rfishbase: exploring, manipulating and visualizing FishBase data from R

Phylogeny, body morphology, and trophic level shape intestinal traits in coral reef fishes

Trait-based approaches are increasingly used to study species assemblages and understand ecosystem functioning. The strength of these approaches lies in the appropriate choice of functional traits that relate to the functions of interest. However, trait-function relationships are often supported by weak empirical evidence.Processes related to digestion and nutrient assimilation are particularly challenging to integrate into trait-based approaches. In fishes, intestinal length is commonly used to describe these functions. Although there is broad consensus concerning the relationship between fish intestinal length and diet, evolutionary and environmental forces have shaped a diversity of intestinal morphologies that is not captured by length alone.Focusing on coral reef fishes, we investigate how evolutionary history and ecology shape intestinal morphology. Using a large dataset encompassing 142 species across 31 families collected in French Polynesia, we test how phylogeny, body morphology, and diet relate to three intestinal morphological traits: intestinal length, diameter, and surface area.We demonstrate that phylogeny, body morphology, and trophic level explain most of the interspecific variability in fish intestinal morphology. Despite the high degree of phylogenetic conservatism, taxonomically unrelated herbivorous fishes exhibit similar intestinal morphology due to adaptive convergent evolution. Furthermore, we show that stomachless, durophagous species have the widest intestines to compensate for the lack of a stomach and allow passage of relatively large undigested food particles.Rather than traditionally applied metrics of intestinal length, intestinal surface area may be the most appropriate trait to characterize intestinal morphology in functional studies.

Meta-Fish-Lib: A generalised, dynamic DNA reference library pipeline for metabarcoding of fishes

The accuracy and reliability of DNA metabarcoding analyses depend on the breadth and quality of the reference libraries that underpin them. However, there are limited options available to obtain and curate the huge volumes of sequence data that are available on public repositories such as NCBI and BOLD. Here, we provide a pipeline to download, clean and annotate mitochondrial DNA sequence data for a given list of fish species. Features of this pipeline include (a) support for multiple metabarcode markers; (b) searches on species synonyms and taxonomic name validation; (c) phylogeny assisted quality control for identification and removal of misannotated sequences; (d) automatically generated coverage reports for each new GenBank release update; and (e) citable, versioned DOIs. As an example we provide a ready-to-use curated reference library for the marine and freshwater fishes of the U.K. To augment this reference library for environmental DNA metabarcoding specifically, we generated 241 new MiFish-12S sequences for 88 U.K. marine species, and make available new primer sets useful for sequencing these. This brings the coverage of common U.K. species for the MiFish-12S fragment to 93%, opening new avenues for scaling up fish metabarcoding across wide spatial gradients. The Meta-Fish-Lib reference library and pipeline is hosted at https://github.com/genner-lab/meta-fish-lib.

Correlated evolution of fish host length and parasite spore size: a tale from myxosporeans inhabiting elasmobranchs

Myxozoa represent a diverse group of microscopic cnidarian endoparasites alternating between invertebrate and vertebrate hosts. Of the approximately 2,600 species described predominantly from teleost fish, only 1.8% have been reported from cartilaginous fishes (Elasmobranchii). As ancestral vertebrate hosts of myxozoans, elasmobranchs may have played an important role in myxozoan evolution, however, they are also some of the largest vertebrate hosts known for this group of parasites. We screened 50 elasmobranchs belonging to nine species and seven families, from various geographical areas, for myxozoan infection. We found a 22% overall prevalence of myxozoans in elasmobranchs and describe five species new to science. We investigated, for the first known time, the evolution of spore size within three phylogenetic clades, Ceratomyxa, Sphaerospora sensu stricto and Parvicapsula. We found that spores from elasmobranch-infecting myxozoans were on average 4.8× (Ceratomyxa), 2.2× (Parvicapsula clade) and 1.8× (Sphaerospora sensu stricto except polysporoplasmic Sphaerospora spp.) larger than those from teleosts. In all analysed clades, spore size was correlated with phylogenetic position. In ceratomyxids, it was further strongly positively correlated with fish body size and habitat depth, independent of cellular composition of the spores and phylogenetic position in the tree. While in macroparasites a host size-correlated increase in parasite size occurs on a large scale and is often related to improved exploitation of host resources, in microscopic parasites size ranges vary at the scale of a few micrometres, disproportionate to the available additional space in a large host. We discuss the ecological role of these changes with regard to transmission under high pressure and an invertebrate fauna that is adapted to deeper marine habitats.

Reduced Global Genetic Differentiation of Exploited Marine Fish Species

Knowledge on genetic structure is key to understand species connectivity patterns and to define the spatiotemporal scales over which conservation management plans should be designed and implemented. The distribution of genetic diversity (within and among populations) greatly influences species ability to cope and adapt to environmental changes, ultimately determining their long-term resilience to ecological disturbances. Yet, the drivers shaping connectivity and structure in marine fish populations remain elusive, as are the effects of fishing activities on genetic subdivision. To investigate these questions, we conducted a meta-analysis and compiled genetic differentiation data (FST/ΦST estimates) for more than 170 fish species from over 200 published studies globally distributed. We modeled the effects of multiple life-history traits, distance metrics, and methodological factors on observed population differentiation indices and specifically tested whether any signal arising from different exposure to fishing exploitation could be detected. Although the myriad of variables shaping genetic structure makes it challenging to isolate the influence of single drivers, results showed a significant correlation between commercial importance and genetic structure, with widespread lower population differentiation in commercially exploited species. Moreover, models indicate that variables commonly used as proxy for connectivity, such as larval pelagic duration, might be insufficient, and suggest that deep-sea species may disperse further. Overall, these results contribute to the growing body of knowledge on marine genetic connectivity and suggest a potential effect of commercial fisheries on the homogenization of genetic diversity, highlighting the need for additional research focused on dispersal ecology to ensure long-term sustainability of exploited marine species.

New scale analyses reveal centenarian African coelacanths

The extant coelacanth was discovered in 1938;¹ its biology and ecology remain poorly known due to the low number of specimens collected. Only two previous studies^1,2 have attempted to determine its age and growth. They suggested a maximum lifespan of 20 years, placing the coelacanth among the fastest growing marine fish. These findings are at odds with the coelacanth's other known biological features including low oxygen-extraction capacity, slow metabolism, ovoviviparity, and low fecundity, typical of fish with slow life histories and slow growth. In this study, we use polarized light microscopy to study growth on scales based on a large sample of 27 specimens. Our results demonstrate for the first time nearly imperceptible annual calcified structures (circuli) on the scales and show that maximal age of the coelacanth was underestimated by a factor of 5. Our validation method suggests that circuli are indeed annual, thus supporting that the coelacanth is among the longest-living fish species, its lifespan being probably around 100 years. Like deep-sea sharks with a reduced metabolism, the coelacanth has among the slowest growth for its size. Further reappraisals of age at first sexual maturity (in the range 40 to 69 years old) and gestation duration (of around 5 years) show that the living coelacanth has one of the slowest life histories of all marine fish and possibly the longest gestation. As long-lived species with slow life histories are extremely vulnerable to natural and anthropogenic perturbations, our results suggest that coelacanths may be more threatened than previously considered.

Evidence for general size-by-habitat rules in actinopterygian fishes across nine scales of observation

Identifying environmental predictors of phenotype is fundamentally important to many ecological questions, from revealing broadscale ecological processes to predicting extinction risk. However, establishing robust environment—phenotype relationships is challenging, as powerful case studies require diverse clades which repeatedly undergo environmental transitions at multiple taxonomic scales. Actinopterygian fishes, with 32,000+ species, fulfil these criteria for the fundamental habitat divisions in water. With four datasets of body size (ranging 10,905–27,226 species), I reveal highly consistent size‐by‐habitat‐use patterns across nine scales of observation. Taxa in marine, marine‐brackish, euryhaline and freshwater‐brackish habitats possess larger mean sizes than freshwater relatives, and the largest mean sizes consistently emerge within marine‐brackish and euryhaline taxa. These findings align with the predictions of seven mechanisms thought to drive larger size by promoting additional trophic levels. However, mismatches between size and trophic‐level patterns highlight a role for additional mechanisms, and support for viable candidates is examined in 3439 comparisons.

Sexual Dichromatism Is Decoupled from Diversification over Deep Time in Fishes

AbstractSexually selected traits have long been thought to drive diversification, but support for this hypothesis has been persistently controversial. In fishes, sexually dimorphic coloration is associated with assortative mating and speciation among closely related species, as shown in classic studies. However, it is unclear whether these results can generalize to explain diversity patterns across ray-finned fishes, which contain the majority of vertebrate species and 96% of fishes. Here, we use phylogenetic approaches to test for an association between sexual dichromatism and diversification rates (speciation minus extinction) in ray-finned fishes. We assembled dichromatism data for 10,898 species, a data set of unprecedented size. We found no difference in diversification rates between monochromatic and dichromatic species when including all ray-finned fishes. However, at lower phylogenetic scales (within orders and families), some intermediate-sized clades did show an effect of dichromatism on diversification. Surprisingly, dichromatism could significantly increase or decrease diversification rates. Moreover, we found no effect in many of the clades initially used to link dichromatism to speciation in fishes (e.g., cichlids) or an effect only at shallow scales (within subclades). Overall, we show how the effects of dichromatism on diversification are highly variable in direction and restricted to certain clades and phylogenetic scales.

The deep sea is a hot spot of fish body shape evolution

Deep-sea fishes have long captured our imagination with striking adaptations to life in the mysterious abyss, raising the possibility that this cold, dark ocean region may be a key hub for physiological and functional diversification. We explore this idea through an analysis of body shape evolution across ocean depth zones in over 3000 species of marine teleost fishes. We find that the deep ocean contains twice the body shape disparity of shallow waters, driven by elevated rates of evolution in traits associated with locomotion. Deep-sea fishes display more frequent adoption of forms suited to slow and periodic swimming, whereas shallow living species are concentrated around shapes conferring strong, sustained swimming capacity and manoeuvrability. Our results support long-standing impressions of the deep sea as an evolutionary hotspot for fish body shape evolution and highlight that factors like habitat complexity and ecological interactions are potential drivers of this adaptive diversification.

The fossil record of extant elasmobranchs

Sharks and their relatives (Elasmobranchii) are highly threatened with extinction due to various anthropogenic pressures. The abundant fossil record of fossil taxa has allowed the tracing of the evolutionary history of modern elasmobranchs to at least 250 MYA; nonetheless, exactly how far back the fossil record of living taxa goes has never been collectively surveyed. In this study, the authors assess the representation and extent of the fossil record of elasmobranchs currently living in our oceans by collecting their oldest records and quantifying first appearance dates at different taxonomic levels (i.e., orders, families, genera and species), ecological traits (e.g., body size, habitat and feeding mechanism) and extinction risks (i.e., threatened, not threatened and data deficient). The results of this study confirm the robust representation of higher taxonomic ranks, with all orders, most of the families and over half of the extant genera having a fossil record. Further, they reveal that 10% of the current global species diversity is represented in the geological past. Sharks are better represented and extend deeper in time than rays and skates. While the fossil record of extant genera (e.g., the six gill sharks, Hexanchus) goes as far back as c. 190 MYA, the fossil record of extant species (e.g., the sand shark, Carcharias taurus Rafinesque 1810) extends c. 66 MYA. Although no significant differences were found in the extent of the fossil record between ecological traits, it was found that the currently threatened species have a significantly older fossil record than the not threatened species. This study demonstrate that the fossil record of extant elasmobranchs extends deep into the geologic time, especially in the case of threatened sharks. As such, the elasmobranch geological history has great potential to advance the understanding of how species currently facing extinction have responded to different stressors in the past, thereby providing a deep-time perspective to conservation.

Delineating reef fish trophic guilds with global gut content data synthesis and phylogeny

Understanding species' roles in food webs requires an accurate assessment of their trophic niche. However, it is challenging to delineate potential trophic interactions across an ecosystem, and a paucity of empirical information often leads to inconsistent definitions of trophic guilds based on expert opinion, especially when applied to hyperdiverse ecosystems. Using coral reef fishes as a model group, we show that experts disagree on the assignment of broad trophic guilds for more than 20% of species, which hampers comparability across studies. Here, we propose a quantitative, unbiased, and reproducible approach to define trophic guilds and apply recent advances in machine learning to predict probabilities of pairwise trophic interactions with high accuracy. We synthesize data from community-wide gut content analyses of tropical coral reef fishes worldwide, resulting in diet information from 13,961 individuals belonging to 615 reef fish. We then use network analysis to identify 8 trophic guilds and Bayesian phylogenetic modeling to show that trophic guilds can be predicted based on phylogeny and maximum body size. Finally, we use machine learning to test whether pairwise trophic interactions can be predicted with accuracy. Our models achieved a misclassification error of less than 5%, indicating that our approach results in a quantitative and reproducible trophic categorization scheme, as well as high-resolution probabilities of trophic interactions. By applying our framework to the most diverse vertebrate consumer group, we show that it can be applied to other organismal groups to advance reproducibility in trait-based ecology. Our work thus provides a viable approach to account for the complexity of predator-prey interactions in highly diverse ecosystems.

Clustered versus catastrophic global vertebrate declines

Recent analyses have reported catastrophic global declines in vertebrate populations^1,2. However, the distillation of many trends into a global mean index obscures the variation that can inform conservation measures and can be sensitive to analytical decisions. For example, previous analyses have estimated a mean vertebrate decline of more than 50% since 1970 (Living Planet Index²). Here we show, however, that this estimate is driven by less than 3% of vertebrate populations; if these extremely declining populations are excluded, the global trend switches to an increase. The sensitivity of global mean trends to outliers suggests that more informative indices are needed. We propose an alternative approach, which identifies clusters of extreme decline (or increase) that differ statistically from the majority of population trends. We show that, of taxonomic-geographic systems in the Living Planet Index, 16 systems contain clusters of extreme decline (comprising around 1% of populations; these extreme declines occur disproportionately in larger animals) and 7 contain extreme increases (around 0.4% of populations). The remaining 98.6% of populations across all systems showed no mean global trend. However, when analysed separately, three systems were declining strongly with high certainty (all in the Indo-Pacific region) and seven were declining strongly but with less certainty (mostly reptile and amphibian groups). Accounting for extreme clusters fundamentally alters the interpretation of global vertebrate trends and should be used to help to prioritize conservation efforts.

PeskAAS: A near-real-time, open-source monitoring and analytics system for small-scale fisheries

Small-scale fisheries are responsible for landing half of the world’s fish catch, yet there are very sparse data on these fishing activities and associated fisheries production in time and space. Fisheries-dependent data underpin scientific guidance of management and conservation of fisheries systems, but it is inherently difficult to generate robust and comprehensive data for small-scale fisheries, particularly given their dispersed and diverse nature. In tackling this challenge, we use open source software components including the Shiny R package to build PeskAAS; an adaptable and scalable digital application that enables the collation, classification, analysis and visualisation of small-scale fisheries catch and effort data. We piloted and refined this system in Timor-Leste; a small island developing nation. The features that make PeskAAS fit for purpose are that it is: (i) fully open-source and free to use (ii) component-based, flexible and able to integrate vessel tracking data with catch records; (iii) able to perform spatial and temporal filtering of fishing productivity by fishing method and habitat; (iv) integrated with species-specific length-weight parameters from FishBase; (v) controlled through a click-button dashboard, that was co-designed with fisheries scientists and government managers, that enables easy to read data summaries and interpretation of context-specific fisheries data. With limited training and code adaptation, the PeskAAS workflow has been used as a framework on which to build and adapt systematic, standardised data collection for small-scale fisheries in other contexts. Automated analytics of these data can provide fishers, managers and researchers with insights into a fisher’s experience of fishing efforts, fisheries status, catch rates, economic efficiency and geographic preferences and limits that can potentially guide management and livelihood investments.

Linking dimensions of data on global marine animal diversity

Recent decades have seen an explosion in the amount of data available on all aspects of biodiversity, which has led to data-driven approaches to understand how and why diversity varies in time and space. Global repositories facilitate access to various classes of species-level data including biogeography, genetics and conservation status, which are in turn required to study different dimensions of diversity. Ensuring that these different data sources are interoperable is a challenge as we aim to create synthetic data products to monitor the state of the world's biodiversity. One way to approach this is to link data of different classes, and to inventory the availability of data across multiple sources. Here, we use a comprehensive list of more than 200 000 marine animal species, and quantify the availability of data on geographical occurrences, genetic sequences, conservation assessments and DNA barcodes across all phyla and broad functional groups. This reveals a very uneven picture: 44% of species are represented by no record other than their taxonomy, but some species are rich in data. Although these data-rich species are concentrated into a few taxonomic and functional groups, especially vertebrates, data are spread widely across marine animals, with members of all 32 phyla represented in at least one database. By highlighting gaps in current knowledge, our census of marine diversity data helps to prioritize future data collection activities, as well as emphasizing the importance of ongoing sustained observations and archiving of existing data into global repositories. This article is part of the theme issue 'Integrative research perspectives on marine conservation'.

Individual back-calculated size-at-age based on otoliths from Pacific coral reef fish species

Somatic growth is a critical biological trait for organismal, population, and ecosystem-level processes. Due to its direct link with energetic demands, growth also represents an important parameter to estimate energy and nutrient fluxes. For marine fishes, growth rate information is most frequently derived from sagittal otoliths, and most of the available data stems from studies on temperate species that are targeted by commercial fisheries. Although the analysis of otoliths is a powerful tool to estimate individual growth, the time-consuming nature of otolith processing is one barrier for collection of comprehensive datasets across multiple species. This is especially true for coral reef fishes, which are extremely diverse. Here, we provide back-calculated size-at-age estimates (including measures of uncertainty) based on sagittal otoliths from 710 individuals belonging to 45 coral reef fish species from French Polynesia. In addition, we provide Von Bertalanffy growth parameters which are useful to predict community level biomass production.

Climate drives the geography of marine consumption by changing predator communities

The global distribution of primary production and consumption by humans (fisheries) is well-documented, but we have no map linking the central ecological process of consumption within food webs to temperature and other ecological drivers. Using standardized assays that span 105° of latitude on four continents, we show that rates of bait consumption by generalist predators in shallow marine ecosystems are tightly linked to both temperature and the composition of consumer assemblages. Unexpectedly, rates of consumption peaked at midlatitudes (25 to 35°) in both Northern and Southern Hemispheres across both seagrass and unvegetated sediment habitats. This pattern contrasts with terrestrial systems, where biotic interactions reportedly weaken away from the equator, but it parallels an emerging pattern of a subtropical peak in marine biodiversity. The higher consumption at midlatitudes was closely related to the type of consumers present, which explained rates of consumption better than consumer density, biomass, species diversity, or habitat. Indeed, the apparent effect of temperature on consumption was mostly driven by temperature-associated turnover in consumer community composition. Our findings reinforce the key influence of climate warming on altered species composition and highlight its implications for the functioning of Earth's ecosystems.

The Effects of Ecological Traits on the Rate of Molecular Evolution in Ray-Finned Fishes: A Multivariable Approach

Myriad environmental and biological traits have been investigated for their roles in influencing the rate of molecular evolution across various taxonomic groups. However, most studies have focused on a single trait, while controlling for additional factors in an informal way, generally by excluding taxa. This study utilized a dataset of cytochrome c oxidase subunit I (COI) barcode sequences from over 7000 ray-finned fish species to test the effects of 27 traits on molecular evolutionary rates. Environmental traits such as temperature were considered, as were traits associated with effective population size including body size and age at maturity. It was hypothesized that these traits would demonstrate significant correlations with substitution rate in a multivariable analysis due to their associations with mutation and fixation rates, respectively. A bioinformatics pipeline was developed to assemble and analyze sequence data retrieved from the Barcode of Life Data System (BOLD) and trait data obtained from FishBase. For use in phylogenetic regression analyses, a maximum likelihood tree was constructed from the COI sequence data using a multi-gene backbone constraint tree covering 71% of the species. A variable selection method that included both single- and multivariable analyses was used to identify traits that contribute to rate heterogeneity estimated from different codon positions. Our analyses revealed that molecular rates associated most significantly with latitude, body size, and habitat type. Overall, this study presents a novel and systematic approach for integrative data assembly and variable selection methodology in a phylogenetic framework.

Foraging habitat determines predator-prey size relationships in marine fishes

Predator-prey size (PPS) relationships are determined by predator behaviour, with the likelihood of prey being eaten dependent on their size relative to that of the consumer. Published PPS relationships for 30 pelagic or benthic marine fish species were analysed using quantile regression to determine how median, lower and upper prey sizes varied with predator size and habitat. Habitat effects on predator foraging activity/mode, morphology, growth and natural mortality are quantified and the effects on PPS relationships explored. Pelagic species are more active, more likely to move by caudal fin propulsion and grow more rapidly but have higher mortality rates than benthic species, where the need for greater manoeuvrability when foraging in more physically complex habitats favours ambush predators using pectoral fin propulsion. Prey size increased with predator size in most species, but pelagic species ate relatively smaller prey than benthic predators. As pelagic predators grew, lower prey size limits changed little, and prey size range increased but median relative prey size declined, whereas the lower limit increased and median relative prey size was constant or increased in benthic species.

Do key innovations unlock diversification? A case-study on the morphological and ecological impact of pharyngognathy in acanthomorph fishes

Key innovations may allow lineages access to new resources and facilitate the invasion of new adaptive zones, potentially influencing diversification patterns. Many studies have focused on the impact of key innovations on speciation rates, but far less is known about how they influence phenotypic rates and patterns of ecomorphological diversification. We use the repeated evolution of pharyngognathy within acanthomorph fishes, a commonly cited key innovation, as a case study to explore the predictions of key innovation theory. Specifically, we investigate whether transitions to pharyngognathy led to shifts in the rate of phenotypic evolution, as well as shifts and/or expansion in the occupation of morphological and dietary space, using a dataset of 8 morphological traits measured across 3,853 species of Acanthomorpha. Analyzing the 6 evolutionarily independent pharyngognathous clades together, we found no evidence to support pharyngognathy as a key innovation; however, comparisons between individual pharyngognathous lineages and their sister clades did reveal some consistent patterns. In morphospace, most pharyngognathous clades cluster in areas that correspond to deeper-bodied morphologies relative to their sister clades, while occupying greater areas in dietary space that reflects a more diversified diet. Additionally, both Cichlidae and Labridae exhibited higher univariate rates of phenotypic evolution compared with their closest relatives. However, few of these results were exceptional relative to our null models. Our results suggest that transitions to pharyngognathy may only be advantageous when combined with additional ecological or intrinsic factors, illustrating the importance of accounting for lineage-specific effects when testing key innovation hypotheses. Moreover, the challenges we experienced formulating informative comparisons, despite the ideal evolutionary scenario of multiple independent evolutionary origins of pharyngognathous clades, illustrates the complexities involved in quantifying the impact of key innovations. Given the issues of lineage specific effects and rate heterogeneity at macroevolutionary scales we observed, we suggest a reassessment of the expected impacts of key innovations may be warranted.

Occupancy-derived thermal affinities reflect known physiological thermal limits of marine species

Predicting how species will respond to increased environmental temperatures is key to understanding the ecological consequences of global change. The physiological tolerances of a species define its thermal limits, while its thermal affinity is a summary of the environmental temperatures at the localities at which it actually occurs. Experimentally derived thermal limits are known to be related to observed latitudinal ranges in marine species, but accurate range maps from which to derive latitudinal ranges are lacking for many marine species. An alternative approach is to combine widely available data on global occurrences with gridded global temperature datasets to derive measures of species-level "thermal affinity"-that is, measures of the central tendency, variation, and upper and lower bounds of the environmental temperatures at the locations at which a species has been recorded to occur. Here, we test the extent to which such occupancy-derived measures of thermal affinity are related to the known thermal limits of marine species using data on 533 marine species from 24 taxonomic classes and with experimentally derived critical upper temperatures spanning 2-44.5°C. We show that thermal affinity estimates are consistently and positively related to the physiological tolerances of marine species, despite gaps and biases in the source data. Our method allows thermal affinity measures to be rapidly and repeatably estimated for many thousands more marine species, substantially expanding the potential to assess vulnerability of marine communities to warming seas.

Quantifying the primary biotic resource use by fisheries: A global assessment

In this paper, the specific primary production required (SPPR expressed as kg-NPP/kg-fish in wet weight) of more than 1700 marine species were calculated directly from 96 published food web models using the newly developed SPPR calculation framework. The relationship between SPPR and other ecological factors were then statistically analyzed. Among- and within-species variability of SPPR were found to be both explained by trophic level (TL), suggesting similar mechanisms underpinning both sources of variability. Among species, we found that harvesting species at higher mean trophic levels (MTL) increases the mean SPPR by a factor of 19 per 1 unit increase in MTL. Based on our empirical relationship, the mean SPPR of more than 9000 marine species were predicted and subsequently used to assess the primary production required (PPR) to support fisheries in five major fishing countries in Europe. The results indicated that conventional approach to estimating PPR, which neglects food web ecology, can underestimate PPR by up to a factor of 5. Within species, we found that harvesting populations occupying a higher TL leads to a higher SPPR. For example, the SPPR of Atlantic cod in the Celtic Sea (TL = 4.75) was 5 times higher than in the Gilbert Bay (TL = 3.3). Our results, which are based on large amounts of field data, highlight the importance of properly accounting for ecological factors during the impact assessment of fisheries.

Trophic innovations fuel reef fish diversification

Reef fishes are an exceptionally speciose vertebrate assemblage, yet the main drivers of their diversification remain unclear. It has been suggested that Miocene reef rearrangements promoted opportunities for lineage diversification, however, the specific mechanisms are not well understood. Here, we assemble near-complete reef fish phylogenies to assess the importance of ecological and geographical factors in explaining lineage origination patterns. We reveal that reef fish diversification is strongly associated with species' trophic identity and body size. Large-bodied herbivorous fishes outpace all other trophic groups in recent diversification rates, a pattern that is consistent through time. Additionally, we show that omnivory acts as an intermediate evolutionary step between higher and lower trophic levels, while planktivory represents a common transition destination. Overall, these results suggest that Miocene changes in reef configurations were likely driven by, and subsequently promoted, trophic innovations. This highlights trophic evolution as a key element in enhancing reef fish diversification.

A database of freshwater fish species of the Amazon Basin

The Amazon Basin is an unquestionable biodiversity hotspot, containing the highest freshwater biodiversity on earth and facing off a recent increase in anthropogenic threats. The current knowledge on the spatial distribution of the freshwater fish species is greatly deficient in this basin, preventing a comprehensive understanding of this hyper-diverse ecosystem as a whole. Filling this gap was the priority of a transnational collaborative project, i.e. the AmazonFish project - https://www.amazon-fish.com/. Relying on the outputs of this project, we provide the most complete fish species distribution records covering the whole Amazon drainage. The database, including 2,406 validated freshwater native fish species, 232,936 georeferenced records, results from an extensive survey of species distribution including 590 different sources (e.g. published articles, grey literature, online biodiversity databases and scientific collections from museums and universities worldwide) and field expeditions conducted during the project. This database, delivered at both georeferenced localities (21,500 localities) and sub-drainages grains (144 units), represents a highly valuable source of information for further studies on freshwater fish biodiversity, biogeography and conservation.

Global determinants of freshwater and marine fish genetic diversity

Genetic diversity is estimated to be declining faster than species diversity under escalating threats, but its spatial distribution remains poorly documented at the global scale. Theory predicts that similar processes should foster congruent spatial patterns of genetic and species diversity, but empirical studies are scarce. Using a mined database of 50,588 georeferenced mitochondrial DNA barcode sequences (COI) for 3,815 marine and 1,611 freshwater fish species respectively, we examined the correlation between genetic diversity and species diversity and their global distributions in relation to climate and geography. Genetic diversity showed a clear spatial organisation, but a weak association with species diversity for both marine and freshwater species. We found a predominantly positive relationship between genetic diversity and sea surface temperature for marine species. Genetic diversity of freshwater species varied primarily across the regional basins and was negatively correlated with average river slope. The detection of genetic diversity patterns suggests that conservation measures should consider mismatching spatial signals across multiple facets of biodiversity.

Biogeographic patterns of genetic diversity are poorly documented, especially for fish species. Here the authors show that (mitochondrial) genetic diversity has global spatial organization patterns with different environmental drivers for marine and freshwater fishes, where genetic diversity is only partly congruent with species richness.

Taxonomy-based differences in feeding guilds of fish

It has been taken for granted that feeding guilds and behavior in animals are linked to the taxonomic relatedness of species, but empirical evidence supporting such relationship is virtually missing. To examine the importance of taxonomy on trophic ecology, I here present the first well-resolved dietary taxonomy analysis based on feeding guilds (predation, herbivory, and filtering) among families and genera within the fish order Perciformes. Taxonomic relatedness in feeding did not vary with ecosystem dimension (marine vs. freshwater). Although predation dominates among Perciformes fishes, this study shows that in most cases taxonomic units (family or genus) are composed by species with several feeding guilds. Related species are more similar in feeding compared with species that are taxonomically more distant, demonstrating that there is a greater variation of feeding guilds within families than genera. Thus, there is no consistency in feeding guilds between family- and genus-level taxonomy. This study provides empirical support for the notion that genera are more informative than families, underlining that family-level taxonomy should be avoided to infer feeding habits of fish species at finer taxonomic resolution. Thus, the choice of taxonomic resolution (family or genus level) in ecological studies is key to avoid information loss and misleading results. I conclude that high-rank taxonomic units (i.e., above the generic level) are not appropriate to test research hypotheses about the feeding of fish.

Population variability under stressors is dependent on body mass growth and asymptotic body size

The recruitment and biomass of a fish stock are influenced by their environmental conditions and anthropogenic pressures such as fishing. The variability in the environment often translates into fluctuations in recruitment, which then propagate throughout the stock biomass. In order to manage fish stocks sustainably, it is necessary to understand their dynamics. Here, we systematically explore the dynamics and sensitivity of fish stock recruitment and biomass to environmental noise. Using an age-structured and trait-based model, we explore random noise (white noise) and autocorrelated noise (red noise) in combination with low to high levels of harvesting. We determine the vital rates of stocks covering a wide range of possible body mass (size) growth rates and asymptotic size parameter combinations. Our study indicates that the variability of stock recruitment and biomass are probably correlated with the stock's asymptotic size and growth rate. We find that fast-growing and large-sized fish stocks are likely to be less vulnerable to disturbances than slow-growing and small-sized fish stocks. We show how the natural variability in fish stocks is amplified by fishing, not just for one stock but for a broad range of fish life histories.

Migratory lineages rapidly evolve larger body sizes than non-migratory relatives in ray-finned fishes

Migratory animals respond to environmental heterogeneity by predictably moving long distances in their lifetime. Migration has evolved repeatedly in animals, and many adaptations are found across the tree of life that increase migration efficiency. Life-history theory predicts that migratory species should evolve a larger body size than non-migratory species, and some empirical studies have shown this pattern. A recent study analysed the evolution of body size between diadromous and non-diadromous shads, herrings, anchovies and allies, finding that species evolved larger body sizes when adapting to a diadromous lifestyle. It remains unknown whether different fish clades adapt to migration similarly. We used an adaptive landscape framework to explore body size evolution for over 4500 migratory and non-migratory species of ray-finned fishes. By fitting models of macroevolution, we show that migratory species are evolving towards a body size that is larger than non-migratory species. Furthermore, we find that migratory lineages evolve towards their optimal body size more rapidly than non-migratory lineages, indicating body size is a key adaption for migratory fishes. Our results show, for the first time, that the largest vertebrate radiation on the planet exhibited strong evolutionary determinism when adapting to a migratory lifestyle.

Homogenization of freshwater lakes: Recent compositional shifts in fish communities are explained by gamefish movement and not climate change

Globally, lake fish communities are being subjected to a range of scale-dependent anthropogenic pressures, from climate change to eutrophication, and from overexploitation to species introductions. As a consequence, the composition of these communities is being reshuffled, in most cases leading to a surge in taxonomic similarity at the regional scale termed homogenization. The drivers of homogenization remain unclear, which may be a reflection of interactions between various environmental changes. In this study, we investigate two potential drivers of the recent changes in the composition of freshwater fish communities: recreational fishing and climate change. Our results, derived from 524 lakes of Ontario, Canada sampled in two periods (1965-1982 and 2008-2012), demonstrate that the main contributors to homogenization are the dispersal of gamefish species, most of which are large predators. Alternative explanations relating to lake habitat (e.g., area, phosphorus) or variations in climate have limited explanatory power. Our analysis suggests that human-assisted migration is the primary driver of the observed compositional shifts, homogenizing freshwater fish community among Ontario lakes and generating food webs dominated by gamefish species.

Where are all the moms? External fertilization predicts the rise of male parental care in bony fishes

Parental care shows remarkable variation across the animal kingdom, but while maternal and biparental care are common in terrestrial organisms, male-only care dominates in aquatic species that provide care. Using the most complete phylogenetic tree of bony fishes to date, we test whether the opportunity for external fertilization in aquatic environments can explain the more frequent evolution of male care in this group. We show that paternal care has evolved at least 30 times independently in fish and is found exclusively in externally fertilizing species. Male care is positively associated with pair spawning, suggesting that confidence in paternity is an important determinant of the evolution of care. Crucially, while female care is constrained by other forms of reproductive investment, male care occurs more frequently when females invest heavily in gamete production. Our results suggest that moving control of fertilization outside of the female reproductive tract raises male confidence in parentage and increases the potential for paternal care, highlighting that in an aquatic environment in which fertilization is external, paternal care is an effective reproductive strategy.

A phylogenomic framework for pelagiarian fishes (Acanthomorpha: Percomorpha) highlights mosaic radiation in the open ocean

The fish clade Pelagiaria, which includes tunas as its most famous members, evolved remarkable morphological and ecological variety in a setting not generally considered conducive to diversification: the open ocean. Relationships within Pelagiaria have proven elusive due to short internodes subtending major lineages suggestive of rapid early divergences. Using a novel sequence dataset of over 1000 ultraconserved DNA elements (UCEs) for 94 of the 286 species of Pelagiaria (more than 70% of genera), we provide a time-calibrated phylogeny for this widely distributed clade. Some inferred relationships have clear precedents (e.g. the monophyly of 'core' Stromateoidei, and a clade comprising 'Gempylidae' and Trichiuridae), but others are unexpected despite strong support (e.g. Chiasmodontidae + Tetragonurus). Relaxed molecular clock analysis using node-based fossil calibrations estimates a latest Cretaceous origin for Pelagiaria, with crown-group families restricted to the Cenozoic. Estimated mean speciation rates decline from the origin of the group in the latest Cretaceous, although credible intervals for root and tip rates are broad and overlap in most cases, and there is higher-than-expected partitioning of body shape diversity (measured as fineness ratio) between clades concentrated during the Palaeocene-Eocene. By contrast, more direct measures of ecology show either no substantial deviation from a null model of diversification (diet) or patterns consistent with evolutionary constraint or high rates of recent change (depth habitat). Collectively, these results indicate a mosaic model of diversification. Pelagiarians show high morphological disparity and modest species richness compared to better-studied fish radiations in contrasting environments. However, this pattern is also apparent in other clades in open-ocean or deep-sea habitats, and suggests that comparative study of such groups might provide a more inclusive model of the evolution of diversity in fishes.

Biological and environmental drivers of trophic ecology in marine fishes - a global perspective

Dietary niche width and trophic position are key functional traits describing a consumer’s trophic ecology and the role it plays in a community. However, our understanding of the environmental and biological drivers of both traits is predominantly derived from theory or geographically restricted studies and lacks a broad empirical evaluation. We calculated the dietary niche width and trophic position of 2,938 marine fishes and examined the relationship of both traits with species’ maximum length and geographic range, in addition to species richness, productivity, seasonality and water temperature within their geographic range. We used Generalized Additive Models to assess these relationships across seven distinct marine habitat types. Fishes in reef associated habitats typically had a smaller dietary niche width and foraged at a lower trophic position than those in pelagic or demersal regions. Species richness was negatively related to dietary niche width in each habitat. Species range and maximum length both displayed positive associations with dietary niche width. Trophic position was primarily related to species maximum length but also displayed a non-linear relationship with dietary niche width, whereby species of an intermediate trophic position (3–4) had a higher dietary niche width than obligate herbivores or piscivores. Our results indicate that trophic ecology of fishes is driven by several interlinked factors. Although size is a strong predictor of trophic position and the diversity of preys a species can consume, dietary niche width of fishes is also related to prey and competitor richness suggesting that, at a local level, consumer trophic ecology is determined by a trade-off between environmental drivers and biological traits.

The Evolution of Color Pattern in Butterflyfishes (Chaetodontidae)

Coral reef fishes constitute one of the most diverse assemblages of vertebrates on the planet. Color patterns are known to serve a number of functions including intra- and inter-specific signaling, camouflage, mimicry, and defense. However, the relative importance of these and other factors in shaping color pattern evolution is poorly understood. Here we conduct a comparative phylogenetic analysis of color pattern evolution in the butterflyfishes (Chaetodontidae). Using recently developed tools for quantifying color pattern geometry as well as machine learning approaches, we investigate the tempo of evolution of color pattern elements and test whether ecological variables relating to defense, depth, and social behavior predict color pattern evolution. Butterflyfishes exhibit high diversity in measures of chromatic conspicuousness and the degrees of fine versus gross scale color patterning. Surprisingly, most diversity in color pattern was not predicted by any of the measures of ecology in our study, although we did find a significant but weak relationship between the level of fine scale patterning and some aspects of defensive morphology. We find that the tempo of color pattern diversification in butterflyfishes has increased toward the present and suggest that rapid evolution, presumably in response to evolutionary pressures surrounding speciation and lineage divergence, has effectively decoupled color pattern geometry from some aspects of ecology. Machine learning classification of color pattern appears to rely on a set of features that are weakly correlated with current color pattern geometry descriptors, but that may be better suited for the detection of discrete components of color pattern. A key challenge for future studies lies in determining whether rapid evolution has generally decoupled color patterns from ecology, or whether convergence in function produces convergence in color pattern at phylogenetic scales.

Data for Fish Stock Assessment Obtained from the CMSY Algorithm for all Global FAO Datasets

Assessing the state of fish stocks requires the determination of descriptors. They correspond to the absolute and relative (to the carrying capacity of the habitat) fish biomasses in the ecosystem, and the absolute and relative (to the intrinsic growth rate of the population) fishing mortality resulting from catches. This allows, among other things, to compare the catch with the maximum sustainability yield. Some fish stocks are well described and monitored, but for many data-limited stocks, catch time series are remaining the only source of data. Recently, an algorithm (CMSY) has been proposed, allowing an estimation of stock assessment variables from catch and resilience. In this paper, we provide stock reference points for all global fisheries reported by Food and Agriculture Organization (FAO) major fishing area for almost 5000 fish stocks. These data come from the CMSY algorithm for 42% of the stock (75% of the global reported fish catch) and are estimated by aggregated values for the remaining 58%.

Comparative Functional and Phylogenomic Analyses of Host Association in the Remoras (Echeneidae), a Family of Hitchhiking Fishes

The family Echeneidae consists of eight species of marine fishes that hitchhike by adhering to a wide variety of vertebrate hosts via a sucking disc. While several studies have focused on the interrelationships of the echeneids and the adhesion performance of a single species, no clear phylogenetic hypothesis has emerged and the morphological basis of adhesion remains largely unknown. We first set out to resolve the interrelationships of the Echeneidae by taking a phylogenomic approach using ultraconserved elements. Then, within this framework, we characterized disc morphology through µ-CT analysis, evaluated host specificity through an analysis of host phylogenetic distance, and determined which axes of disc morphological variation are associated with host diversity, skin surface properties, mean pairwise phylogenetic distance (MPD obs.), and swimming regime. We recovered an extremely well-supported topology, found that the specificity of host choice is more variable in a pelagic group and less variable in a reef-generalist group than previously proposed, and that axes of disc morphospace are best explained by models that include host skin surface roughness, host MPD obs., and maximum host Reynolds number. This suggests that ecomorphological diversification was driven by the selection pressures of host skin surface roughness, host specialization, and hydrodynamic regime.

Impacts of historical warming on marine fisheries production

Climate change is altering habitats for marine fishes and invertebrates, but the net effect of these changes on potential food production is unknown. We used temperature-dependent population models to measure the influence of warming on the productivity of 235 populations of 124 species in 38 ecoregions. Some populations responded significantly positively (n = 9 populations) and others responded significantly negatively (n = 19 populations) to warming, with the direction and magnitude of the response explained by ecoregion, taxonomy, life history, and exploitation history. Hindcasts indicate that the maximum sustainable yield of the evaluated populations decreased by 4.1% from 1930 to 2010, with five ecoregions experiencing losses of 15 to 35%. Outcomes of fisheries management—including long-term food provisioning—will be improved by accounting for changing productivity in a warmer ocean.

Susceptibility of European freshwater fish to climate change: Species profiling based on life-history and environmental characteristics

Climate change is expected to strongly affect freshwater fish communities. Combined with other anthropogenic drivers, the impacts may alter species spatio-temporal distributions and contribute to population declines and local extinctions. To provide timely management and conservation of fishes, it is relevant to identify species that will be most impacted by climate change and those that will be resilient. Species traits are considered a promising source of information on characteristics that influence resilience to various environmental conditions and impacts. To this end, we collated life-history traits and climatic niches of 443 European freshwater fish species and compared those identified as susceptible to climate change to those that are considered to be resilient. Significant differences were observed between the two groups in their distribution, life history, and climatic niche, with climate-change-susceptible species being distributed within the Mediterranean region, and being characterized by greater threat levels, lesser commercial relevance, lower vulnerability to fishing, smaller body and range size, and warmer thermal envelopes. Based on our results, we establish a list of species of highest priority for further research and monitoring regarding climate-change susceptibility within Europe. The presented approach represents a promising tool to efficiently assess large groups of species regarding their susceptibility to climate change and other threats, and to identify research and management priorities.

Taxonomically constrained reporting framework limits biodiversity data for aquarium fish imports to Australia

Context Biological resource use represents the most common direct threat to biodiversity. Despite this, there is a paucity of comprehensive and overarching data relating to the biological resource use. The global aquarium trade encompasses millions of individual live fishes representing thousands of marine and freshwater species traded on an annual basis. The lack of specific data systems for recording information where fish are exported or imported has resulted in limited accessible trade data. An evaluation of the data-reporting frameworks presently employed by countries engaged in the aquarium trade is warranted to better understand the means by which comprehensive data on the aquarium trade can be made more accessible. Aims This study examines the data-reporting framework of The Australian Government Department of Agriculture and Water Resources (DAWR) used to collate aquarium fish import data, and its capacity to inform on the aquarium trade biodiversity imported to Australia. Methods Aquarium import records from 2010–16 were provided by DAWR and used to determine the quantity of individual fishes and consignments imported to Australia. The potential biodiversity of imports was determined from the Australian Government’s List of Permitted Live Freshwater/Marine Fish Suitable for Import 2018 (Number 69, F2017C00079), the legislative document identifying species permitted import to Australia for the aquarium trade. Species permitted import were cross-referenced with the International Union for Conservation of Nature (IUCN) Red List to address whether the Australian aquarium trade is importing threatened species. Key results A total of 10320 consignments encompassing more than 78.6 million aquarium fishes were imported to Australia between 2010 and 2016. A total of 4628 species of fishes were permitted import to Australia for the aquarium trade with 73 of the marine species (2.0%) and 81 of the freshwater species (7.5%) found to be threatened with some degree of extinction risk. The data-reporting framework for aquarium fish imports offered limited capacity to taxonomically differentiate imports and only 12.5% of all aquarium fishes imported could be identified to species. Conclusions The aquarium fish import records provided by DAWR had limited taxonomic resolution and, consequently, limited capacity to contribute to an improved understanding of the biodiversity imported to Australia for the aquarium fish trade. While more detailed information is available than is presently collated by DAWR, the availability of this information is constrained by the laws around protected information and the resources available to DAWR. Implications Accessible, detailed information on aquarium fish imports is necessary to support comprehensive research capable of addressing threats to biodiversity loss from the aquarium trade. To this end, the means by which Australian aquarium import data can be reported at greater taxonomic resolution under the existing legislative and resource restraints should be explored further.

Creating functional groups of marine fish from categorical traits

Background

Functional groups serve two important functions in ecology: they allow for simplification of ecosystem models and can aid in understanding diversity. Despite their important applications, there has not been a universally accepted method of how to define them. A common approach is to cluster species on a set of traits, validated through visual confirmation of resulting groups based primarily on expert opinion. The goal of this research is to determine a suitable procedure for creating and evaluating functional groups that arise from clustering nominal traits.

Methods

To do so, we produced a species by trait matrix of 22 traits from 116 fish species from Tasman Bay and Golden Bay, New Zealand. Data collected from photographs and published literature were predominantly nominal, and a small number of continuous traits were discretized. Some data were missing, so the benefit of imputing data was assessed using four approaches on data with known missing values. Hierarchical clustering is utilised to search for underlying data structure in the data that may represent functional groups. Within this clustering paradigm there are a number of distance matrices and linkage methods available, several combinations of which we test. The resulting clusters are evaluated using internal metrics developed specifically for nominal clustering. This revealed the choice of number of clusters, distance matrix and linkage method greatly affected the overall within- and between- cluster variability. We visualise the clustering in two dimensions and the stability of clusters is assessed through bootstrapping.

Results

Missing data imputation showed up to 90% accuracy using polytomous imputation, so was used to impute the real missing data. A division of the species information into three functional groups was the most separated, compact and stable result. Increasing the number of clusters increased the inconsistency of group membership, and selection of the appropriate distance matrix and linkage method improved the fit.

Discussion

We show that the commonly used methodologies used for the creation of functional groups are fraught with subjectivity, ultimately causing significant variation in the composition of resulting groups. Depending on the research goal dictates the appropriate strategy for selecting number of groups, distance matrix and clustering algorithm combination.

Drivers and rates of stock assessments in the United States

Fisheries management is most effective when based on scientific estimates of sustainable fishing rates. While some simple approaches allow estimation of harvest limits, more data-intensive stock assessments are generally required to evaluate the stock's biomass and fishing rates relative to sustainable levels. Here we evaluate how stock characteristics relate to the rate of new assessments in the United States. Using a statistical model based on time-to-event analysis and 569 coastal marine fish and invertebrate stocks landed in commercial fisheries, we quantify the impact of region, habitat, life-history, and economic factors on the annual probability of being assessed. Although the majority of landings come from assessed stocks in all regions, less than half of the regionally-landed species currently have been assessed. As expected, our time-to-event model identified landed tonnage and ex-vessel price as the dominant factors determining increased rates of new assessments. However, we also found that after controlling for landings and price, there has been a consistent bias towards assessing larger-bodied species. A number of vulnerable groups such as rockfishes (Scorpaeniformes) and groundsharks (Carcharhiniformes) have a relatively high annual probability of being assessed after controlling for their relatively small tonnage and low price. Due to relatively low landed tonnage and price of species that are currently unassessed, our model suggests that the number of assessed stocks will increase more slowly in future decades.

Pulsed evolution shaped modern vertebrate body sizes

The diversity of forms found among animals on Earth is striking. Despite decades of study, it has been difficult to reconcile the patterns of diversity seen between closely related species with those observed when studying single species on ecological timescales. We propose a set of models, called Lévy processes, to attempt to reconcile rapid evolution between species with the relatively stable distributions of phenotypes seen within species. These models, which have been successfully used to model stock market data, allow for long periods of stasis followed by bursts of rapid change. We find that many vertebrate groups are well fitted by Lévy models compared with models for which traits evolve toward a stationary optimum or evolve in an incremental and wandering manner.

The relative importance of different modes of evolution in shaping phenotypic diversity remains a hotly debated question. Fossil data suggest that stasis may be a common mode of evolution, while modern data suggest some lineages experience very fast rates of evolution. One way to reconcile these observations is to imagine that evolution proceeds in pulses, rather than in increments, on geological timescales. To test this hypothesis, we developed a maximum-likelihood framework for fitting Lévy processes to comparative morphological data. This class of stochastic processes includes both an incremental and a pulsed component. We found that a plurality of modern vertebrate clades examined are best fitted by pulsed processes over models of incremental change, stationarity, and adaptive radiation. When we compare our results to theoretical expectations of the rate and speed of regime shifts for models that detail fitness landscape dynamics, we find that our quantitative results are broadly compatible with both microevolutionary models and observations from the fossil record.

A global database on freshwater fish species occurrence in drainage basins

A growing interest is devoted to global-scale approaches in ecology and evolution that examine patterns and determinants of species diversity and the threats resulting from global change. These analyses obviously require global datasets of species distribution. Freshwater systems house a disproportionately high fraction of the global fish diversity considering the small proportion of the earth's surface that they occupy, and are one of the most threatened habitats on Earth. Here we provide complete species lists for 3119 drainage basins covering more than 80% of the Earth surface using 14953 fish species inhabiting permanently or occasionally freshwater systems. The database results from an extensive survey of native and non-native freshwater fish species distribution based on 1436 published papers, books, grey literature and web-based sources. Alone or in combination with further datasets on species biological and ecological characteristics and their evolutionary history, this database represents a highly valuable source of information for further studies on freshwater macroecology, macroevolution, biogeography and conservation.

Improving understanding of the functional diversity of fisheries by exploring the influence of global catch reconstruction

Functional diversity is thought to enhance ecosystem resilience, driving research focused on trends in the functional composition of fisheries, most recently with new reconstructions of global catch data. However, there is currently little understanding of how accounting for unreported catches (e.g. small-scale and illegal fisheries, bycatch and discards) influences functional diversity trends in global fisheries. We explored how diversity estimates varied among reported and unreported components of catch in 2010, and found these components had distinct functional fingerprints. Incorporating unreported catches had little impact on global-scale functional diversity patterns. However, at smaller, management-relevant scales, the effects of incorporating unreported catches were large (changes in functional diversity of up to 46%). Our results suggest there is greater uncertainty about the risks to ecosystem integrity and resilience from current fishing patterns than previously recognized. We provide recommendations and suggest a research agenda to improve future assessments of functional diversity of global fisheries.