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

Responses of coral reef fishes to past climate changes are related to life‐history traits

Coral reefs and their associated fauna are largely impacted by ongoing climate change. Unravelling species responses to past climatic variations might provide clues on the consequence of ongoing changes. Here, we tested the relationship between changes in sea surface temperature and sea levels during the Quaternary and present-day distributions of coral reef fish species. We investigated whether species- specific responses are associated with life-history traits. We collected a database of coral reef fish distribution together with life-history traits for the Indo-Pacific Ocean. We ran species distribution models (SDMs) on 3,725 tropical reef fish species using contemporary environmental factors together with a variable describing isolation from stable coral reef areas during the Quaternary. We quantified the variance explained independently by isolation from stable areas in the SDMs and related it to a set of species traits including body size and mobility. The variance purely explained by isolation from stable coral reef areas on the distribution of extant coral reef fish species largely varied across species. We observed a triangular relationship between the contribution of isolation from stable areas in the SDMs and body size. Species, whose distribution is more associated with historical changes, occurred predominantly in the Indo-Australian archipelago, where the mean size of fish assemblages is the lowest. Our results suggest that the legacy of habitat changes of the Quaternary is still detectable in the extant distribution of many fish species, especially those with small body size and the most sedentary. Because they were the least able to colonize distant habitats in the past, fish species with smaller body size might have the most pronounced lags in tracking ongoing climate change

Functional diversity of sharks and rays is highly vulnerable and supported by unique species and locations worldwide

Elasmobranchs (sharks, rays and skates) are among the most threatened marine vertebrates, yet their global functional diversity remains largely unknown. Here, we use a trait dataset of >1000 species to assess elasmobranch functional diversity and compare it against other previously studied biodiversity facets (taxonomic and phylogenetic), to identify species- and spatial- conservation priorities. We show that threatened species encompass the full extent of functional space and disproportionately include functionally distinct species. Applying the conservation metric FUSE (Functionally Unique, Specialised, and Endangered) reveals that most top-ranking species differ from the top Evolutionarily Distinct and Globally Endangered (EDGE) list. Spatial analyses further show that elasmobranch functional richness is concentrated along continental shelves and around oceanic islands, with 18 distinguishable hotspots. These hotspots only marginally overlap with those of other biodiversity facets, reflecting a distinct spatial fingerprint of functional diversity. Elasmobranch biodiversity facets converge with fishing pressure along the coast of China, which emerges as a critical frontier in conservation. Meanwhile, several components of elasmobranch functional diversity fall in high seas and/or outside the global network of marine protected areas. Overall, our results highlight acute vulnerability of the world’s elasmobranchs’ functional diversity and reveal global priorities for elasmobranch functional biodiversity previously overlooked

Ecological constraints coupled with deep-time habitat dynamics predict the latitudinal diversity gradient in reef fishes

We develop a spatially explicit model of diversification based on palaeohabitat to explore the predictions of four major hypotheses potentially explaining the latitudinal diversity gradient (LDG), namely, the ‘time-area’, ‘tropical niche conservatism’, ‘ecological limits’ and ‘evolutionary speed’ hypotheses. We compare simulation outputs to observed diversity gradients in the global reef fish fauna. Our simulations show that these hypotheses are non-mutually exclusive and that their relative influence depends on the time scale considered. Simulations suggest that reef habitat dynamics produced the LDG during deep geological time, while ecological constraints shaped the modern LDG, with a strong influence of the reduction in the latitudinal extent of tropical reefs during the Neogene. Overall, this study illustrates how mechanistic models in ecology and evolution can provide a temporal and spatial understanding of the role of speciation, extinction and dispersal in generating biodiversity patterns

Quantifying biodiversity using eDNA from water bodies : general principles and recommendations for sampling designs

Reliable and comparable estimates of biodiversity are the foundation for understanding ecological systems and informing policy and decision-making, especially in an era of massive anthropogenic impacts on biodiversity. Environmental DNA (eDNA) metabarcoding is at the forefront of technological advances in biodiversity monitoring, and the last few years have seen major progress and solutions to technical challenges from the laboratory to bioinformatics. Water eDNA has been shown to allow the fast and efficient recovery of biodiversity signals, but the rapid pace of technological development has meant that some important principles regarding sampling design, which are well established in traditional biodiversity inventories, have been neglected. Using a spatially explicit river flow model, we illustrate how sampling must be adjusted to the size of the watercourse to increase the quality of the biodiversity signal recovered. We additionally investigate the effect of sampling parameters (volume, number of sites, sequencing depth) on detection probability in an empirical data set. Based on traditional sampling principles, we propose that aquatic eDNA sampling replication and volume must be scaled to match the organisms' and ecosystems' properties to provide reliable biodiversity estimates. We present a generalizable conceptual equation describing sampling features as a function of the size of the ecosystem monitored, the abundance of target organisms, and the properties of the sequencing procedure. The aim of this formalization is to enhance the standardization of critical steps in the design of biodiversity inventory studies using eDNA. More robust sampling standards will generate more comparable biodiversity data from eDNA, which is necessary for the method's long-term plausibility and comparability

The marine fish food web is globally connected

The productivity of marine ecosystems and the services they provide to humans are largely dependent on complex interactions between prey and predators. These are embedded in a diverse network of trophic interactions, resulting in a cascade of events following perturbations such as species extinction. The sheer scale of oceans, however, precludes the characterization of marine feeding networks through de novo sampling. This effort ought instead to rely on a combination of extensive data and inference. Here we investigate how the distribution of trophic interactions at the global scale shapes the marine fish food web structure. We hypothesize that the heterogeneous distribution of species ranges in biogeographic regions should concentrate interactions in the warmest areas and within species groups. We find that the inferred global metaweb of marine fish—that is, all possible potential feeding links between co-occurring species—is highly connected geographically with a low degree of spatial modularity. Metrics of network structure correlate with sea surface temperature and tend to peak towards the tropics. In contrast to open-water communities, coastal food webs have greater interaction redundancy, which may confer robustness to species extinction. Our results suggest that marine ecosystems are connected yet display some resistance to perturbations because of high robustness at most locations.Using a global interaction dataset, the authors quantify the distribution of trophic interactions among marine fish, finding a high degree of geographic connectivity but low spatial modularity.C.A. was supported by a MELS-FQRNT Postdoctoral Fellowship and a Ressources Aquatique Québec (RAQ) fellowship during the conception and writing of this manuscript. T.P., D.G. and D.B.S. acknowledge financial support by the CIEE through their working group programme. M.B.A. is funded through FCT project No. PTDC/AAG-MAA/3764/2014. A.R.C. is funded by a Natural Sciences and Engineering Research Council of Canada (NSERC) PGS-D scholarship. D.G., T.P., M.-J.F., P.A. and S.J.L. are supported by NSERC Discovery Grants. T.P. also acknowledges a FRQNT New Investigator award and a Université de Montréal starting grant. D.B.S. acknowledges support from the Royal Society of New Zealand (via Marsden Fast-Start No. UOC-1101 and a Rutherford Discovery Fellowship)

Cross-ocean patterns and processes in fish biodiversity on coral reefs through the lens of eDNA metabarcoding

Increasing speed and magnitude of global change threaten the world's biodiversity and particularly coral reef fishes. A better understanding of large-scale patterns and processes on coral reefs is essential to prevent fish biodiversity decline but it requires new monitoring approaches. Here, we use environmental DNA metabarcoding to reconstruct well-known patterns of fish biodiversity on coral reefs and uncover hidden patterns on these highly diverse and threatened ecosystems. We analysed 226 environmental DNA (eDNA) seawater samples from 100 stations in five tropical regions (Caribbean, Central and Southwest Pacific, Coral Triangle and Western Indian Ocean) and compared those to 2047 underwater visual censuses from the Reef Life Survey in 1224 stations. Environmental DNA reveals a higher (16%) fish biodiversity, with 2650 taxa, and 25% more families than underwater visual surveys. By identifying more pelagic, reef-associated and crypto-benthic species, eDNA offers a fresh view on assembly rules across spatial scales. Nevertheless, the reef life survey identified more species than eDNA in 47 shared families, which can be due to incomplete sequence assignment, possibly combined with incomplete detection in the environment, for some species. Combining eDNA metabarcoding and extensive visual census offers novel insights on the spatial organization of the richest marine ecosystems

Modelling scenario for fish biodiversity in the Mediterranean Sea : Influence of global change and trophic consequences, application to marine reserves and exploited ecosystems

Un des enjeux majeurs en écologie est de comprendre les effets du changement climatique sur la biodiversité et le fonctionnement des écosystèmes. En milieu marin, la surexploitation des ressources par l'homme est un autre facteur de forçage sur les assemblages d'espèces. La thèse propose, par une approche multi-composantes de la biodiversité, de projeter les modifications attendues sur la structure des assemblages de poissons côtiers méditerranéens soumis au changement climatique mais aussi aux différentes pressions de pêche. L'originalité de ce travail est de considérer la dynamique de la structure en taille, de la diversité des espèces mais aussi des lignées (diversité phylogénétique), des traits fonctionnels (diversité fonctionnelle) et des interactions (diversité des liens trophiques) des assemblages de poissons à différentes échelles au sein du bassin méditerranéen, ces trois dernières composantes étant largement ignorées dans les projections face au changement climatique alors qu'elles sont essentielles pour le viabilité des écosystèmes et des services associés au delà du simple nombre d'espèces.Nous avons donc projeté les futures aires de répartition des poissons côtiers méditerranéens grâce à l’implémentation d’un nouveau modèle climatique (NEMOMED8) et de modèles de niche basés sur les enveloppes bioclimatiques. Les projections des aires de distribution des poissons côtiers méditerranéens mettent en évidence que pour la fin du siècle (i) 54 espèces devraient perdre leur niche climatique, (ii) la richesse en espèces pourrait diminuer sur 70,4% du plateau continental, en particulier en Méditerranée occidentale et en mer Égée, et (iii) la taille maximale moyenne des assemblages de poissons pourrait augmenter dans 74,8% des cellules du plateau continental. Les espèces de petite taille non ciblées par la pêche pourraient être les espèces les plus menacées par le changement climatique alors que les espèces de grande taille seraient les plus vulnérables face à l'effort de pêche. Nos projections, au niveau de l’ensemble de la Méditerranée, suggérent l'érosion importante de quelques lignées comme la famille des gobidae. Même si l'érosion de PD et de FD est en partie liée à la perte de richesse spécifique (moins d'espèces moins de lignées ou de fonctions), nous avons établi, notamment dans le bassin ouest, que les assemblages de poissons perdraient plus de diversité phylogénétique et fonctionnelle que prévu simplement suite à l’érosion de la richesse spécifique.Pour appréhender les effets du changement climatique sur la structure du réseau trophique nous avons mis en place une méthodologie basée sur la robustesse d'une relation entre la taille des proies et des prédateurs. Nous avons pu ainsi mettre en évidence les modifications potentielles des réseaux trophiques au sein des assemblages de poissons face au changement global pour l’ensemble du plateau continental méditerranéen. Nous avons constaté qu'une partie importante du plateau continental méditerranéen serait confrontée à une diminution du nombre de liens trophiques, de la vulnérabilité (nombre de prédateurs par proie) et de généralité (nombre de proies par prédateur) moyennes des espèces, tandis que la connectance et le niveau trophique dans les assemblages de poissons pourraient augmenter d'ici la fin du XXIème siècle.Au-delà des modifications de richesse spécifique, les assemblages de poissons méditerranéens côtiers pourraient être modifiés dans les fonctions qu’ils jouent au sein de l’écosystème, dans leur histoire évolutive ainsi que dans les interactions structurant les réseaux trophiques. La thèse est donc une ouverture vers la biogéographie du fonctionnement des écosystèmes à partir de modèles parcimonieux et hybrides permettant d'intégrer différentes composantes de la biodiversité, l'océanographie physique, et le niveau d'exploitation des ressources pour inférer le devenir des systèmes marins côtiers face aux pressions multiples qui s'y exercent déjà.One of the main goals in ecology is to understand the effects of climate change on biodiversity and ecosystem functioning. In marine environments the overexploitation of resources by human activities is another forcing factor on species assemblages. This PhD thesis suggested, within a multicomponentsbiodiversity approach, to project expected changes in the structure of Mediterranean coastal fish assemblages under climate change but also under different fishing pressures. The originality of this work is to consider the dynamics of size structure, diversity of species, but also lineages (phylogenetic diversity), functional traits (functional diversity) and interactions (diversity of trophic links) in fish assemblages at different scales within the Mediterranean basin, the latter three components being largely ignored in climate change projections whereas they are essential for maintaining the viability of ecosystems and associated services beyond the simple number of species. We therefore projected future geographic ranges of Mediterranean coastal fish through theimplementation of a new climate model (NEMOMED8) and based on bioclimatic envelopes models. Projected range shifts of Mediterranean coastal fish show that for the end of the century (i) 54 species would lose their climatic niche, (ii) species richness may decline on 70.4% of the continental shelf, particularly in the Western Mediterranean basin and in the Aegean Sea, and (iii) the average maximum size of fish assemblages would increase on 74.8% of the continental shelf. The small species, not targeted by fishing activities, would be the species most threatened by climate change, while larger species are most vulnerable to fishing effort.Our projections at the whole Mediterranean scale show a decrease of 13.6% for the phylogenetic diversity (PD) of coastal fish and 12.6% for their functional diversity (FD) by the end of this century and suggest a significant erosion of some lineages like the gobidae family. While erosion of PD and FD is partly due to the loss of species richness (fewer species implies less lineage and functions) we obseved, especially in the western basin, that the fish assemblages would loss more phylogenetic and functional diversity than expected simply due to the erosion of species richness. These two components, were largely ignored in conservation of marine species assemblages and appear to be strongly impacted by global change.To understand the effects of climate change on food web structure we developed a new methodology based on the robust relationship between the size of preys and predators. We were able to highlight potential changes in food webs of fish assemblages under climate change for the Mediterranean continental shelf. We found that a significant portion of the Mediterranean continental shelf would face a reduction in the number of trophic links, vulnerability (number of predators per prey) and generality (number of preys per predator) of species on average, while connectance and trophic level within fish assemblages would increase by the end of the XXIth century.Beyond changes in species richness, the Mediterranean coastal fish assemblages may be modified, in the functions that they play in ecosystem, in the amount evolutionary history they support, as well as in their interactions structuring food webs. This PhD thesis paves the way towards the biogeography of ecosystem functioning using parsimonious and hybrid models to integrate different components of biodiversity, physical oceanography, and the level of exploitation of ressouces to infer the futur of marine systems cfunctioning facing multiple pressures that are already there

eDNA complements scientific trawling in surveys of marine fish biodiversity components.

 Environmental DNA (eDNA) metabarcoding is a method to detect taxa from environmental samples. It is increasingly used for marine biodiversity surveys. As it only requires water collection, eDNA metabarcoding is less invasive than scientific trawling and might be more cost-effective. Here, we analysed data from both sampling methods applied in the same scientific survey targeting Northeast Atlantic fishes in the Bay of Biscay. We compared the methods in terms of spatial patterns of taxonomic, phylogenetic and functional diversity. We found that eDNA captured more taxonomic and phylogenetic richness than bottom trawling and more functional richness at the local scale. eDNA was less selective than trawling and detected species in local communities spanning larger phylogenetic and functional breadths, especially as it detected large pelagic species that escaped the trawl, even though trawling detected more flat fish. eDNA indicated differences in fish community composition that were comparable to those based on trawling. However, consistency between abundance estimates provided by eDNA metabarcoding and trawl catches was low, even after accounting for allometric scaling in eDNA production. We conclude that eDNA metabarcoding is an efficient method that can complement scientific trawling for multi-component biodiversity monitoring based on presence/absence. Here with provide the eDNA data set that support these findings. </p