Biological invasions are a major driver of global biodiversity loss, with the Mediterranean Sea among the most heavily invaded marine regions. However, identification and monitoring of Non-Indigenous Species (NIS) are hindered by taxonomic uncertainty and cryptic diversity, especially in taxonomic groups whose complexity remains poorly explored, such as polychaete annelids. In this study, specimens morphologically identified as Dorvillea similis (Crossland, 1924) according to the current identification keys, were collected from the Mediterranean Sea, Red Sea, Arabian Gulf, and north-western Indian Ocean. Combined morphological and molecular analyses revealed eight distinct molecular operational taxonomic units (MOTUs), four of which are NIS in the Mediterranean. Five of these MOTUs (MOTUs 4–8) form a morphologically homogeneous group, designated here as the Dorvillea similis species complex. Two distinct lineages were shown to represent two new species, with one recently formalized as D. phoenicia Putignano et al. 2026 (MOTU 2), and another formally described herein as Dorvillea ariannae sp. nov. (MOTU 3). The MOTU 1 also belongs to a distinct but as yet unidentified Dorvillea sp. Although species previously identified as D. similis show a relatively homogeneous morphology of chaetae and jaw pieces, our results highlight the diagnostic value of both live colouration and arrangement of sub-epidermal glandular tissue for their distinction. This study further supports previous findings that marine annelid invasions in the Mediterranean Sea are currently underestimated and underscores the pivotal role of integrative taxonomy in improving our understanding of biological invasions.

Gen3 is an open-source data platform for building data commons. A data commons is a cloud-based data platform for managing, analyzing, and sharing data with a research community. Gen3 has been used to build over 30 data commons by different organizations around the world. To set up a Gen3 data commons, you first define a data model. Gen3 then autogenerates 1) a data portal for searching and exploring data in the commons; 2) a data portal for submitting data to the commons; and 3) FAIR APIs for accessing the data programmatically. Gen3 is built over a small number of standards-based software services, which are designed to support current and future Gen3 components so that Gen3 can interoperate with other data platforms and data ecosystems.

Brachiopods are a group of shelled, filter-feeding marine invertebrates. Though they superficially resemble bivalve mollusks, brachiopods fall within the clade Lophophorata (Brachiopoda, Bryozoa, Phoronida) and possess an abundant and diverse fossil record spanning more than 500 million years. This long evolutionary history makes Brachiopoda particularly important for understanding the evolution of the morphologically disparate superphylum Lophotrochozoa. Brachiopods also stand to provide insight into the evolution of biomineralization, as most lineages produce skeletons of calcium carbonate while linguliforms use calcium phosphate. However, genomic resources for brachiopods are limited. To enable comparative and evolutionary genomic studies of this clade, we generated a chromosome-level assembly for the discinid brachiopod Discradisca antillarum. Sequencing was performed using PacBio HiFi and Hi-C to produce both a primary (N = 8) and haplotype-resolved (2N = 16) assembly. The primary assembly comprises 208 scaffolds with the 8 chromosome-level scaffolds representing 96.6% of the genome. The primary assembly has a BUSCO genome completeness score of 95.5% (94.4% single copy, 1.0% duplicated, 0.9% fragmented). Annotation of protein-coding genes yielded 29,208 genes with a BUSCO protein completeness score of 95.6% (87.6% single copy, 8.0% duplicated, 2.8% fragmented). Comparative synteny between D. antillarum and other lophotrochozoans shows that, at the macrosyntenic level, the genome conserves all proposed ancestral lophotrochozoan fusion-with-mixing events while also revealing new fusions involving several bilaterian ancestral linkage groups. The genome of D. antillarum will enable significant insights into brachiopod evolution.

Both human populations and marine biodiversity are concentrated along coastlines, with growing conservation interest in how these ecosystems can survive intense anthropogenic impacts. Tropical urban centres provide valuable research opportunities because these megacities are often adjacent to mega-diverse coral reef systems. The Pearl River Delta is a prime exemplar, as it encompasses one of the most densely populated and impacted regions in the world and is located just northwest of the Coral Triangle. However, the spatial and taxonomic complexity of this biodiversity, most of which is small, cryptic in habitat and poorly known, make comparative analyses challenging. We deployed standardized settlement structures at seven sites differing in the intensity of human impacts and used COI metabarcoding to characterize benthic biodiversity, with a focus on metazoans. We found a total of 7184 OTUs, with an average of 665 OTUs per sampling unit; these numbers exceed those observed in many previous studies using comparable methods, despite the location of our study in an urbanized environment. Beta diversity was also high, with 52% of the OTUs found at just one site. As expected, we found that the sites close to point sources of pollution had substantially lower diversity (44% less) relative to sites bathed in less polluted oceanic waters. However, the polluted sites contributed substantially to the total animal diversity of the region, with 25% of all OTUs occurring only within polluted sites. Further analysis of Arthropoda, Annelida and Mollusca showed that phylogenetic clustering within a site was common, suggesting that environmental filtering reduced biodiversity to a subset of lineages present within the region, a pattern that was most pronounced in polluted sites and for the Arthropoda. The water quality gradients surrounding the PRD highlight the unique role of in situ studies for understanding the impacts of complex urbanization pressures on biodiversity.

With the on-going efforts in digitising museum collections, increased participation of citizen scientists, and greater accessibility to research data, accurately determining global patterns of diversity has become more achievable. Here, we used occurrence records from the Global Biodiversity Information Facility, with annotation of authoritative taxonomy, to evaluate the taxonomic richness of marine gastropods and to identify global species hotspots for this group. We also reviewed the availability of genetic resources within hotspots to detect potentially important regions where reference sequences for identifying these organisms are wanting. We find 33,268 unique and valid species under 3291 genera belonging to 380 gastropod families that have been recorded from 1662 to 2023. Globally, only 12.1% of reported species are linked to a COI barcode, whilst 27.1% of the families are represented with complete mitogenomes. Georeferenced records show the wide albeit disparate distribution of observations and species counts. The compiled dataset, published by organisations that are restricted to 55 countries, reveal a seeming lack of local submissions, but nonetheless demonstrates the growing contribution of citizen science platforms. We present 28 marine provinces across the globe as putative gastropod species hotspots and call for further work and stronger involvement, particularly within COI barcoding cold spots, to address the observed genetic reference inequity. Lastly, we highlight the important and relevant role of open and inclusive science to biodiversity monitoring and research.

Microbes play vital roles across coral reefs both in the environment and inside and upon macrobes (holobionts), where they support critical functions such as nutrition and immune system modulation. These roles highlight the potential ecosystem-level importance of microbes, yet most knowledge of microbial functions on reefs is derived from a small set of holobionts such as corals and sponges. Declining seawater pH — an important global coral reef stressor — can cause ecosystem-level change on coral reefs, providing an opportunity to study the role of microbes at this scale. We use an in situ experimental approach to test the hypothesis that under such ocean acidification (OA), known shifts among macrobe trophic and functional groups may drive a general ecosystem-level response extending across macrobes and microbes, leading to reduced distinctness between the benthic holobiont community microbiome and the environmental microbiome. We test this hypothesis using genetic and chemical data from benthic coral reef community holobionts sampled across a pH gradient from CO2 seeps in Papua New Guinea. We find support for our hypothesis; under OA, the microbiome and metabolome of the benthic holobiont community become less compositionally distinct from the sediment microbiome and metabolome, suggesting that benthic macrobe communities are colonised by environmental microbes to a higher degree under OA conditions. We also find a simplification and homogenisation of the benthic photosynthetic community, and an increased abundance of fleshy macroalgae, consistent with previously observed reef microbialisation. We demonstrate a novel structural shift in coral reefs involving macrobes and microbes: that the microbiome of the benthic holobiont community becomes less distinct from the sediment microbiome under OA. Our findings suggest that microbialisation and the disruption of macrobe trophic networks are interwoven general responses to environmental stress, pointing towards a universal, undesirable, and measurable form of ecosystem changed.

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][1]-[5][2]]. However, our evolutionary understanding of this iconic symbiosis comes almost entirely from studies on clownfishes— a charismatic group of 28 described species in the genus Amphiprion [[2][3]]. Adaptation to venomous sea anemones (Anthozoa: Actiniaria) provided clownfishes with novel habitat space, ultimately triggering the adaptive radiation of the group [[2][3]]. Clownfishes diverged from their free-living ancestors 25-30 MYA with their adaptive radiation to sea anemones dating to 13.2 MYA [[2][3], [3][4]]. 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], [5][2]]. 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][6]). 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][6]). 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.### Competing Interest StatementThe authors have declared no competing interest. [1]: #ref-1 [2]: #ref-5 [3]: #ref-2 [4]: #ref-3 [5]: #ref-4 [6]: #F1

We document aggregations of an undescribed benthic solitary tunicate of the family Pyuridae from the Arabian Sea. This new genus was found forming dense thickets in shallow rocky substrates around Masirah Island and the Dhofar area in Oman. Such aggregations of tunicates have not been reported before from coral reefs in the Indo-West Pacific region and the Atlantic. This observation contributes to our understanding of the ecology and biogeography of ascidians, setting the stage for a comprehensive species description and in-depth analysis of this species.

Environmental DNA (eDNA) data make it possible to measure and monitor biodiversity at unprecedented resolution and scale. As use-cases multiply and scientific consensus grows regarding the value of eDNA analysis, public agencies have an opportunity to decide how and where eDNA data fit into their mandates. Within the United States, many federal and state agencies are individually using eDNA data in various applications and developing relevant scientific expertise. A national strategy for eDNA implementation would capitalize on recent scientific developments, providing a common set of next-generation tools for natural resource management and public health protection. Such a strategy would avoid patchwork and possibly inconsistent guidelines in different agencies, smoothing the way for efficient uptake of eDNA data in management. Because eDNA analysis is already in widespread use in both ocean and freshwater settings, we focus here on applications in these environments. However, we foresee the broad adoption of eDNA analysis to meet many resource management issues across the nation because the same tools have immediate terrestrial and aerial applications.

Longtail tuna (Thunnus tonggol), one of the neritic tuna species commonly found in the coastal areas of the IndoPacific region, is known to be in an overfishing state in certain areas, including in Indonesia. Understanding the condition of the T. tonggol population within Indonesia is very important in managing its fisheries policy. This research aims to understand the population genetic structure of T. tonggol across Indonesia's Fisheries Management Areas (FMAs), as well as to investigate the phylogeography of T. tonggol within the Indo-Pacific region. A total of 586 samples were collected from 18 locations within Indonesia's six FMAs, and two locations from Malaysian waters. A 520 bp portion of mtDNA control region was amplified and sequenced. Data analysis was conducted using 586 total sequences generated from this study, and 336 sequences retrieved from GenBank, as well as provided by the author of previous study. Population structure analysis indicated a panmictic population of T. tonggol within six Indonesian FMAs and within the neighboring countries (Malaysia, Andaman Sea, Vietnam, Philippines, and India), with an indication of population expansion. These data do, however, reveal two potentially distinctive clades, one showing an affinity among samples from certain parts of Indonesia (East Aceh, West Aceh, Medan - FMA571 & FMA572) and India. Based on this finding, the T. tonggol fisheries should be managed as a single management unit both within Indonesia's FMA and within neighboring countries, while also emphasizing localized genetic diversity to protect the sustainability of the species and its fishery.

Abstract The democratisation of next‐generation sequencing has vastly increased the availability of sequencing data from metabarcoding. However, to effectively prepare these metabarcoding data for subsequent analysis, researchers must consistently apply several different bioinformatic tools—including those which denoise reads, cluster sequences and assign taxonomic identities. This often creates a bioinformatics bottleneck in workflows for non‐specialists due to obstacles around: (a) integrating different tools, (b) the inability to easily modify and rerun bioinformatic pipelines involving non‐scripted (‘point‐and‐click’) elements and (c) the multiple outputs that may be required of a single dataset (e.g. amplicon sequence variants [ASVs] and operational taxonomic units [OTUs]), which often results in users running pipelines multiple times. Here, we introduce SimpleMetaPipeline, an open‐source bioinformatics pipeline implemented in R, which addresses these obstacles. SimpleMetaPipeline integrates the most robust and commonly used existing bioinformatic tools in a single reproducible pipeline, with a streamlined choice of parameters, to generate a sequence data table containing alternative clustering and assignment options. SimpleMetaPipeline accepts demultiplexed paired‐end and single reads from multiple sequencing runs. We describe the pipeline and demonstrate how alternative annotations enable the easy implementation of multi‐algorithm agreement tests to strengthen inferences. SimpleMetaPipeline represents a valuable addition to the existing library of pipelines, providing easy and reproducible bioinformatics, including a range of commonly desired clustering and assignment options, such as OTUs and ASVs.

Background: Congenital heart disease (CHD) is the most common major congenital anomaly and causes significant morbidity and mortality. Epidemiologic evidence supports a role of genetics in the development of CHD. Genetic diagnoses can inform prognosis and clinical management. However, genetic testing is not standardized among individuals with CHD. We sought to develop a list of validated CHD genes using established methods and to evaluate the process of returning genetic results to research participants in a large genomic study. Methods: Two-hundred ninety-five candidate CHD genes were evaluated using a ClinGen framework. Sequence and copy number variants involving genes in the CHD gene list were analyzed in Pediatric Cardiac Genomics Consortium participants. Pathogenic/likely pathogenic results were confirmed on a new sample in a clinical laboratory improvement amendments-certified laboratory and disclosed to eligible participants. Adult probands and parents of probands who received results were asked to complete a post-disclosure survey. Results: A total of 99 genes had a strong or definitive clinical validity classification. Diagnostic yields for copy number variants and exome sequencing were 1.8% and 3.8%, respectively. Thirty-one probands completed clinical laboratory improvement amendments-confirmation and received results. Participants who completed postdisclosure surveys reported high personal utility and no decision regret after receiving genetic results. Conclusions: The application of ClinGen criteria to CHD candidate genes yielded a list that can be used to interpret clinical genetic testing for CHD. Applying this gene list to one of the largest research cohorts of CHD participants provides a lower bound for the yield of genetic testing in CHD.

Omic BON is a thematic Biodiversity Observation Network under the Group on Earth Observations Biodiversity Observation Network (GEO BON), focused on coordinating the observation of biomolecules in organisms and the environment. Our founding partners include representatives from national, regional, and global observing systems; standards organizations; and data and sample management infrastructures. By coordinating observing strategies, methods, and data flows, Omic BON will facilitate the co-creation of a global omics meta-observatory to generate actionable knowledge. Here, we present key elements of Omic BON's founding charter and first activities.

Coral reefs are declining worldwide primarily because of bleaching and subsequent mortality resulting from thermal stress. Currently, extensive efforts to engage in more holistic research and restoration endeavors have considerably expanded the techniques applied to examine coral samples. Despite such advances, coral bleaching and restoration studies are often conducted within a specific disciplinary focus, where specimens are collected, preserved, and archived in ways that are not always conducive to further downstream analyses by specialists in other disciplines. This approach may prevent the full utilization of unexpended specimens, leading to siloed research, duplicative efforts, unnecessary loss of additional corals to research endeavors, and overall increased costs. A recent US National Science Foundation-sponsored workshop set out to consolidate our collective knowledge across the disciplines of Omics, Physiology, and Microscopy and Imaging regarding the methods used for coral sample collection, preservation, and archiving. Here, we highlight knowledge gaps and propose some simple steps for collecting, preserving, and archiving coral-bleaching specimens that can increase the impact of individual coral bleaching and restoration studies, as well as foster additional analyses and future discoveries through collaboration. Rapid freezing of samples in liquid nitrogen or placing at −80 °C to −20 °C is optimal for most Omics and Physiology studies with a few exceptions; however, freezing samples removes the potential for many Microscopy and Imaging-based analyses due to the alteration of tissue integrity during freezing. For Microscopy and Imaging, samples are best stored in aldehydes. The use of sterile gloves and receptacles during collection supports the downstream analysis of host-associated bacterial and viral communities which are particularly germane to disease and restoration efforts. Across all disciplines, the use of aseptic techniques during collection, preservation, and archiving maximizes the research potential of coral specimens and allows for the greatest number of possible downstream analyses.

DNA barcoding is critical to conservation and biodiversity research, yet public reference databases are incomplete. Existing barcode databases are biased toward cytochrome oxidase subunit I (COI) and frequently lack associated voucher specimens or geospatial metadata, which can hinder reliable species assignments. The emergence of metabarcoding approaches such as environmental DNA (eDNA) has necessitated multiple marker techniques combined with barcode reference databases backed by voucher specimens. Reference barcodes have traditionally been generated by Sanger sequencing, however sequencing multiple markers is costly for large numbers of specimens, requires multiple separate PCR reactions, and limits resulting sequences to targeted regions. High-throughput sequencing techniques such as genome skimming enable assembly of complete mitogenomes, which contain the most commonly used barcoding loci (e.g., COI, 12S, 16S), as well as nuclear ribosomal repeat regions (e.g., ITS1&2, 18S). We evaluated the feasibility of genome skimming to generate barcode references databases for marine fishes by assembling complete mitogenomes and nuclear ribosomal repeats. We tested genome skimming across a taxonomically diverse selection of 12 marine fish species from the collections of the National Museum of Natural History, Smithsonian Institution. We generated two sequencing libraries per species to test the impact of shearing method (enzymatic or mechanical), extraction method (kit-based or automated), and input DNA concentration. We produced complete mitogenomes for all non-chondrichthyans (11/12 species) and assembled nuclear ribosomal repeats (18S-ITS1-5.8S-ITS2-28S) for all taxa. The quality and completeness of mitogenome assemblies was not impacted by shearing method, extraction method or input DNA concentration. Our results reaffirm that genome skimming is an efficient and (at scale) cost-effective method to generate all mitochondrial and common nuclear DNA barcoding loci for multiple species simultaneously, which has great potential to scale for future projects and facilitate completing barcode reference databases for marine fishes.

Preassembly of Gymnothorax fimbriatus (UNSM 395396) based on SRA data (SRR14433904), derived using SPAdes 3.15.2. All contigs less than 200 bp removed.