Search

• Genomic capture methods can resolve clades that lack decades of molecular marker development. • An enhanced bait setfor Hexacorallia recovers >2400 UCE/exon loci in stony corals. • Phylogenomics resolves coral relationships at deep and shallow time scales. • Well-supported clades in Acropora are not supported by macromorphological features. Targeted enrichment of genomic DNA can profoundly increase the phylogenetic resolution of clades and inform taxonomy. Here, we redesign a custom bait set previously developed for the cnidarian class Anthozoa to more efficiently target and capture ultraconserved elements (UCEs) and exonic loci within the subclass Hexacorallia. We test this enhanced bait set (targeting 2476 loci) on 99 specimens of scleractinian corals spanning both the "complex" (Acroporidae, Agariciidae) and "robust" (Fungiidae) clades. Focused sampling in the staghorn corals (genus Acropora) highlights the ability of sequence capture to inform the taxonomy of a clade previously deficient in molecular resolution. A mean of 1850 (±298) loci were captured per taxon (955 UCEs, 894 exons), and a 75% complete concatenated alignment of 96 samples included 1792 loci (991 UCE, 801 exons) and ~1.87 million base pairs. Maximum likelihood and Bayesian analyses recovered robust molecular relationships and revealed that species-level relationships within the Acropora are incongruent with traditional morphological groupings. Both UCE and exon datasets delineated six well-supported clades within Acropora. The enhanced bait set will facilitate investigations of the evolutionary history of many important groups of reef corals, particularly where previous molecular marker development has been unsuccessful. [ABSTRACT FROM AUTHOR]

[Display omitted] • Sea anemone diversity is understudied at a regional level for French Polynesia and at a local level for the island of Moorea. • Target capture of ultra-conserved elements is more reliable in lineages where conventional mitochondrial barcodes fail, such as Actiniaria. • Phylogenetic identification of sea anemone samples collected during a "BioBlitz" recovers the genera Andvakia and Aiptasiomorpha for the first time in Moorea. Sea anemones (Order Actiniaria) are a diverse group of marine invertebrates ubiquitous across marine ecosystems. Despite their wide distribution and success, a knowledge gap persists in our understanding of their diversity within tropical systems, owed to sampling bias of larger and more charismatic species overshadowing cryptic lineages. This study aims to delineate the sea anemone diversity in Mo'orea (French Polynesia) with the use of a dataset from the Mo'orea Biocode's "BioBlitz" initiative, which prioritized the sampling of more cryptic and understudied taxa. Implementing a target enrichment approach, we integrate 71 newly sequenced samples into an expansive phylogenetic framework and contextualize Mo'orea's diversity within global distribution patterns of sea anemones. Our analysis corroborates the presence of several previously documented sea anemones in French Polynesia and identifies for the first time the occurrence of members of genera Andvakia and Aiptasiomorpha. This research unveils the diverse sea anemone ecosystem in Mo'orea, spotlighting the area's ecological significance and emphasizing the need for continued exploration. Our methodology, encompassing a broad BLAST search coupled with phylogenetic analysis, proved to be a practical and effective approach for overcoming the limitations posed by the lack of comprehensive sequence data for sea anemones. We discuss the merits and limitations of current molecular methodologies and stress the importance of further research into lesser-studied marine organisms like sea anemones. Our work sets a precedent for future phylogenetic studies stemming from BioBlitz endeavors. [ABSTRACT FROM AUTHOR]

[Display omitted] • Proposition of Bathyporidae fam. nov. • Description of a new species of Madrepora. • High gene flow within Madrepora populations in the Southwestern Atlantic. Deep-water coral reefs are found worldwide and harbor biodiversity levels that are comparable to their shallow-water counterparts. However, the genetic diversity and population structure of deep-water species remain poorly explored, and historical taxonomical issues still need to be resolved. Here we used microsatellite markers as well as ultraconserved elements (UCE) and exons to shed light on the population structure, genetic diversity, and phylogenetic position of the genus Madrepora , which contains M. oculata , one of the most widespread scleractinian species. Population structure of 107 samples from three Southwestern Atlantic sedimentary basins revealed the occurrence of a cryptic species, herein named M. piresae sp. nov. (authored by Kitahara, Capel and Zilberberg), which can be found in sympatry with M. oculata. Phylogeny reconstructions based on 134 UCEs and exon regions corroborated the population genetic data, with the recovery of two well-supported groups, and reinforced the polyphyly of the family Oculinidae. In order to better accommodate the genus Madrepora , while reducing taxonomical confusion associated with the name Madreporidae, we propose the monogeneric family Bathyporidae fam. nov. (authored by Kitahara, Capel, Zilberberg and Cairns). Our findings advance the knowledge on the widespread deep-water genus Madrepora , resolve a long-standing question regarding the phylogenetic position of the genus , and highlight the need of a worldwide review of the genus. [ABSTRACT FROM AUTHOR]

[Display omitted] • For the first time, deep nodes are resolved within the Keratoisididae, a prolific deep-sea family of octocorals. • Nuclear phylogenies built with hundreds of genes conflict with previously published single and multi-gene mitochondrial phylogenies. • Some currently recognised keratoisidid groups appear polyphyletic using nuclear phylogenies built with hundreds of markers. • Sclerite microstructure and ornamentation could be future informative taxonomic features for bamboo corals. Keratoisididae is a globally distributed, and exclusively deep-sea, family of octocorals that contains species and genera that are polyphyletic. An alphanumeric system, based on a three-gene-region phylogeny, is widely used to describe the biodiversity within this family. That phylogeny identified 12 major groups although it did not have enough signal to explore the relationships among groups. Using increased phylogenomic resolution generated from Ultraconserved Elements and exons (i.e. conserved elements), we aim to resolve deeper nodes within the family and investigate the relationships among those predefined groups. In total, 109 libraries of conserved elements were generated from individuals representing both the genetic and morphological diversity of our keratoisidids. In addition, the conserved element data of 12 individuals from previous studies were included. Our taxon sampling included 11 of the 12 keratoisidid groups. We present two phylogenies, constructed from a 75% (231 loci) and 50% (1729 loci) taxon occupancy matrix respectively, using both Maximum Likelihood and Multiple Species Coalescence methods. These trees were congruent at deep nodes. As expected, S1 keratoisidids were recovered as a well-supported sister clade to the rest of the bamboo corals. S1 corals do not share the same mitochondrial gene arrangement found in other members of Keratoisididae. All other bamboo corals were recovered within two major clades. Clade I comprises individuals assigned to alphanumeric groups B1, C1, D1&D2, F1, H1, I4, and J3 while Clade II contains representatives from A1, I1, and M1. By combining genomics with already published morphological data, we provide evidence that group H1 is not monophyletic, and that the division between other groups – D1 and D2, and A1 and M1 – needs to be reconsidered. Overall, there is a lack of robust morphological markers within Keratoisididae, but subtle characters such as sclerite microstructure and ornamentation seem to be shared within groups and warrant further investigation as taxonomically diagnostic characters. [ABSTRACT FROM AUTHOR]

The development of coalescent-based and other multilocus methods for species delimitation has facilitated the identification of cryptic species complexes across the tree of life. A recent taxonomic revision of the ecologically important soft coral genus Ovabunda validated 11 morphospecies, all with type localities and overlapping geographic ranges in the Red Sea. A subsequent molecular phylogenetic analysis using mitochondrial and 28S nrDNA genes divided the genus into just two clades, with no apparent genetic distinctions among morphospecies. To further explore species boundaries among morphospecies of Ovabunda we sequenced three additional nuclear genes ( ITS , ATPS α, ATPS β), and obtained data for 1332 unlinked SNPs from restriction-site associated DNA sequencing. Both coalescent-based and allele-sharing species delimitation analyses supported four species of Ovabunda , each of which included multiple morphotypes encompassing the full range of morphological variation observed within the genus. All four species occurred over the same depth range of 5–41 m, and were sympatric at sites separated by 1100 km in the Red Sea. The only characters that have been found to distinguish three of the four species are diagnostic substitutions in the nuclear genome; the fourth differs by exhibiting polyp pulsation, a behavioral trait that can be assessed only in live colonies. The lack of any obvious morphological, life history, ecological or geographical differences among these four species begs the question of what drove the evolution and maintenance of reproductive isolating mechanisms in this cryptic species complex. [ABSTRACT FROM AUTHOR]