Genetic diversity is a crucial component of biodiversity, and as such, its maintenance and preservation is of high conservation concern. Tropical environments are undergoing intense rates of environmental change, and these changes may be driving large declines in genetic diversity. However, data on genetic diversity are highly skewed towards temperate regions. The degree to which diversity loss has occurred in tropical species, particularly marine species, remains an open and important question. Here, we directly compare genomic data from modern and museum collections of two commercially harvested nearshore marine fishes ( (Equulites laterofenestra and Gazza minuta) gathered from a single location in the Philippines, spanning a century of intense environmental change. These data reveal a marked loss in genetic diversity and evidence for multiple orders of magnitude reductions in effective population size (Ne) in both species, indicating substantial genomic erosion. Such a decline highlights the long-lasting genomic consequences of anthropogenic activity and sheds light on an, until-now, invisible loss of diversity from the most biodiverse ocean region.

The spotted spiny eel, Macrognathus siamensis is an economically important freshwater fish in the Mekong River basin, which is undergoing dramatic biodiversity changes due to anthropogenic impacts. The species is non-migratory, with a moderate larval duration that facilitates downstream genetic connectivity. Restriction site-associated DNA sequence datasets that includes 3736 and 1244 single nucleotide polymorphisms representing putatively neutral loci, from all geographic sites and without the Tachileik site, indicate strong population structure in this sedentary fish, with a significant isolation-by-distance signature. This structure reflects isolation of tributary populations and downstream dispersal of these distinct populations to mix in the Mekong mainstem and contributes to increased genetic diversity in the lower reaches of the Mekong basin. Genetic data indicates that the dispersal of eggs and larvae downstream is not impeded by Khone Falls and that the falls prevent upstream dispersal of eggs and larvae. Despite this downstream connectivity, there is a strong population structure among above- and below-Khone Falls groups. An analysis of outlier loci putatively under selection provides evidence that the difference between connected metapopulations above and below the falls is due to the fundamental differences in environmental regimes. We hypothesize that instead of a physical barrier, the falls simply represents a demarcation between previously recognized upstream limited-floodplain environments and downstream extensive-floodplain environments. These findings emphasize the need to monitor genetic diversity of key sedentary fishery species to assess whether proposed dams along the river could affect genetic diversity downstream. This genetic diversity is particularly important for the resilience of downstream populations because of the many environmental impacts caused by dams, land use, and climate change. Early detection of reduced downstream genetic diversity could trigger remediation programs to ensure resilience and continued fisheries productivity of important non-migratory fish resources.

Nations have committed to reductions in the global rate of species extinctions through the Sustainable Development Goals 14 and 15, for ocean and terrestrial species, respectively. Biodiversity loss is worsening despite rapid growth in the number and extent of protected areas, both at sea and on land. Resolving this requires targeting the locations and actions that will deliver positive conservation outcomes for biodiversity. The Species Threat Abatement and Restoration (STAR) metric, developed by a consortium of experts, quantifies the contributions that abating threats and restoring habitats in specific places offer towards reducing extinction risk based on the IUCN Red List of Threatened SpeciesTM. STAR is now recommended as an appropriate metric by recent disclosure frameworks for companies to report their impacts on nature and STAR has seen widespread uptake within the private sector. However, it is currently only available for the terrestrial realm. We extend the coverage of the threat abatement component of the STAR metric (START), used to identify locations where positive interventions could make a large contribution to reducing global species extinction risk and where developments that increase threats to species should be mitigated, to the marine realm for 1646 marine species. Reducing unsustainable fishing provides the greatest opportunity to lower species extinction risk, comprising 43% of the marine START score. Three-quarters (75%) of the global marine START score falls entirely outside the boundaries of protected areas and only 2.7% falls within no-take protected areas. The STAR metric can be used both to guide protected area expansion and to target other actions, such as establishment and enforcement of fishing limits, to recover biodiversity.

The Mekong River Basin, a critical biodiversity hotspot, is facing growing threats from environmental degradation and human activities, particularly dam construction. This study investigates the population structure and migratory behavior of Labeo chrysophekadion, an important food fish and widespread migratory species found in varied habitats, using restriction-site associated DNA sequencing. Treemix, Structure, and PCA analyses using an EzRAD derived neutral SNP dataset supported the subdivision of populations into three distinct zones corresponding to the Upper, Middle, and Lower Mekong regions. The analyses also provided evidence of both upstream and downstream migration pathways, including upstream through the Khone Falls. Active upstream adult migration apparently supports a peak in observed heterozygosity within the middle Mekong. Downstream dispersal best explains a large proportion of genetic material originating from the Upper into the Middle and Lower Mekong regions, and Middle into the Lower Mekong region. These findings emphasize the importance of managing this species as migratory, with special attention to the impacts of dam construction, to maintain healthy levels of genetic diversity.

Accurate identification of fishes is essential for understanding their biology and to ensure food safety for consumers. DNA barcoding is an important tool because it can verify identifications of both whole and processed fishes that have had key morphological characters removed (e.g., filets, fish meal); however, DNA reference libraries are incomplete, and public repositories for sequence data contain incorrectly identified sequences. During a nine-year sampling program in the Philippines, a global biodiversity hotspot for marine fishes, we developed a verified reference library of cytochrome c oxidase subunit I (COI) sequences for 2,525 specimens representing 984 species. Specimens were primarily purchased from markets, with additional diversity collected using rotenone or fishing gear. Species identifications were verified based on taxonomic, phenotypic, and genotypic data, and sequences are associated with voucher specimens, live-color photographs, and genetic samples catalogued at Smithsonian Institution, National Museum of Natural History. The Biodiversity of Philippine Marine Fishes dataset is released herein to increase knowledge of species diversity and distributions and to facilitate accurate identification of market fishes.

Biodiversity loss is a major global challenge and minimizing extinction rates is the goal of several multilateral environmental agreements. Policy decisions require comprehensive, spatially explicit information on species' distributions and threats. We present an analysis of the conservation status of 14,669 European terrestrial, freshwater and marine species (ca. 10% of the continental fauna and flora), including all vertebrates and selected groups of invertebrates and plants. Our results reveal that 19% of European species are threatened with extinction, with higher extinction risks for plants (27%) and invertebrates (24%) compared to vertebrates (18%). These numbers exceed recent IPBES (Intergovernmental Platform on Biodiversity and Ecosystem Services) assumptions of extinction risk. Changes in agricultural practices and associated habitat loss, overharvesting, pollution and development are major threats to biodiversity. Maintaining and restoring sustainable land and water use practices is crucial to minimize future biodiversity declines.

Being introduced in 2010, fingolimod was among the first oral therapies for relapsing multiple sclerosis (MS). Since that time, postmarketing surveillance has noted several case reports of various cryptococcal infections associated with fingolimod use. To date, approximately 15 such case reports have been published. We present the first and unique case of cryptococcal chest wall mass and rib osteomyelitis associated with fingolimod use. The patient presented with left-side chest pain and was found to have a lower left chest wall mass. Computerized tomography (CT) showed chest wall mass with the destruction of left 7th rib. Aspirate from the mass grew Cryptococcus neoformans. The isolate was serotype A. Fingolimod was stopped. The patient received liposomal amphotericin B for 2 weeks and started on fluconazole with a plan to continue for 6-12 months. The follow-up CT in 6 weeks showed a marked decrease in the size of the chest wall mass. In conclusion, our case highlights the atypical and aggressive form of cryptococcal infection possibly related to immunosuppression from fingolimod use.

Oil and gas extraction activities occur across the globe, yet species-specific toxicological information on the biological and ecological impacts of exposure to petrochemicals is lacking for the vast majority of marine species. To help prioritize species for recovery, mitigation, and conservation in light of significant toxicological data gaps, a trait-based petrochemical vulnerability index was developed and applied to the more than 1700 marine fishes present across the entire Gulf of Mexico, including all known bony fishes, sharks, rays and chimaeras. Using life history and other traits related to likelihood of exposure, physiological sensitivity to exposure, and population resiliency, final calculated petrochemical vulnerability scores can be used to provide information on the relative sensitivity, or resilience, of marine fish populations across the Gulf of Mexico to oil and gas activities. Based on current knowledge of traits, marine fishes with the highest vulnerability scores primarily occur in areas of high petrochemical activity, are found at or near the surface, and have low reproductive turnover rates and/or highly specialized diet and habitat requirements. Relative population vulnerability scores for marine fishes can be improved with additional toxicokinetic studies, including those that account for the synergistic or additive effect of multiple stressors, as well as increased research on ecological and life history traits, especially for deep living species.

Global biodiversitytargets require us to identify species at risk of extinction and quantify status and trends of biodiversity. The Red List Index (RLI) tracks trends in the conservation status of entire species groups over time by monitoring changes in categories assigned to species. Here, we calculate this index for the world’s fishes in 2010, using a sampled approach to the RLI based on a randomly selected sample of 1,500 species, and also present RLI splits for freshwater and marine systems separately. We further compare specific traits of a worldwide fish list to our sample to assess its representativeness. Overall, 15.1% of species in the sample were estimated to be threatened with extinction, resulting in a sampled RLI of 0.914 for all species, 0.968 in marine and 0.862 in freshwater ecosystems. Our sample showed fishing as the principal threat for marine species, and pollution by agricultural and forestry effluents for freshwater fishes. The sampled list provides a robust representation for tracking trends in the conservation status of the world’s fishes, including disaggregated sampled indices for marine and freshwater fish. Reassessment and backcasting of this index is urgent to check the achievement of the commitments proposed in global biodiversity targets.

The use of high-throughput sequencing technologies to produce genome-scale data sets was expected to settle some long-standing controversies across the Tree of Life, particularly in areas where short branches occur at deep timescales. Instead, these data sets have often yielded many well-supported but conflicting topologies, and highly variable gene-tree distributions. A variety of branch-support metrics beyond the nonparametric bootstrap are now available to assess how robust a phylogenetic hypothesis may be, as well as new methods to quantify gene-tree discordance. We applied multiple branch-support metrics to a study of an ancient group of marine fishes (Teleostei: Pelagiaria) whose interfamilial relationships have proven difficult to resolve due to a rapid accumulation of lineages very early in its history. We analyzed hundreds of loci including published ultraconserved elements and newly generated exonic data along with their flanking regions to represent all 16 extant families for more than 150 out of 284 valid species in the group. Branch support was typically lower at inter- than intra-familial relationships regardless of the type of marker used. Several nodes that were highly supported with bootstrap had a very low site and gene-tree concordance, revealing underlying conflict. Despite this conflict, we were able to identify four consistent interfamilial clades, each comprised of two or three families. Combining exons with their flanking regions also produced increased branch lengths at the deep branches of the pelagiarian tree. Our results demonstrate the limitations of employing current metrics of branch support and species-tree estimation when assessing the confidence of ancient evolutionary radiations and emphasize the necessity to embrace alternative measurements to explore phylogenetic uncertainty and discordance in phylogenomic data sets.[Concatenation; exons; introns; phylogenomics; species-tree methods; target capture.].

Extensive damage to reefs and exploitation of threatened species of the South China Sea raise questions regarding national obligations under international treaties. An historic test of these obligations under the United Nations Convention on the Law of the Sea (UNCLOS) was presented by the Philippine government before the Permanent Court of Arbitration at the International Court of Justice at the Peace Palace in Den Hague in November 2015. High resolution satellite imagery and on-site photographs, videos, and eye witness accounts provide ample evidence of unparalleled direct environmental damage to highly productive and biodiverse coral reefs of the South China Sea. Experts witness testimony indicated that this damage is a result of extensive island building on reef flats and sedimentation from dredging activities. Scientific evidence also indicates that this damage to coral reefs is likely to influence reef productivity throughout the region, including in adjacent Exclusive Economic Zones. Additional evidence of unrestrained exploitation targeting giant clams, corals, and reef fishes was presented that are indicative of irresponsible fishing practices and pose additional threats to endangered species. The decision of the Tribunal of the Permanent Court of Arbitration was handed down in July 2016 that upheld the claims of the Philippines government and has far-reaching policy implications for environmental actions in international waters. An evaluation of the ruling of the tribunal shows that nearly all points presented under UNCLOS were merited, with the possible exception of claims of connectivity of reefs of the South China Seas with adjacent Exclusive Economic Zones. Further research is needed to provide evidence for this claim.

Understanding the extinction risk of taxonomic groups increases our ability to prioritize efforts to address biodiversity loss. Over 400 species of herrings, shads, sardines, anchovies, menhadens, and relatives belong to the Order Clupeiformes and include many of the most important forage fishes. These small, schooling fishes are ecologically, economically, and culturally significant. However, despite their global contribution to fisheries and our increasing reliance on them for food and modern commodities, we lack critical information regarding basic biology and population trends for most species. We applied the IUCN Red List methodology, a comprehensive and systematic approach to assess extinction risk, to all clupeiform species. The best estimate suggests nearly 11% of species are of elevated conservation concern, although this could be as high as 36%. Two regions, the Caribbean and the Indo-Malay-Philippine Archipelago have high concentrations of threatened and Data Deficient species and are areas of conservation concern. Major threats include overexploitation, pollution, and habitat modification. Immediate conservation priorities include: 1) increasing research and mitigative action directed toward species assessed as threatened or Data Deficient; 2) improving fisheries management regulations for the understudied but heavily exploited species, and 3) promoting local, intensive habitat restoration to reduce pollution and remove dams. These extinction risk assessments and subsequent analyses should be used as an informative tool for fisheries and conservation managers and to monitor conservation progress.

Increasing rates of Anthropocene biodiversity extinctions suggest a possible sixth mass extinction event. Conservation planners are seeking effective ways to protect species, hotspots of biodiversity, and dynamic ecosystems to reduce and eventually eliminate the degradation and loss of diversity at the scale of genes, species, and ecosystems. While well-established, adequately enforced protected areas (PAs) increase the likelihood of preserving species and habitats, traditional placement methods are frequently inadequate in protecting biodiversity most at risk. Consequently, the Key Biodiversity Area (KBA) Partnership developed a set of science-based criteria and thresholds that iteratively identify sites where biodiversity is most in need of protection. KBA methodology has been rarely applied in the marine realm, where data are often extremely limited. We tested the feasibility of KBA population metrics in the Greater Caribbean marine region using occurrence and population data and threat statuses for 1669 marine vertebrates. These data identified areas where site-specific conservation measures can effectively protect biodiversity. Using KBA criteria pertaining to threatened and irreplaceable biodiversity, we identified 90 geographically unique potential KBAs, 34 outside and 56 within existing PAs. These provide starting points for local conservation managers to verify that KBA thresholds are met and to delineate site boundaries. Significant data gaps, such as population sizes, life history characteristics, and extent of habitats, prevent the full application of the KBA criteria to data-poor marine species. Increasing the rate and scope of marine sampling programs and digital availability of occurrence datasets will improve identification and delineation of KBAs in the marine environment.

This protocol describes the methodologies used for DNA extraction, quantification, restriction digestion, and make libraries from non-model organisms following Toonen el al. (2013). Toonen, R. J., Puritz, J. B., Forsman, Z. H., Whitney, J. L., Fernandez-Silva, I., Andrews, K. R., et al. (2013). ezRAD: a simplified method for genomic genotyping in non-model organisms. PeerJ 1, e203. doi:10.7717/peerj.203.

The Western Indian Ocean is comprised of productive and highly diverse marine ecosystems that are rich sources of food security, livelihoods, and natural wonder. The ecological services that species provide are vital to the productivity of these ecosystems and healthy biodiversity is essential for the continued support of economies and local users. The stability of these valuable resources, however, is being eroded by growing threats to marine life from overexploitation, habitat degradation and climate change, all of which are causing serious reductions in marine ecosystem services and the ability of these ecosystems to support human communities. Quantifying the impacts of these threats and understanding the conservation status of the region’s marine biodiversity is a critical step in applying informed management and conservation measures to mitigate loss and retain the ecological value of these systems. This report highlights trends in research needs for species in the region, including priorities for fundamental biological and ecological research and quantifying trends in the populations of species. The assessments and analyses submitted in this report should inform conservation decision-making processes and will be valuable to policymakers, natural resource managers, environmental planners and NGOs.

Impacts of urban development on aquatic populations are often complex and difficult to ascertain, but population genetic analysis has allowed researchers to monitor and estimate gene flow in the context of existing and future hydroelectric projects. The Lower Mekong Basin is undergoing rapid hydroelectric development with around 50 completed and under-construction dams and 95 planned dams. The authors investigated the baseline genetic diversity of two exploited migratory fishes, the mud carpHenicorhynchus lobatus(five locations), and the rat-faced pangasiid catfish,Helicophagus leptorhynchus(two locations), in the Lower Mekong Basin using the genomic double digest restriction site-associated DNA (ddRAD) sequencing method. In both species, fish sampled upstream of Khone Falls were differentiated from those collected at other sites, andN(e)estimates at the site above the falls were lower than those at other sites. This was the first study to utilize thousands of RAD-generated single nucleotide polymorphisms to indicate that the Mekong's Khone Falls are a potential barrier to gene flow for these two moderately migratory species. The recent completion of the Don Sahong dam across one of the only channels for migratory fishes through Khone Falls may further exacerbate signatures of isolation and continue to disrupt the migration patterns of regionally vital food fishes. In addition,H. lobatuspopulations downstream of Khone Falls, including the 3S Basin and Tonle Sap system, displayed robust connectivity. Potential obstruction of migration pathways between these river systems resulting from future dam construction may limit dispersal, which has led to elevated inbreeding rates and even local extirpation in other fragmented riverine species.

A comprehensive understanding of the status of marine organisms in the Gulf of Mexico is critical to the conservation and improved management of marine biodiversity in the region. Threats and extinction risk, based on application of the IUCN Red List Categories and Criteria at the global level, were analyzed for 1,300 Gulf of Mexico marine species. These species include all known marine mammals, sea birds, marine reptiles, cartilaginous fishes, bony shorefishes, corals, mangroves, seagrasses and complete clades of select invertebrates. Analyses showed that 6% of these species are threatened, 2% Near Threatened, 9% Data Deficient, and 83% Least Concern. However, the majority of these species are not endemic to the Gulf, and therefore are globally impacted by threats that may or may not be particularly intense within the Gulf. For example, many of these species are impacted by fisheries in much of their global range; however, the intensity of fishing pressure varies across their ranges, and some of these exploited species are well managed in the Gulf of Mexico. Other anthropogenic impacts, including industrial development, pollution, and habitat loss also vary in intensity across species’ global ranges. Here we provide recommendations for interpreting the application of global IUCN Red List Categories at the sub-global/regional scale, while highlighting conservation measures needed for marine species specific to the Gulf region.

A fundamental understanding of the impact of petrochemicals and other stressors on marine biodiversity is critical for effective management, restoration, recovery, and mitigation initiatives. As species-specific information on levels of petrochemical exposure and toxicological response are lacking for the majority of marine species, a trait-based assessment to rank species vulnerabilities to petrochemical activities in the Gulf of Mexico can provide a more comprehensive and effective means to prioritize species, habitats, and ecosystems for improved management, restoration and recovery. To initiate and standardize this process, we developed a trait-based framework, applicable to a wide range of vertebrate and invertebrate species, that can be used to rank relative population vulnerabilities of species to petrochemical activities in the Gulf of Mexico. Through expert consultation, 18 traits related to likelihood of exposure, individual sensitivity, and population resilience were identified and defined. The resulting multi-taxonomic petrochemical vulnerability framework can be adapted and applied to a wide variety of species groups and geographic regions. Additional recommendations and guidance on the application of the framework to rank species vulnerabilities under specific petrochemical exposure scenarios, management needs or data limitations are also discussed.

Significance Body shape is a strong predictor of habitat occupation in fishes, which changes rapidly at microevolutionary scales in well-studied freshwater systems such as sticklebacks and cichlids. Deep-bodied forms tend to occur in benthic habitats, while pelagic species typically have streamlined body plans. The recurrent evolution of this pattern across distantly related groups suggests that limited sets of high-fitness solutions exist due to environmental constraints. We rigorously test these observations showing that similar constraints operate at deeper evolutionary scales in a clade (Lutjanidae) of primarily benthic fish dwellers that repeatedly transitioned into midwater habitats in all major oceans throughout its 45-million-year history. Midwater species strongly converge in body shape, emphasizing evolutionary determinism in form and function along the benthic–pelagic axis.

A new species of the genus Acropoma, A. arafurensis sp. nov., is described based on two specimens (57.3–76.2 mm standard length: SL) collected from the Arafura Sea. The present species is distinguished from other congeners by a combination of the following characters: luminous gland U-shaped extending from throat to posterior tip of pectoral fin; luminous-gland length 29.5–32.0% SL; symphysis of lower jaw not sharply protruded; proximal radial of first anal-fin pterygiophore with concavity on anterior surface; anus situated closer to pelvic-fin insertion than to origin of anal fin; cycloid scales on lateral side of posterior half of body; vertical line on cheek absent; scales between first dorsal-fin base and lateral line 4; pectoral-fin rays 15; and gill rakers 20–21. Acropoma leobergi is redescribed based on 60 specimens (38.6–143.5 mm SL) from Taiwan, Philippines, and northern and west coast of Australia. Additionally, two specimens (94.9–103.1 mm SL) of A. boholensis collected from Luzon, Philippines, represent the first record of this species from the South China Sea.