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Largely understudied, mesophotic coral ecosystems lie below shallow reefs (at30 m depth) and comprise ecologically distinct communities. Brooding reproductive modes appear to predominate among mesophotic-specialist corals and may limit genetic connectivity among populations. Using reduced representation genomic sequencing, we assessed spatial population genetic structure at 50 m depth in an ecologically important mesophotic-specialist species Agaricia grahamae, among locations in the Southern Caribbean. We also tested for hybridisation with the closely related (but depth-generalist) species Agaricia lamarcki, within their sympatric depth zone (50 m). In contrast to our expectations, no spatial genetic structure was detected between the reefs of Curaçao and Bonaire (~40 km apart) within A. grahamae. However, cryptic taxa were discovered within both taxonomic species, with those in A. lamarcki (incompletely) partitioned by depth and those in A. grahamae occurring sympatrically (at the same depth). Hybrid analyses and demographic modelling identified contemporary and historical gene flow among cryptic taxa, both within and between A. grahamae and A. lamarcki. These results (1) indicate that spatial connectivity and subsequent replenishment may be possible between islands of moderate geographic distances for A. grahamae, an ecologically important mesophotic species, (2) that cryptic taxa occur in the mesophotic zone and environmental selection along shallow to mesophotic depth gradients may drive divergence in depth-generalists such as A. lamarcki, and (3) highlight that gene flow links taxa within this relativity diverse Caribbean genus.

Nearly a billion people depend on tropical seascapes. The need to ensure sustainable use of these vital areas is recognised, as one of 17 policy commitments made by world leaders, in Sustainable Development Goal (SDG) 14 (‘Life below Water’) of the United Nations. SDG 14 seeks to secure marine sustainability by 2030. In a time of increasing social-ecological unpredictability and risk, scientists and policymakers working towards SDG 14 in the Asia–Pacific region need to know: (1) How are seascapes changing? (2) What can global society do about these changes? and (3) How can science and society together achieve sustainable seascape futures? Through a horizon scan, we identified nine emerging research priorities that clarify potential research contributions to marine sustainability in locations with high coral reef abundance. They include research on seascape geological and biological evolution and adaptation; elucidating drivers and mechanisms of change; understanding how seascape functions and services are produced, and how people depend on them; costs, benefits, and trade-offs to people in changing seascapes; improving seascape technologies and practices; learning to govern and manage seascapes for all; sustainable use, justice, and human well-being; bridging communities and epistemologies for innovative, equitable, and scale-crossing solutions; and informing resilient seascape futures through modelling and synthesis. Researchers can contribute to the sustainability of tropical seascapes by co-developing transdisciplinary understandings of people and ecosystems, emphasising the importance of equity and justice, and improving knowledge of key cross-scale and cross-level processes, feedbacks, and thresholds.

Global environmental change is happening at unprecedented rates. Coral reefs are among the ecosystems most threatened by global change and for wild populations to persist, they must adapt. However, little is known about corals’ complex ecological and evolutionary dynamics making prediction about potential adaptation to future conditions precarious. Here, we review the process of adaptation through the lens of quantitative genetics and make suggestions about how incorporating genomic tools can help to both understand and predict adaptive potential in corals. In many cases, small changes in experimental design may provide large increases in the power, precision, and accuracy of information produced for predicting corals’ adaptation to environmental changes. We also outline where quantitative genetic principles may be incorporated into current research programs that aim to bolster coral tolerance to future warming conditions.

Genetic diversity within species represents a fundamental yet underappreciated level of biodiversity. Because genetic diversity can indicate species and population resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies of evolutionary biology, molecular ecology and conservation genetics produce large amounts of genome-scale genetic diversity data for wild populations. While open data policies have ensured an abundance of freely available genomic data stored in the databases of the International Nucleotide Sequence Database Collaboration (INSDC), only about 13% of current accessions have the associated spatial and temporal metadata in INSDC necessary to be reused in monitoring programs, macrogenetic studies, or for acknowledging the sovereignty of nations or Indigenous Peoples. We undertook a “distributed datathon” to quantify the availability of these missing metadata in sources external to the INSDC and to test the hypothesis that these metadata decay with time. We also worked to remediate these missing metadata by extracting them, when present, from associated published papers, online repositories, and/or from direct communication with authors. Starting with 848 programmatically identified candidate datasets (INSDC BioProjects), we manually determined that 561 contained samples from wild populations. We successfully restored spatiotemporal metadata (locality name and/or geospatial coordinates and collection year) for 78% of these 561 datasets (N = 440 BioProjects comprising 45,105 individuals or BioSamples from 762 species in 17 phyla). We also quantified the availability of 33 additional categories of metadata in sources external to the INSDC. Information about associated publications and the type of habitat from which the samples were taken was the most easily found; information about sampling permits was the most challenging to locate. Looking at papers and online repositories was much more fruitful than contacting authors, who only replied to our email requests 45% of the time. Overall, 23% of our email queries to authors discovered useful metadata. Importantly, we found that the probability of retrieving spatiotemporal metadata declines significantly with the age of the dataset, with a 13.5% yearly decrease for metadata located in published papers or online repositories and up to a 22% yearly decrease for metadata that were only available from authors. This observable metadata decay, mirrored in studies of other types of biological data, should motivate swift updates to data sharing policies and researcher practices to ensure that the valuable context provided by metadata is not lost forever.

Aim: Globally distributed pelagic fishes are typified by very low to negligible genetic differentiation at oceanic scales arising from high gene flow and (or) large population sizes. However, genomic approaches employing thousands of loci to characterise genetic variation can illuminate subtle patterns of genetic structure and facilitate demographic inference, such that effects arising from gene flow and population size can be partially decoupled. We used a population genomics approach to identify putative stocks in a circumtropical pelagic fish, wahoo, and to assess global connectivity in this species. Location: Indo-Pacific and Atlantic Oceans. Taxon: Wahoo, Acanthocybium solandri (Cuvier, 1832). Methods: Globally distributed wahoo samples from 11 locations (representing a total of 296 individuals) were sequenced using a pool-seq ezRAD approach to obtain 1289–9825 genome-wide SNP loci per population pair for analyses of genetic structure at a minor allele frequency (MAF) >0.05. Demographic inference using a diffusion approximation method (∂a∂i) was performed using 11,495–12,812 SNPs per population pair at a MAF >0.02. Results: Genetic structure, measured as F , was overall low, suggesting very little heterogeneity amongst sample pairs (pairwise F ≤ 0.021). However, there was a clear signal of regional genetic structuring between ocean basins. A principal coordinate analysis separated samples from the Indo-Pacific with those from the Atlantic and an analysis of molecular variance suggested that ~77% of variation in genetic structure was amongst regions. Our demographic analyses found greater support for models including migration over simple models of isolation. Main conclusions: Our study provides the most thorough genetic investigation of wahoo to date. We provide evidence for global connectivity of wahoo populations over their evolutionary history, but we also provide the first indication of subtle regional structure between the Indo-Pacific and Atlantic Oceans, which occurs against a background of high gene flow. The identification of regional stocks will inform new management strategies and guide future investigations in wahoo, an increasingly important species in global fisheries. ST ST

Extreme environmental conditions, such as temperature, can lead to meristic trait variation and skeletal deformities, which may have major impacts on individual fitness. As intertidal ecosystems experience rapid temperature and physicochemical fluctuations, intertidal fish living and reproducing in these environmental conditions may have phenotypes influenced by such variable environments. The impact of intertidal variability on fish development, however, has not been previously investigated. Skeletal deformities and meristic traits were assessed for Bathygobius cocosensis, a common intertidal fish living across the Indo-Pacific region, using a clearing and staining method on 72 individuals. Over 87% of individuals presented meristic variation and over 70% exhibited at least one type of skeletal deformity, mostly recorded in the caudal fin area. The unexpected prevalence of skeletal deformities among this intertidal fish population suggests that such deformities may be suitable markers to evaluate an individual's stress exposure during development and the subsequent fitness effects.

Genetic data represent a relatively new frontier for our understanding of global biodiversity. Ideally, such data should include both organismal DNA‐based genotypes and the ecological context where the organisms were sampled. Yet most tools and standards for data deposition focus exclusively either on genetic or ecological attributes. The Genomic Observatories Metadatabase (GEOME: geome‐db.org) provides an intuitive solution for maintaining links between genetic data sets stored by the International Nucleotide Sequence Database Collaboration (INSDC) and their associated ecological metadata. GEOME facilitates the deposition of raw genetic data to INSDCs sequence read archive (SRA) while maintaining persistent links to standards‐compliant ecological metadata held in the GEOME database. This approach facilitates findable, accessible, interoperable and reusable data archival practices. Moreover, GEOME enables data management solutions for large collaborative groups and expedites batch retrieval of genetic data from the SRA. The article that follows describes how GEOME can enable genuinely open data workflows for researchers in the field of molecular ecology., Development of GEOME has been supported by NESCent, the National Evolutionary Synthesis Center (2012 Catalysis Meeting to EDC and CR; 2013‐2014 Working Group to CR, EDC and RJT); the National Science Foundation (OISE‐1243541 to CM, DEB‐0956426 to CM and JD, and DEB‐1457848 to EDC and RJT); the Gordon and Betty Moore Foundation (CM and JD), the Berkeley Natural History Museums, and contracts from the Smithsonian National Museum of Natural History as components of the Global ARMS Programme, Global Genome Initiative and the SI Barcoding Network. The implementation of some metadata fields in GEOME were jointly initiated by the Ira Moana – Genes of the Sea – Project (www.massey.ac.nz/iramoana) and the project ‘Te Tuākiri o te Tāonga: Recognizing Indigenous Interests in Genetic Resources' both supported by Catalyst Seeding funds provided by the New Zealand Ministry of Business, Innovation and Employment and administered by the Royal Society Te Apārangi (17‐MAU‐309‐CSG to LL, CR, EDC, MRG, JD, RJT and seven others; and 19‐UOW‐008‐CSG to Maui Hudson and Jane Anderson, respectively), as well as a Massey University Research Fund to L.L. We thank Dr Karen Chambers and Dr Benjamin Sibbett from Wiley for providing encouragement and suggestions, alongside reviewers including Dr Shawn Narum and Dr Nick Fountain‐Jones. NESCent, we miss you.

Patterns of genetic structure in highly mobile marine vertebrates may be accompanied by phenotypic variation. Most studies in marine turtles focused on population genetic structure have been performed at rookeries. We studied whether genetic and morphological variation of the endangered green turtle (Chelonia mydas) is consistent geographically, focusing on foraging grounds. An association between population genetic structure and body shape variation at broad (inter-lineage) and fine (foraging grounds) scales was predicted and analysed using mitochondrial DNA and geometric morphometrics. Although genetic and phenotypic differentiation patterns were congruent between lineages, no fine-scale association was found, suggesting adaptive divergence. Connectivity among Pacific foraging grounds found here suggests that temperatures of ocean surface currents may influence the genetic structure of C. mydas on a broad scale. Our results suggest that vicariance, dispersal, life-history traits and ecological conditions operating in foraging grounds have shaped the intraspecific morphology and genetic diversity of this species. Considering a range of geographic and temporal scales is useful when management strategies are required for cosmopolitan species. Integrating morphological and genetic tools at different spatial scales, conservation management is proposed based on protection of neutral and adaptive diversity. This approach opens new questions and challenges, especially regarding conservation genetics in cosmopolitan species.

Rate of colour change and background matching capacity are important functional traits for avoiding predation and hiding from prey. Acute changes in environmental temperature are known to impact the rate at which animals change colour, and therefore may affect their survival. Many ectotherms have the ability to acclimate performance traits such as locomotion, metabolic rate and growth rate with changes in seasonal temperature. However, it remains unclear how other functional traits that are directly linked to behaviour and survival respond to long-term changes in temperature (within an individual's lifetime). We assessed whether the rate of colour change is altered by long-term changes in temperature (seasonal variation) and if rate of colour change can acclimate to seasonal thermal conditions. We used an intertidal rock-pool goby Bathygobius cocosensis, to test this and exposed individuals to representative seasonal mean temperatures (16 or 31°C, herein referred to cold- and warm-exposed fish respectively) for 9 weeks and then tested their rate of luminance change when placed on white and black backgrounds at acute test temperatures 16 and 31°C. We modelled rate of luminance change using the visual sensitives of a coral trout Plectropmus leopardus to determine how well gobies matched their backgrounds in terms of luminance contrast to a potential predator. After exposure to long-term seasonal conditions, the warm-exposed fish had faster rates of luminance change and matched their background more closely when tested at 31 than at 16°C. Similarly, the cold-exposed fish had faster rates of luminance change and matched their backgrounds more closely at 16°C than at 31°C. This demonstrates that rate of luminance change can be adjusted to compensate for long-term changes in seasonal temperature. This is the first study to show that animals can acclimate rate of colour change for background matching to seasonal thermal conditions. We also show that rapid changes in acute temperature reduce background matching capabilities. Stochastic changes in climate are likely to affect the frequency of predator-prey interactions which may have substantial knock-on effects throughout ecosystems.

This datasheet on Mytilus galloprovincialis covers Identity, Overview, Associated Diseases, Pests or Pathogens, Distribution, Dispersal, Biology & Ecology, Environmental Requirements, Natural Enemies, Impacts, Uses, Management, Genetics and Breeding, Economics, Further Information.

Offshore platforms, subsea pipelines, wells and related fixed structures supporting the oil and gas (O&G) industry are prevalent in oceans across the globe, with many approaching the end of their operational life and requiring decommissioning. Although structures can possess high ecological diversity and productivity, information on how they interact with broader ecological processes remains unclear. Here, we review the current state of knowledge on the role of O&G infrastructure in maintaining, altering or enhancing ecological connectivity with natural marine habitats. There is a paucity of studies on the subject with only 33 papers specifically targeting connectivity and O&G structures, although other studies provide important related information. Evidence for O&G structures facilitating vertical and horizontal seascape connectivity exists for larvae and mobile adult invertebrates, fish and megafauna; including threatened and commercially important species. The degree to which these structures represent a beneficial or detrimental net impact remains unclear, is complex and ultimately needs more research to determine the extent to which natural connectivity networks are conserved, enhanced or disrupted. We discuss the potential impacts of different decommissioning approaches on seascape connectivity and identify, through expert elicitation, critical knowledge gaps that, if addressed, may further inform decision making for the life cycle of O&G infrastructure, with relevance for other industries (e.g. renewables). The most highly ranked critical knowledge gap was a need to understand how O&G structures modify and influence the movement patterns of mobile species and dispersal stages of sessile marine species. Understanding how different decommissioning options affect species survival and movement was also highly ranked, as was understanding the extent to which O&G structures contribute to extending species distributions by providing rest stops, foraging habitat, and stepping stones. These questions could be addressed with further dedicated studies of animal movement in relation to structures using telemetry, molecular techniques and movement models. Our review and these priority questions provide a roadmap for advancing research needed to support evidence-based decision making for decommissioning O&G infrastructure.

Humans have long sought to restore species, but little attention has been directed at how to best select a subset of foundation species for maintaining rich assemblages that support ecosystems, like coral reefs and rainforests that are increasingly threatened by environmental change.We propose a two-part hedging approach that selects optimized sets of species for restoration. The first part acknowledges that biodiversity supports ecosystem functions and services, and so it takes precaution against loss by ensuring an even spread of phenotypic traits. The second part maximizes species and ecosystem persistence by weighting species based on characteristics that are known to improve ecological persistence—e.g., abundance, species range and tolerance to environmental change.Using existing phenotypic trait and ecological characteristic data for reef building corals, we identified sets of ecologically persistent species by examining marginal returns in occupancy of phenotypic trait space. We compared optimal sets of species with those from the world’s southern-most coral reef which naturally harbors low coral diversity to show these occupy much of the trait space. Comparison with an existing coral restoration program indicated that current corals used for restoration only cover part of the desired trait space and may be improved by including species with different traits.Synthesis and applications. While there are many possible criteria for selecting species for restoration, the approach proposed here addresses the need to insure against unpredictable losses of ecosystem services by focusing on a wide range of phenotypic traits and ecological characteristics. Furthermore, the flexibility of the approach enables the functional goals of restoration to vary depending on environmental context, stakeholder values, and the spatial and temporal scales at which meaningful impacts can be achieved.

Investigating the history of natural selection among closely related species can elucidate how genomes diverge in response to disparate environmental pressures. Molecular evolutionary approaches can be integrated with knowledge of gene functions to examine how evolutionary divergence may affect ecologically-relevant traits such as temperature tolerance and species distribution limits. Here, we integrate transcriptome-wide analyses of molecular evolution with knowledge from physiological studies to develop hypotheses regarding the functional classes of genes under positive selection in one of the world's most widespread invasive species, the warm-tolerant marine mussel Mytilus galloprovincialis. Based on existing physiological information, we test the hypothesis that genomic functions previously linked to divergent temperature adaptation at the whole-organism level show accelerated molecular divergence between warm-adapted M. galloprovincialis and cold-adapted congeners. Combined results from codon model tests and analyses of polymorphism and divergence reveal that divergent selection has affected genomic functions previously associated with species-specific expression responses to heat stress, namely oxidative stress defense and cytoskeletal stabilisation. Examining specific loci implicated in thermal tolerance among Mytilus species (based on interspecific biochemical or expression patterns), we find close functional similarities between known thermotolerance candidate genes under positive selection and positively selected loci under predicted genomic functions (those associated with divergent expression responses). Taken together, our findings suggest a contribution of temperature-dependent selection in the molecular divergence between warm- and cold-adapted Mytilus species that is largely consistent with results from physiological studies. More broadly, this study provides an example of how independent experimental evidence from ecophysiological investigations can inform evolutionary hypotheses about molecular adaptation in closely related non-model species.

Aim: Widespread coral bleaching, crown-of-thorns seastar outbreaks, and tropical storms all threaten foundational coral species of the Great Barrier Reef, with impacts differing over time and space. Yet, dispersal via larval propagules could aid reef recovery by supplying new settlers and enabling the spread of adaptive variation among regions. Documenting and predicting spatial connections arising from planktonic larval dispersal in marine species, however, remains a formidable challenge. Location: The Great Barrier Reef, Australia. Methods: Contemporary biophysical larval dispersal models were used to predict long-distance multigenerational connections for two common and foundational coral species (Acropora tenuis and Acropora millepora). Spatially extensive genetic surveys allowed us to infer signatures of asymmetric dispersal for these species and evaluate concordance against expectations from biophysical models using coalescent genetic simulations, directions of inferred gene flow, and spatial eigenvector modelling. Results: At long distances, biophysical models predicted a preponderance of north-south connections and genetic results matched these expectations: coalescent genetic simulations rejected an alternative scenario of historical isolation; the strongest signals of inferred gene flow were from north-south; and asymmetric eigenvectors derived from north-south connections in the biophysical models were significantly better predictors of spatial genetic patterns than eigenvectors derived from symmetric null spatial models. Main conclusions: Results are consistent with biophysical dispersal models yielding approximate summaries of past multigenerational gene flow conditioned upon directionality of connections. For A. tenuis and A. millepora, northern and central reefs have been important sources to downstream southern reefs over the recent evolutionary past and should continue to provide southward gene flow. Endemic genetic diversity of southern reefs suggests substantial local recruitment and lack of long-distance gene flow from south to north.

Most marine fish species disperse during a planktonic larval stage where individuals exhibit variation in pelagic duration, growth rate and settlement size. Extreme predation risk is predicted to select for rapid growth rates and decreased pelagic duration as a strategy for increasing survival to settlement. How larval traits affect post-metamorphic performance, however, has been a contentious topic over the past 50 yrs. Some studies suggest that larval traits have carry-over effects to later life stages, where larval traits can be positively or negatively correlated with post-metamorphic performance. For example, individuals with rapid larval growth rates may settle at larger sizes and have faster post-metamorphic locomotion than slow-growing individuals. Alternatively, trade-offs between life stages might exist, where rapid larval growth rate may be negatively correlated with post-metamorphic locomotion, potentially due to energetic resource allocation trade-offs. In addition, other studies suggest that larval traits are decoupled from later life stages to allow for a transition in morphology and habitat. We tested how Bathygobius cocosensis hatch size, larval growth rates, settlement size and pelagic duration correlated with post-metamorphic thermal performance of burst swimming speed, routine metabolic rate and critical thermal maximum. We found that larval growth rate was negatively correlated with juvenile routine metabolic rate and burst swimming speed across a range of test temperatures. That is, fast-growing larvae had slower burst swimming speeds and lower routine metabolic rates across temperature as juveniles compared to slower-growing larvae. We also found that hatch size and pelagic larval duration were not correlated with post-metamorphic performance. Thus, we provide evidence both for larval traits having carry-over effects on later life stages and also for larval traits being decoupled with thermal performance post-metamorphosis. This is the first study to show that rapid larval growth rate is costly for post-metamorphic thermal performance.

In this study, we sequenced the full mitochondrial genome of Bathygobius cocosensis, an abundant intertidal fish species, which may provide insights into the evolutionary genetics of chaotic genetic patchiness and range expansion in marine systems. The mitochondrial genome is 16,692 bp, and contains 13 protein-coding genes along with 22 tRNA and 2 rRNA genes and a D-loop region, arranged similarly to other Gobiidae species. A Bayesian phylogeny of Gobiidae species indicates close relationships to the genus Glossogobius. The B. cocosensis mitochondrial genome is now available through GenBank (Accession = MG704838).

Interactions among selection, gene flow, and drift affect the trajectory of adaptive evolution. In natural populations, the direction and magnitude of these processes can be variable across different spatial, temporal, or ontogenetic scales. Consequently, variability in evolutionary processes affects the predictability or stochasticity of microevolutionary outcomes. We studied an intertidal fish, Bathygobius cocosensis (Bleeker, 1854), to understand how space, time, and life stage structure genetic and phenotypic variation in a species with potentially extensive dispersal and a complex life cycle (larval dispersal preceding benthic recruitment). We sampled juvenile and adult life stages, at three sites, over three years. Genome-wide SNPs uncovered a pattern of chaotic genetic patchiness, that is, weak-but-significant patchy spatial genetic structure that was variable through time and between life stages. Outlier locus analyses suggested that targets of spatially divergent selection were mostly temporally variable, though a significant number of spatial outlier loci were shared between life stages. Head shape, a putatively ecologically responsive (adaptive) phenotype in B. cocosensis also exhibited high temporal variability within sites. However, consistent spatial relationships between sites indicated that environmental similarities among sites may generate predictable phenotype distributions across space. Our study highlights the complex microevolutionary dynamics of marine systems, where consideration of multiple ecological dimensions can reveal both predictable and stochastic patterns in the distributions of genetic and phenotypic variation. Such considerations probably apply to species that possess short, complex life cycles, have large dispersal potential and fecundities, and that inhabit heterogeneous environments.

International audience; Despite increasing awareness of issues affecting inclusivity, equity and diversity, change has been slow in science and academia, and gender disparities remain significant. Biogeography has not escaped this pattern. Here, we present a virtual issue compiling some of the most cited papers led by women that have been published in the Journal of Biogeography since 2009 in an effort to equalize visibility of women's influential work. We summarize leading gender disparities and their potential underlying causes, and present our motivation and methodology in compiling this issue. We further provide a blog, website and social media links to highlight the research of the authors whose work is showcased here. Highlighting influential contributions by women biogeographers is a small step towards equalizing visibility across genders. We hope that this virtual issue will also contribute in some way to creating a greater sense of belonging for women biogeographers.

The most remarkable feature of our planet is the diversity of its life forms, ranging from viruses and nanobacteria to blue whales and giant sequoias to satanic leaf‐tailed geckos and leafy seadragons (look them up!). Life is found in essentially all environments on earth, and the number of species living on our planet is many times greater than we could have imagined a century ago. A well‐regarded estimate pegs the number of eukaryotic species on earth at 8.7 million (±1.3 million), of which fewer than 15% are currently described (Mora et al., 2011). The diversity of prokaryotes is less clear (and highly controversial), but an analysis of 1.6 billion 16S ribosomal RNA sequences estimated that 0.8–1.6 million prokaryotic operational taxonomic units exist globally (Louca et al., 2019). While we do not know how many species are currently extant, or have existed in the past, we do know that this biodiversity is valuable, providing food, fibre and medicine, furnishing ecosystem services such as water and air purification, nutrient cycling, pollination and carbon uptake, and contributing to technological innovations ranging from biotechnology to robotics to material science. Moreover, biodiversity underlies the cultural identity of human populations and is important to human health and well‐being. Geographically, species richness increases from the Polar Regions to the tropics in terrestrial and surface marine ecosystems. Thus, some countries, especially those in tropical and subtropical regions, are endowed with much greater biodiversity than others. Unfortunately, benefits arising from the access and utilization of this biodiversity have been unequally shared, with (paradoxically) biodiversity‐poor countries often accruing the lion's share of economic gains. There can be imbalances within countries as well, wherein some segments of the population obtain greater economic benefits from biodiversity and associated traditional knowledge than indigenous peoples. The “Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization,” which came into force in 2014, is an international agreement designed to ensure that the benefits arising from biodiversity are shared equitably (https://www.cbd.int/abs/). However, few scientific journals require compliance with the Nagoya Protocol or the reporting of benefits from biodiversity research. In this editorial, we (the editors of Molecular Ecology and Molecular Ecology Resources) express support for the Nagoya Protocol and the principle of benefit sharing. We believe that scientific journals publishing research on biodiversity can play an important role in implementing the Nagoya Protocol and in reporting on benefits generated from such research. Below, we provide background on the Nagoya Protocol, discuss the kinds of benefits that may arise from biodiversity research, describe the rationale for reporting on these benefits and introduce changes to the journals’ Data Accessibility Statements to incorporate the requirements and goals of the Nagoya Protocol.

Molecular genetic estimates of population effective size (Ne ) lose accuracy and precision when insufficient numbers of samples or loci are used. Ideally, researchers would like to forecast the necessary power when planning their project. neogen (genetic Ne for Overlapping Generations) enables estimates of precision and accuracy in advance of empirical investigation and allows exploration of the power available in different user-specified age-structured sampling schemes. neogen provides a population simulation and genetic power analysis framework that simulates the demographics, genetic composition, and Ne , from species-specific life history, mortality, population size, and genetic priors. neogen guides the user to establish a tractable sampling regime and to determine the numbers of samples and microsatellite or SNP loci required for accurate and precise genetic Ne estimates when sampling a natural population. neogen is useful at multiple stages of a study's life cycle: when budgeting, as sampling and locus development progresses, and for corroboration when empirical Ne estimates are available. The underlying model is applicable to a wide variety of iteroparous species with overlapping generations (e.g., mammals, birds, reptiles, long-lived fishes). In this paper, we describe the neogen model, detail the workflow for the point-and-click software, and explain the graphical results. We demonstrate the use of neogen with empirical Australian east coast zebra shark (Stegostoma fasciatum) data. For researchers wishing to make accurate and precise genetic Ne estimates for overlapping generations species, neogen facilitates planning for sample and locus acquisition, and with existing empirical genetic Ne estimates neogen can corroborate population demographic and life history properties.

Complex life cycles may evolve to dissociate distinct developmental phases in an organism's lifetime. However, genetic or environmental factors may restrict trait independence across life stages, constraining ontogenetic trajectories. Quantifying covariance across life stages and their temporal variability is fundamental in understanding life-history phenotypes and potential distributions and consequences for selection. We studied developmental constraints in an intertidal fish (Bathygobius cocosensis: Gobiidae) with a discrete pelagic larval phase and benthic juvenile phase. We tested whether traits occurring earlier in life affected those expressed later, and whether larval traits were decoupled from postsettlement juvenile traits. Sampling distinct cohorts from three annual breeding seasons afforded tests of temporally variability in trait covariance. From otoliths (fish ear stones), we measured hatch size, larval duration, pelagic growth (larval traits) and early postsettlement growth (juvenile trait) in 124 juvenile B. cocoensis. We used path analyses to model trait relationships with respect to their chronological expression, comparing models among seasons. We also modelled the effect of season and hatch date on each individual trait to quantify their inherent variability. Our path analyses demonstrated a decoupling of larval traits on juvenile growth. Within the larval phase, longer larval durations resulted in greater pelagic growth, and larger size-at-settlement. There was also evidence that larger hatch size might reduce larval durations, but this effect was only marginally significant. Although pelagic and postsettlement growth were decoupled, pelagic growth had postsettlement consequences: individuals with high pelagic growth were among the largest fish at settlement, and remained among the largest early postsettlement. We observed no evidence that trait relationships varied among breeding seasons, but larval duration differed among breeding seasons, and was shorter for larvae hatching later within each season. Overall, we demonstrate mixed support for the expectation that traits in different life stages are independent. While postsettlement growth was decoupled from larval traits, pelagic development had consequences for the size of newly settled juveniles. Temporal consistency in trait covariances implies that genetic and/or environmental factors influencing them were stable over our three-year study. Our work highlights the importance of individual developmental experiences and temporal variability in understanding population distributions of life-history traits.

Aim: Several biogeographic hypotheses seek to explain the extreme species diversity of the coral reefs in the Coral Triangle (CT) of the Indo-West Pacific (IWP). Here, we investigate processes implicit to the Centre of Origin, Centre of Overlap and Centre of Survival hypotheses. We focus on intraspecific genetic data, where intraspecific diversity can provide information regarding directionality of past dispersal (gene flow) and changes in population size such as expansion from refugia. Location: Indian Ocean, Coral Triangle and West Pacific Ocean. Methods: We use existing mitochondrial DNA data augmented with new samples from the Philippines, thus filling in key sampling gaps from previous studies, to examine nine reef species. We first test if genetic diversity peaks in the CT. We then estimate gene flow between regions—CT vs. Indian Ocean (IO) and CT vs. Pacific Ocean (PO)—to assess concordance with predicted directions of movement (i.e. into the CT or out of the CT). Finally, we investigate the historical demography of these species and evaluate population expansions to ascertain whether genetic diversity is correlated with putative Pleistocene refugia. Results: Genetic diversity in the CT was not greater than genetic diversity in the IO and PO, and we found highly variable spatial patterns of genetic diversity when species were evaluated individually. Gene flow estimates indicated very limited exchange between regions, consistent with peripheral isolation and/or signals of historical divergence. For some species, however, there were signals of movement out of the CT. While there was no significant correlation between genetic diversity and putative refugia, genetic patterns suggested that some populations have experienced population expansions. The locations of expansion were also variable across species. Overall, there was no signal of concordant processes shaping intraspecific genetic diversity. Main conclusions: Genetic patterns across species were highly variable with some species lending weak support for processes aligned with each of the “Centre” of diversity hypotheses. But overall there was no compelling evidence for uniform processes underlying all species, which possibly indicate that processes underlying the different “Centre” have not strongly affected IWP species within the recent past.

Coral reef fishes are famous for their fantastic colors and forms. Easily overlooked are the cryptic and diminutive (cryptobenthic) bottom-dwelling fishes that also call coral reefs home. By linking empirical data and ecosystem modeling, Brandl et al. (1), on page 1189 of this issue, propose that pelagic (open-water) larvae of cryptobenthic fishes and their small juveniles that recently settled on reefs constitute a key food source for other reef residents. Such a scenario could help explain why coral reefs in nutrientpoor waters teem with life.

Aim: To test the influence of historical and contemporary environment in shaping the genetic diversity of freshwater fauna we contrast genetic structure in two co-distributed, but ecologically distinct, rainbowfish; a habitat generalist (Melanotaenia splendida) and a habitat specialist (M. trifasciata). Location: Fishes were sampled from far northern Australia (Queensland and Northern Territory). Methods: We used sequence data from one mitochondrial gene and one nuclear gene to investigate patterns of genetic diversity in M. splendida and M. trifasciata to determine how differences in habitat preference and historical changes in drainage boundaries affected patterns of connectivity. Results: Melanotaenia splendida showed high levels of genetic diversity and little population structure across its range. In contrast, M. trifasciata showed high levels of population structure. Whereas phylogeographic patterns differed, both species showed a strong relationship between geographical distance and genetic differentiation between populations. Melanotaenia splendida showed a shallower relationship with geographical distance, and genetic differentiation was best explained by stream length and a lower scaled ocean distance (11.98 times coast length). For M. trifasciata, genetic differentiation was best explained by overwater distance between catchments and ocean distance scaled at 1.16 × 10 times coast length. Main conclusions: Connectivity of freshwater populations inhabiting regions periodically interconnected during glacial periods appears to have been affected by ecological differences between species. Species-specific differences are epitomized here by the contrast between co-distributed congeners with different habitat requirements: for the habitat generalist, M. splendida, there was evidence for greater historical genetic connectivity with oceans as a weaker barrier to gene exchange in contrast with the habitat specialist, M. trifasciata.

Protected areas buffer species from anthropogenic threats and provide places for the processes that generate and maintain biodiversity to continue. However, genetic variation, the raw material for evolution, is difficult to capture in conservation planning, not least because genetic data require considerable resources to obtain and analyze. Here we show that freely available environmental and geographic distance variables can be highly effective surrogates in conservation planning for representing adaptive and neutral intraspecific genetic variation. We obtained occurrence and genetic data from the IntraBioDiv project for 27 plant species collected over the European Alps using a gridded sampling scheme. For each species, we identified loci that were potentially under selection using outlier loci methods, and mapped their main gradients of adaptive and neutral genetic variation across the grid cells. We then used the cells as planning units to prioritize protected area acquisitions. First, we verified that the spatial patterns of environmental and geographic variation were correlated, respectively, with adaptive and neutral genetic variation. Second, we showed that these surrogates can predict the proportion of genetic variation secured in randomly generated solutions. Finally, we discovered that solutions based only on surrogate information secured substantial amounts of adaptive and neutral genetic variation. Our work paves the way for widespread integration of surrogates for genetic variation into conservation planning.

Larval dispersal by ocean currents is a critical component of systematic marine protected area (MPA) design. However, there is a lack of quantitative methods to incorporate larval dispersal in support of increasingly diverse management objectives, including local population persistence under multiple types of threats (primarily focused on larval retention within and dispersal between protected locations) and benefits to unprotected populations and fisheries (primarily focused on larval export from protected locations to fishing grounds). Here, we present a flexible MPA design approach that can reconcile multiple such potentially conflicting management objectives by balancing various associated treatments of larval dispersal information. We demonstrate our approach based on alternative dispersal patterns, combinations of threats to populations, management objectives, and two different optimization strategies (site vs. network-based). Our outcomes highlight a consistently high effectiveness in selecting priority locations that are self-replenishing, inter-connected, and/or important larval sources. We find that the opportunity to balance these three dispersal attributes flexibly can help not only to prevent meta-population collapse, but also to ensure effective fisheries recovery, with average increases in the number of recruits at fishing grounds at least two times higher than achieved by standard habitat-based or ad-hoc MPA designs. Future applications of our MPA design approach should therefore be encouraged, specifically where management tools other than MPAs are not feasible.

International audience; Non-native species experience novel selection pressures in introduced environments and may interbreed with native lineages. Species introductions therefore provide opportunities to investigate repeated patterns of adaptation and introgression across replicated contact zones. Here, we investigate genetic parallelism between multiple introduced populations of the invasive marine mussel, Mytilus galloprovincialis, in the absence (South Africa and California) and presence of hybridisation with a native congener (Mytilus planulatus in Batemans Bay and Sydney Harbour, Australia). Repeatability in post-introduction differentiation from native-range populations varied between genetically distinct Atlantic and Mediterranean lineages, with Atlantic-derived introductions displaying high differentiation (maxFST>0.4) and parallelism at outlier loci. Identification of long non-coding RNA transcripts (lncRNA) additionally allowed us to clarify that parallel responses are largely limited to protein-coding loci, with lncRNAs likely evolving under evolutionary constraints. Comparisons of independent hybrid zones revealed differential introgression most strongly in Batemans Bay, with an excess of M. galloprovincialis ancestry and resistance to introgression at loci differentiating parental lineages (M. planulatus and Atlantic M. galloprovincialis). Additionally, contigs putatively introgressed with divergent alleles from a closely related species, Mytilus edulis, showed stronger introgression asymmetries compared to genome-wide trends and also diverged in parallel in both Atlantic-derived introductions. These results suggest that divergent demographic histories experienced by introduced lineages, including pre-introduction introgression, influences contemporary admixture dynamics. Our findings build on previous investigations reporting contributions of historical introgression to intrinsic reproductive architectures shared between marine lineages and illustrate that interspecific introgression history can shape differentiation between colonising populations and their hybridisation with native congeners.

Aim: To test hypothesized biogeographic partitions of the tropical Indo-Pacific Ocean with phylogeographic data from 56 taxa, and to evaluate the strength and nature of barriers emerging from this test. Location: The Indo-Pacific Ocean. Time period: Pliocene through the Holocene. Major taxa studied: Fifty-six marine species. Methods: We tested eight biogeographic hypotheses for partitioning of the Indo-Pacific using a novel modification to analysis of molecular variance. Putative barriers to gene flow emerging from this analysis were evaluated for pairwise ΦST, and these ΦST distributions were compared to distributions from randomized datasets and simple coalescent simulations of vicariance arising from the Last Glacial Maximum. We then weighed the relative contribution of distance versus environmental or geographic barriers to pairwise ΦST with a distance-based redundancy analysis (dbRDA). Results: We observed a diversity of outcomes, although the majority of species fit a few broad biogeographic regions. Repeated coalescent simulation of a simple vicariance model yielded a wide distribution of pairwise ΦST that was very similar to empirical distributions observed across five putative barriers to gene flow. Three of these barriers had median ΦST that were significantly larger than random expectation. Only 21 of 52 species analysed with dbRDA rejected the null model. Among these, 15 had overwater distance as a significant predictor of pairwise ΦST, while 11 were significant for geographic or environmental barriers other than distance. Main conclusions: Although there is support for three previously described barriers, phylogeographic discordance in the Indo-Pacific Ocean indicates incongruity between processes shaping the distributions of diversity at the species and population levels. Among the many possible causes of this incongruity, genetic drift provides the most compelling explanation: given massive effective population sizes of Indo-Pacific species, even hard vicariance for tens of thousands of years can yield ΦSTvalues that range from 0 to nearly 0.5.

Population genomic approaches are making rapid inroads in the study of non-model organisms, including marine taxa. To date, these marine studies have predominantly focused on rudimentary metrics describing the spatial and environmental context of their study region (e.g., geographical distance, average sea surface temperature, average salinity). We contend that a more nuanced and considered approach to quantifying seascape dynamics and patterns can strengthen population genomic investigations and help identify spatial, temporal, and environmental factors associated with differing selective regimes or demographic histories. Nevertheless, approaches for quantifying marine landscapes are complicated. Characteristic features of the marine environment, including pelagic living in flowing water (experienced by most marine taxa at some point in their life cycle), require a well-designed spatial-temporal sampling strategy and analysis. Many genetic summary statistics used to describe populations may be inappropriate for marine species with large population sizes, large species ranges, stochastic recruitment, and asymmetrical gene flow. Finally, statistical approaches for testing associations between seascapes and population genomic patterns are still maturing with no single approach able to capture all relevant considerations. None of these issues are completely unique to marine systems and therefore similar issues and solutions will be shared for many organisms regardless of habitat. Here, we outline goals and spatial approaches for landscape genomics with an emphasis on marine systems and review the growing empirical literature on seascape genomics. We review established tools and approaches and highlight promising new strategies to overcome select issues including a strategy to spatially optimize sampling. Despite the many challenges, we argue that marine systems may be especially well suited for identifying candidate genomic regions under environmentally mediated selection and that seascape genomic approaches are especially useful for identifying robust locus-by-environment associations.

Connectivity underpins the persistence and recovery of marine ecosystems. The Great Barrier Reef (GBR) is the world's largest coral reef ecosystem and managed by an extensive network of no-take zones; however, information about connectivity was not available to optimize the network's configuration. We use multivariate analyses, Bayesian clustering algorithms and assignment tests of the largest population genetic data set for any organism on the GBR to date (Acropora tenuis, >2500 colonies; >50 reefs, genotyped for ten microsatellite loci) to demonstrate highly congruent patterns of connectivity between this common broadcast spawning reef-building coral and its congener Acropora millepora (~950 colonies; 20 reefs, genotyped for 12 microsatellite loci). For both species, there is a genetic divide at around 19°S latitude, most probably reflecting allopatric differentiation during the Pleistocene. GBR reefs north of 19°S are essentially panmictic whereas southern reefs are genetically distinct with higher levels of genetic diversity and population structure, most notably genetic subdivision between inshore and offshore reefs south of 19°S. These broadly congruent patterns of higher genetic diversities found on southern GBR reefs most likely represent the accumulation of alleles via the southward flowing East Australia Current. In addition, signatures of genetic admixture between the Coral Sea and outer-shelf reefs in the northern, central and southern GBR provide evidence of recent gene flow. Our connectivity results are consistent with predictions from recently published larval dispersal models for broadcast spawning corals on the GBR, thereby providing robust connectivity information about the dominant reef-building genus Acropora for coral reef managers.

Rhynchobatus spp. (wedgefishes) are large benthopelagic shark-like rays with fins that are highly prized in the international shark fin trade. They are among the most threatened groups of sharks and rays globally. While Rhynchobatus spp. are known to be under considerable fishing pressure as a group, taxonomic confusion among species within the genus has compromised species-specific fishery and demographic data that are urgently needed for developing effective management strategies. Rhynchobatus australiae (Whitley, 1939) is a large Indo-West Pacific species reaching 2 to 3 m that is classified as Vulnerable on the IUCN Red List. This study combines new empirical data from field surveys with data obtained from verified reference specimens to investigate genetic and phenotypic variation in R. australiae and its relative incidence in fisheries. R. australiae dominated Rhynchobatus catch in fisheries surveys across Southeast Asia, and was the most commonly recorded species of the genus in Australia (94% and 58% of captures respectively, n = 207). Study specimens were consistent with a single species with moderate spatial mtDNA variation (Phi(ST) = 0.198, p < 0.0001). We show that R. australiae can be reliably differentiated from other Indo-Pacific species with nadh2 (1044bp), and a section of the control region (456bp) short enough to amplify DNA from processed fins in international trade. We document aspects of morphological variability to assist in the description of external characters that differentiate this species. This is the first range-wide intraspecific study on any wedgefish species, and provides the most complete synthesis of mtDNA data to date for identifying Rhynchobatus fins in the global shark fin trade.

Species introductions promote secondary contacts between taxa with long histories of allopatric divergence. Anthropogenic contact zones thus offer valuable contrasts to speciation studies in natural systems where past spatial isolations may have been brief or intermittent. Investigations of anthropogenic hybridization are rare for marine animals, which have high fecundity and high dispersal ability, characteristics that contrast to most terrestrial animals. Genomic studies indicate that gene flow can still occur after millions of years of divergence, as illustrated by invasive mussels and tunicates. In this context, we highlight three issues: (i) the effects of high propagule pressure and demographic asymmetries on introgression directionality, (ii) the role of hybridization in preventing introduced species spread, and (iii) the importance of postzygotic barriers in maintaining reproductive isolation. Anthropogenic contact zones offer evolutionary biologists unprecedented large scale hybridization experiments. In addition to breaking the highly effective reproductive isolating barrier of spatial segregation, they allow researchers to explore unusual demographic contexts with strong asymmetries. The outcomes are diverse, from introgression swamping to strong barriers to gene flow, and lead to local containment or widespread invasion. These outcomes should not be neglected in management policies of marine invasive species. This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers’.

Seventy-one per cent of the earth’s surface is covered by ocean which contains almost 80% of the world’s phyla – “seascape genomics” is the study of how spatial dependence and environmental features in the ocean influence the geographic structure of genomic patterns in marine organisms. The field extends from seascape genetics where the study of small numbers of neutral loci predominates, to additionally consider larger numbers of loci from throughout the genome that may be of some functional or adaptive significance and are subject to selection. Seascape genomics is conceptually similar to landscape genomics; the disciplines share theoretical underpinnings, and the genetic measures and analytical methods are often the same. However, the spatio-temporal variability of the physical ocean environment and the biological characteristics of marine organisms (e.g. large population sizes and high dispersal ability) present some characteristic challenges and opportunities for spatial population genomics studies. This chapter provides an overview of the field of seascape genomics, outlines concepts and methods to consider when conducting seascape genomics studies, and highlights future research avenues and opportunities for the application of seascape genomics to global issues affecting our marine environment.