systematic questions, further our understanding of the timing of diversifications and help resolve long-standing controversial relationships in the class Anthozoa.

The Holo-Transcriptome of the Zoantharian Protopalythoa variabilis (Cnidaria: Anthozoa): A Plentiful Source of Enzymes for Potential Application in Green Chemistry, Industrial and Pharmaceutical Biotechnology

“…This species has been mentioned by some authors as Palythoa variabilis , in reason of a proposed synonymy for the genera Palythoa and Protopalythoa [ 75 ]. However, the issue of distinctive genera is not completely solved yet (see, for example, [ 76 ]), despite new molecular phylogenetic approach, based on the universal target-enrichment baits, has been recently developed to help resolve long-standing controversial relationships in the class Anthozoa [ 77 ]. Thus, until an extensive revision of the group is not definitively resolved with morphological and molecular data precisely combined, with inclusion of species of both genera, the binomial nomenclature Protopalythoa variabilis is used herein, as for decades.…”

Sequence capture phylogenomics of historical ethanol‐preserved museum specimens: Unlocking the rest of the vault

“…For the older museum specimens (>30 years) only four to seven individual samples were included in a hybridization pool depending on the amount of extracted DNA. Adjusting the number of samples in a hybridization pool is effectively similar to adjusting the concentration of probes in the hybridization reaction (Quattrini et al, 2018). Samples included in this study were sequenced over multiple plates and sequencing experiments.…”

Biochemical characterization of diverse deep-sea anthozoan bioluminescence systems

“…For example, Anthomastus ritteri has been reclassified as Heteropolypus ritteri (Molodtsova 2013), and it remains unclear which species of the parent family might be bioluminescent. Recent phylogenetic analyses suggest polyphyly of Alcyonacea (Quattrini et al 2018), but we still do not have a reliable phylogeny including a rich enough set of luminous species to fully evaluate the origins of bioluminescence in this lineage. Hence, in this study, we follow the classification presently accepted by WoRMS (marinespecies.org).…”