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Documentation of biodiversity and its geographical distribution is necessary to understand the processes and drivers of evolutionary diversification as well as to guide conservation and management initiatives. Among the most emblematic patterns of biodiversity in the world’s oceans is the Coral Triangle (Indo-Australian Archipelago), widely recognized to be the center of species richness for a variety of marine life forms. The distribution of biodiversity remains incompletely documented, however, for a majority of reef-associated invertebrate taxa, including the zooxanthellate soft corals (Octocorallia) that dominate hard substrate on many Indo-Pacific reefs. We used a genetic approach to document the diversity of Indo-Pacific soft corals, sequencing two single-locus barcoding markers for > 4400 soft coral specimens and assigning individuals to molecular operational taxonomic units as proxies of species. We document two centers of species richness for zooxanthellate soft corals, one in the Indo-Australian Archipelago and a second, equally diverse center in the Western Indian Ocean. Centers of endemicity for soft corals are coincident with these centers of species richness, although the peripheral Red Sea and Hawaii also support high proportions of endemic taxa. The patterns documented here suggest that biogeographic distributions of soft coral families may be driven in part by larval dispersal potential: taxa with benthic larvae are absent from most oceanic islands of the central Pacific and are represented by higher proportions of endemic taxa in other geographic regions. Our findings demonstrate the distinct biogeographic patterns among reef taxa and underscore the need to document and analyze species distributions of more reef-associated invertebrate groups to derive a complete picture of reef biogeography. 

Abstract The mutualism between clownfishes (or anemonefishes) and their giant host sea anemones are among the most immediately recognizable animal interactions on the planet and have attracted a great deal of popular and scientific attention [1-5]. However, our evolutionary understanding of this iconic symbiosis comes almost entirely from studies on clownfishes— a charismatic group of 28 described species in the genusAmphiprion[2]. Adaptation to venomous sea anemones (Anthozoa: Actiniaria) provided clownfishes with novel habitat space, ultimately triggering the adaptive radiation of the group [2]. Clownfishes diverged from their free-living ancestors 25-30 MYA with their adaptive radiation to sea anemones dating to 13.2 MYA [2, 3]. Far from being mere habitat space, the host sea anemones also receive substantial benefits from hosting clownfishes, making the mutualistic and co-dependent nature of the symbiosis well established [4, 5]. Yet the evolutionary consequences of mutualism with clownfishes have remained a mystery from the host perspective. Here we use bait-capture sequencing to fully resolve the evolutionary relationships among the 10 nominal species of clownfish-hosting sea anemones for the first time (Figure 1). Using time-calibrated divergence dating analyses we calculate divergence times of less than 25 MYA for each host species, with 9 of 10 host species having divergence times within the last 13 MYA (Figure 1). The clownfish-hosting sea anemones thus diversified coincidently with clownfishes, potentially facilitating the clownfish adaptive radiation, and providing the first strong evidence for co-evolutionary patterns in this iconic partnership. 

The octocoral genusChrysogorgia(Duchassaing and Michelotti, 1864) contains 81 nominal species that are ecologically important components of benthic communities. Taxonomic examination of a large set of samples revealed many provisional new species, exhibiting a wide range of morphological variation. We established nine, distinct morphological groups ofChrysogorgia s.l.that were hypothesized to represent distinct genera. Here, we applied a recently developed universal target enrichment bait method for octocoral exons and ultraconserved elements (UCEs) on 96 specimens varying in morphology, collection ages and DNA quality and quantity to determine whether there was genetic support for these morphologically defined groups. Following Illumina sequencing and SPAdes assembly we recovered 1,682 of 1,700 targeted exon loci and 1,333 of 1,340 targeted UCE loci. Locus recovery per sample was highly variable and significantly correlated with time since specimen collection (2–60 years) and DNA quantity and quality. Phylogenetically informative sites in UCE and exon loci were ∼35% for 50% and 75% taxon-occupancy matrices. Maximum likelihood analyses recovered highly resolved trees with topologies supporting the recognition of 11 candidate genera, corresponding with morphological groups assigneda priori, nine of which are novel. Our results also demonstrate that this target-enrichment approach can be successfully applied to degraded museum specimens of up to 60 years old. This study shows that an integrative approach consisting of molecular and morphological methods will be essential to a proper revision ofChrysogorgiataxonomy and to understand regional diversity of these ecologically important corals. 

Abstract Numerous genomic methods developed over the past two decades have enabled the discovery and extraction of orthologous loci to help resolve phylogenetic relationships across various taxa and scales. Genome skimming (or low‐coverage genome sequencing) is a promising method to not only extract high‐copy loci but also 100s to 1000s of phylogenetically informative nuclear loci (e.g., ultraconserved elements [UCEs] and exons) from contemporary and museum samples. The subphylum Anthozoa, including important ecosystem engineers (e.g., stony corals, black corals, anemones, and octocorals) in the marine environment, is in critical need of phylogenetic resolution and thus might benefit from a genome‐skimming approach. We conducted genome skimming on 242 anthozoan corals collected from 1886 to 2022. Using existing target‐capture baitsets, we bioinformatically obtained UCEs and exons from the genome‐skimming data and incorporated them with data from previously published target‐capture studies. The mean number of UCE and exon loci extracted from the genome skimming data was 1837 ± 662 SD for octocorals and 1379 ± 476 SD loci for hexacorals. Phylogenetic relationships were well resolved within each class. A mean of 1422 ± 720 loci was obtained from the historical specimens, with 1253 loci recovered from the oldest specimen collected in 1886. We also obtained partial to whole mitogenomes and nuclear rRNA genes from >95% of samples. Bioinformatically pulling UCEs, exons, mitochondrial genomes, and nuclear rRNA genes from genome skimming data is a viable and low‐cost option for phylogenetic studies. This approach can be used to review and support taxonomic revisions and reconstruct evolutionary histories, including historical museum and type specimens.