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Aim: The aim was to determine reef connectivity and future coral cover levels under global scenarios of coral bleaching loss and potential recovery. Location: Global coral reefs. Time period: Present‐day to 2100. Major taxa studied: Scleractinian coral. Methods: We used a global coral larval dispersal model that describes population connectivity among reefs at a resolution of ⅙° × ⅙° (c. 18 km × 18 km) cells. To simulate different patterns of bleaching events, we ran three scenarios at different levels of coral reef habitat loss followed by a reseeding of coral larvae from surviving reefs to simulate recovery. Results: We found a total of 604 distinct reef networks, but more than half of the world's reef cells are contained in six large coral reef networks (294–5,494 cells), whereas the rest form smaller networks. In the bleaching scenario where previously identified predicted climate refugia were maintained, initial connectivity was largely preserved even when 71% of global coral reef habitat was lost, but the relict reef cells were unable to reseed even 50% of former coral reef habitat because many of the relict reefs are in the same networks as each other. In scenarios where refugia were lost first or with random loss, less of the initial connectivity was maintained, but more widespread reseeding was possible because more reef cells within smaller networks were maintained. Main conclusions: Our findings highlight the importance of maintaining functional coral reef habitat outside of predicted climate refugia to sustain connectivity globally, and suggest an important role for "stepping stone" reefs between the climate refugia. Without attention to these issues of habitat loss and connectivity, much of global coral reef habitat might not be reseeded without human intervention. [ABSTRACT FROM AUTHOR]

Spatial conservation prioritization (SCP) is a planning framework used to identify new conservation areas on the basis of the spatial distribution of species, ecosystems, and their services to human societies. The ongoing accumulation of intraspecific genetic data on a variety of species offers a way to gain knowledge of intraspecific genetic diversity and to estimate several population characteristics useful in conservation, such as dispersal and population size. Here, we review how intraspecific genetic data have been integrated into SCP and highlight their potential for identifying conservation area networks that represent intraspecific genetic diversity comprehensively and that ensure the long-term persistence of biodiversity in the face of global change. Conservation area networks on land and sea need to be expanded to meet the objectives of the post-2020 global biodiversity framework. Spatial conservation prioritization (SCP) is a rigorous framework to identify suitable areas for protection on the basis of scientific data. Integrating intraspecific genetic data in SCP can help identify networks of conservation areas that are more representative of biological diversity and likely better at ensuring its long-term persistence. [ABSTRACT FROM AUTHOR]

Many model organisms were chosen and achieved prominence because of an advantageous combination of their life‐history characteristics, genetic properties and also practical considerations. Discoveries made in Arabidopsis thaliana, the most renowned noncrop plant model species, have markedly stimulated studies in other species with different biology. Within the family Brassicaceae, the arctic–alpine Arabis alpina has become a model complementary to Arabidopsis thaliana to study the evolution of life‐history traits, such as perenniality, and ecological genomics in harsh environments. In this review, we provide an overview of the properties that facilitated the rapid emergence of A. alpina as a plant model. We summarize the evolutionary history of A. alpina, including genomic aspects, the diversification of its mating system and demographic properties, and we discuss recent progress in the molecular dissection of developmental traits that are related to its perennial life history and environmental adaptation. From this published knowledge, we derive open questions that might inspire future research in A. alpina, other Brassicaceae species or more distantly related plant families. [ABSTRACT FROM AUTHOR]

As human activities on the world's oceans intensify, mapping human pressure is essential to develop appropriate conservation strategies and prioritize investments with limited resources. Here, we map six human (nonclimatic) pressures on coral reefs using the latest quantitative data on fishing, water pollution (nitrogen and sediments), coastal population, industrial development, and tourism. Using a percentile approach to rank different stressors, we identify the top‐ranked local pressure and estimate a cumulative pressure index for 54,596 global coral reef pixels at 0.05° (∼5 km) resolution. We find that coral reefs are exposed to multiple intense local pressures: fishing and water pollution (nutrients and sediments) are the most common top‐ranked pressures worldwide (in 30.8% and 32.3% of reef cells, respectively), although each pressure was ranked as a top pressure in some locations. We also find that local pressures are similar inside and outside a proposed global portfolio of coral reef climate refugia, suggesting that even potential climate refugia have high levels of local human pressure that require effective management. Our findings and datasets provide the best available information that can ensure local pressures are effectively managed across the world's coral reefs. [ABSTRACT FROM AUTHOR]

The Kunming-Montreal Global Biodiversity Framework recognised the urgency of taking action to conserve intraspecific genetic diversity (IGD) as an insurance against habitat degradation and environmental change. Recent work suggests that 90–99 % of IGD should be conserved to safeguard viability of future generations. Here, we addressed such a conservation issue in three forest tree species in Italy: silver fir (Abies alba Mill.), Heldreich's pine (Pinus heldreichii H. Christ), and pedunculate oak (Quercus robur L.). We used microsatellite markers to measure IGD of 36 (A. alba), 15 (P. heldreichii) and 25 (Q. robur) natural sites, including several putative glacial refugia. We developed a spatial conservation planning (SCP) analysis to quantify the genetic irreplaceability of each site and identify the minimum set coverage ensuring IGD protection. Finally, we compared SCP results with the contributions to allelic diversity within and between sites, total allelic diversity and private allelic richness. We found that between 44 % and 73 % of sites were required to conserve 90–99 % of the alleles, and that this conservation effort held even when targeting lower percentages of alleles to protect (50–75 %). Glacial refugia were often included in the minimum set coverage, confirming biogeographical expectations. Finally, sites with high genetic irreplaceability were found to have higher private allelic richness on average. These results are discussed in the light of the biogeographic history of the species studied and the current policies for the conservation of forest genetic resources. • Intraspecific genetic diversity (IGD) must be protected to avoid extirpation. • Spatial conservation planning of IGD in forest trees from a multi-refugial area. • ½ to ¾ of sites are to be conserved to achieve adequate protection for IGD. • Setting unambitious conservation targets has limited impact on conservation costs. • Glacial refugia are priority candidates for maximising IGD conservation. [ABSTRACT FROM AUTHOR]

Locations for new protected areas should be identified with consideration of intraspecific genetic diversity because genetic variation enhances the adaptability of species to novel environmental conditions. The process of siting new protected areas is called spatial conservation prioritization and is often formulated as a mathematical problem to be solved with the aid of computer software. Integrating multidimensional continuous metrics of genome-wide genetic diversity in spatial conservation prioritization involves significant challenges in terms of computation speed and memory requirements. In this study, we tested and compared several approaches to approximate the multidimensional continuous metrics of genetic diversity using multidimensional discrete genetic clusters or unidimensional discrete conservation features. To this end, we applied two tools for spatial conservation prioritization, raptr and prioritizr , to genomic datasets of two fish species (the white seabream Diplodus sargus and the red mullet Mullus surmuletus) sampled throughout most of their distribution range in the Mediterranean Sea. We found that most of the approximations tested either did not achieve all genetic conservation targets or resulted in excessively high conservation costs. Nonetheless, approaches based on multidimensional genetic clusters allowed generating prioritizations with relatively small gaps in genetic objectives at very high computation speed. This might be an interesting option for exploratory or interactive analyses such as those performed in workshop with stakeholders. • Genome-wide genetic diversity helps species persist against environmental change. • Siting new protected areas should consider genome-wide genetic diversity. • We explore different approaches to integrate it in conservation prioritization. • We used two Mediterranean species as example. • No approach was best in terms of computation efficiency and objectives met. [ABSTRACT FROM AUTHOR]

Multilocus genetic processes in subdivided populations can be complex and difficult to interpret using theoretical population genetics models. Genetic simulators offer a valid alternative to study multilocus genetic processes in arbitrarily complex scenarios. However, the use of forward‐in‐time simulators in realistic scenarios involving high numbers of individuals distributed in multiple local populations is limited by computation time and memory requirements. These limitations increase with the number of simulated individuals. We developed a genetic simulator, MetaPopGen 2.0, to model multilocus population genetic processes in subdivided populations of arbitrarily large size. It allows for spatial and temporal variation in demographic parameters, age structure, adult and propagule dispersal, variable mutation rates and selection on survival and fecundity. We developed MetaPopGen 2.0 in the R environment to facilitate its use by non‐modeler ecologists and evolutionary biologists. We illustrate the capabilities of MetaPopGen 2.0 for studying adaptation to water salinity in the striped red mullet Mullus surmuletus. [ABSTRACT FROM AUTHOR]

Demographic compensation arises when vital rates change in opposite directions across populations, buffering the variation in population growth rates, and is a mechanism often invoked to explain the stability of species geographic ranges. However, studies on demographic compensation have disregarded the effects of temporal variation in vital rates and their temporal correlations, despite theoretical evidence that stochastic dynamics can affect population persistence in temporally varying environments. We carried out a seven‐year‐long demographic study on the perennial plant Arabis alpina (L.) across six populations encompassing most of its elevational range. We discovered demographic compensation in the form of negative correlations between the means of plant vital rates, but also between their temporal coefficients of variation, correlations and elasticities. Even if their contribution to demographic compensation was small, this highlights a previously overlooked, but potentially important, role of stochastic processes in stabilising population dynamics at range margins. [ABSTRACT FROM AUTHOR]

Climate change can affect the habitat resources available to species by changing habitat quantity, suitability and spatial configuration, which largely determine population persistence in the landscape. In this context, dispersal is a central process for species to track their niche. Assessments of the amount of reachable habitat (ARH) using static snap‐shots do not account, however, for the temporal overlap of habitat patches that may enhance stepping‐stone effects. Here, we quantified the impacts of climate change on the ARH using a spatio–temporal connectivity model. We first explored the importance of spatio–temporal connectivity relative to purely spatial connectivity in a changing climate by generating virtual species distributions and analyzed the relative effects of changes in habitat quantity, suitability and configuration. Then, we studied the importance of spatio–temporal connectivity in three vertebrate species with divergent responses to climate change in North America (grey wolf, Canadian lynx and white‐tailed deer). We found that the spatio–temporal connectivity could enhance the stepping‐stone effect for species predicted to experience range contractions, and the relative importance of the spatio–temporal connectivity increased with the reduction in habitat quantity and suitability. Conversely, for species that are likely to expand their ranges, spatio–temporal connectivity had no additional contribution to improve the ARH. We also found that changes in habitat amount (quantity and suitability) were more influential than changes in habitat configuration in determining the relative importance of spatio–temporal connectivity. We conclude that spatio–temporal connectivity may provide less biased and more realistic estimates of habitat connectivity than purely spatial connectivity. [ABSTRACT FROM AUTHOR]

Abstract: Genetic variation, as a basis of evolutionary change, allows species to adapt and persist in different climates and environments. Yet, a comprehensive assessment of the drivers of genetic variation at different spatial scales is still missing in marine ecosystems. Here, we investigated the influence of environment, geographic isolation, and larval dispersal on the variation in allele frequencies, using an extensive spatial sampling (47 locations) of the striped red mullet (Mullus surmuletus) in the Mediterranean Sea. Univariate multiple regressions were used to test the influence of environment (salinity and temperature), geographic isolation, and larval dispersal on single nucleotide polymorphism (SNP) allele frequencies. We used Moran's eigenvector maps (db‐MEMs) and asymmetric eigenvector maps (AEMs) to decompose geographic and dispersal distances in predictors representing different spatial scales. We found that salinity and temperature had only a weak effect on the variation in allele frequencies. Our results revealed the predominance of geographic isolation to explain variation in allele frequencies at large spatial scale (>1,000 km), while larval dispersal was the major predictor at smaller spatial scale (<1,000 km). Our findings stress the importance of including spatial scales to understand the drivers of spatial genetic variation. We suggest that larval dispersal allows to maintain gene flows at small to intermediate scale, while at broad scale, genetic variation may be mostly shaped by adult mobility, demographic history, or multigenerational stepping‐stone dispersal. These findings bring out important spatial scale considerations to account for in the design of a protected area network that would efficiently enhance protection and persistence capacity of marine species. [ABSTRACT FROM AUTHOR]

Abstract: Genome–environment association methods aim to detect genetic markers associated with environmental variables. The detected associations are usually analysed separately to identify the genomic regions involved in local adaptation. However, a recent study suggests that single‐locus associations can be combined and used in a predictive way to estimate environmental variables for new individuals on the basis of their genotypes. Here, we introduce an original approach to predict the environmental range (values and upper and lower limits) of species genotypes from the genetic markers significantly associated with those environmental variables in an independent set of individuals. We illustrate this approach to predict aridity in a database constituted of 950 individuals of wild beets and 299 individuals of cultivated beets genotyped at 14,409 random single nucleotide polymorphisms (SNPs). We detected 66 alleles associated with aridity and used them to calculate the fraction (I) of aridity‐associated alleles in each individual. The fraction I correctly predicted the values of aridity in an independent validation set of wild individuals and was then used to predict aridity in the 299 cultivated individuals. Wild individuals had higher median values and a wider range of values of aridity than the cultivated individuals, suggesting that wild individuals have higher ability to resist to stress‐aridity conditions and could be used to improve the resistance of cultivated varieties to aridity. [ABSTRACT FROM AUTHOR]

Summary: Spatial differences in environmental selective pressures interact with the genomes of organisms, ultimately leading to local adaptation. Landscape genomics is an emergent research area that uncovers genome–environment associations, thus allowing researchers to identify candidate loci for adaptation to specific environmental variables. In the present study, we used latent factor mixed models (LFMMs) and Moran spectral outlier detection/randomization (MSOD‐MSR) to identify candidate loci for adaptation to 10 environmental variables (climatic, soil and atmospheric) among 43 515 single nucleotide polymorphisms (SNPs) from 202 accessions of the model legume Medicago truncatula. Soil variables were associated with a large number of candidate loci identified through both LFMMs and MSOD‐MSR. Genes tagged by candidate loci associated with drought and salinity are involved in the response to biotic and abiotic stresses, while those tagged by candidates associated with soil nitrogen and atmospheric nitrogen, participate in the legume‐rhizobia symbiosis. Candidate SNPs identified through both LFMMs and MSOD‐MSR explained up to 56% of variance in flowering traits. Our findings highlight the importance of soil in driving adaptation in the system and elucidate the basis of evolutionary potential of M. truncatula to respond to global climate change and anthropogenic disruption of the nitrogen cycle. [ABSTRACT FROM AUTHOR]

Abstract: Land management is critical for biodiversity conservation in mountain grasslands. It should be both ecologically effective and economically efficient. We provide an economic analysis of different options (spring and autumn grazing, mowing and abandonment) and their effects on population viability of a rare plant species, Eryngium alpinum (Apiaceae), in two French mountain grassland sites (Fournel and Pralognan). Using data collected in a 10‐year individual‐based demographic study, we estimated the effects of land management options on the population growth rate and simulated the effect of combinations of options. Income earned through each option was estimated using data on associated costs (price of consumables, working time and wages) and benefits (forage production, quality and price), and we assessed the economic effects of agri‐environment subsidies (AESs). We also simulated the effects of increased frequencies of extreme climatic events (such as the 2003 heatwave). Spring grazing was the worst option for E. alpinum demography but the best in economic terms, as it provided net positive incomes. Autumn grazing was the best option, resulting in positive growth rates and incomes, even if the latter were lower than for spring grazing. Mowing was the second best option for demography but resulted in economic losses for farmers. Abandonment provided zero income and was not favourable to population growth. In Fournel, AESs allowed for economically and ecologically near‐optimal combinations of management options. In Pralognan, alternating years of grazing with mowing resulted in an acceptable compromise, with positive growth rates and incomes, but AESs were not sufficient to cover the opportunity cost of spring and autumn grazing. Mowing was also unattractive because of the inaccessibility of the site and impossibility to recover the hay to make forage. Simulations with increased frequency of extreme climatic events resulted in negative growth rates in Pralognan, questioning the continuation of AESs in extinction‐prone populations. Synthesis and applications. The conservation effectiveness and economic efficiency of grassland management could be improved by alternating practices over several years. However, existing agri‐environment subsidies would barely be sufficient to increase uptake of the most favourable land management options for biodiversity. [ABSTRACT FROM AUTHOR]

Abstract: Current methods in conservation planning for promoting the persistence of biodiversity typically focus on either representing species geographic distributions or maintaining connectivity between reserves, but rarely both, and take a focal species, rather than a multispecies, approach. Here, we link prioritization methods with population models to explore the impact of integrating both representation and connectivity into conservation planning for species persistence. Using data on 288 Mediterranean fish species with varying conservation requirements, we show that: (1) considering both representation and connectivity objectives provides the best strategy for enhanced biodiversity persistence and (2) connectivity objectives were fundamental to enhancing persistence of small‐ranged species, which are most in need of conservation, while the representation objective benefited only wide‐ranging species. Our approach provides a more comprehensive appraisal of planning applications than approaches focusing on either representation or connectivity, and will hopefully contribute to build more effective reserve networks for the persistence of biodiversity. [ABSTRACT FROM AUTHOR]

Key message: Using a much higher number of SNP markers and larger sample sizes than all the previous studies, we characterized the genetic relationships among wild and cultivated plants of section Beta. Abstract: We analyzed the genetic variation of Beta section Beta, which includes wild taxa ( Beta macrocarpa, B. patula, B. vulgaris subsp. adanensis and B. vulgaris subsp. maritima) and cultivars (fodder beet, sugar beet, garden beet, leaf beet, and swiss chards), using 9724 single nucleotide polymorphism markers. The analyses conducted at the individual level without a priori groups confirmed the strong differentiation of B. macrocarpa and B. vulgaris subsp. adanensis from the other taxa. B. vulgaris subsp. maritima showed a complex genetic structure partly following a geographical pattern, which confounded the differences between this taxon and the cultivated varieties. Cultivated varieties were structured into three main groups: garden beets, fodder and sugar beets, and leaf beets and swiss chards. The genetic structure described here will be helpful to correctly estimate linkage disequilibrium and to test for statistical associations between genetic markers and environmental variables. [ABSTRACT FROM AUTHOR]

Aim We set out to identify the determinants of the variation in genetic diversity among fish species and test whether multi-species genetic diversity is randomly distributed in space. Location Mediterranean Sea. Methods We collected genetic diversity data from 39 published studies on Mediterranean fishes (31 species) along with the spatial coordinates of the sampling sites. We focused on microsatellite heterozygosity (151 data points) and mitochondrial haplotype diversity (201 data points). We used linear regressions to link genetic diversity and 11 ecological traits. We also tested for spatial autocorrelation and trends in the residuals. Results Among-species variation in microsatellite heterozygosity was explained by three ecological traits: vertical distribution, migration type and body length. Variation in mitochondrial haplotype diversity was also explained by vertical distribution and migration type, and by reproductive strategy (semelparity). However, vertical distribution and migration type showed opposite effects on microsatellites and mitochondrial diversity. After accounting for the effects of ecological traits, no spatial pattern was detected, except for one of the species considered. Main conclusions Ecological factors explain an important proportion of the among-species genetic diversity. These results suggest that life history strategies of the species influence the variation of microsatellite diversity indirectly through their effect on effective population size, while the spatial variations of genetic diversity seem to be too complex to be identified in our analysis. We found very different effects of traits on mitochondrial and nuclear DNA diversity, which can be explained by the specificities of mitochondrial DNA (absence of recombination, maternal inheritance and non-neutrality). [ABSTRACT FROM AUTHOR]

Key message: The genetic variation of Beta section Beta is structured into four taxonomic and spatial clusters. There are significant associations between molecular markers and environmental variables. Abstract: We investigated the genetic diversity of Beta section Beta, which includes the wild and cultivated relatives of the sugar beet. The taxa included in the study were: Beta vulgaris subsp. maritima, B. vulgaris subsp. adanensis, B. macrocarpa, B. patula and B. vulgaris subsp. vulgaris (garden beet, leaf beet and swiss chards). We collected 1264 accessions originating from the entire distribution area of these taxa and genotyped them for 4436 DArT markers (DArTs). We showed that the genetic variation of these accessions is structured into four taxonomic and spatial clusters: (1) samples of Beta macrocarpa, (2) samples of Beta vulgaris subsp. adanensis, (3) Mediterranean and Asian samples and (4) Atlantic and Northern European samples. These last two clusters were mainly composed of samples of Beta vulgaris subsp. maritima. We investigated in deeper detail the genetic structure of B. vulgaris subsp. maritima, which constituted the majority (80 %) of the wild samples. This subspecies exhibited a clinal genetic variation from South-East to North-West. We detected some markers significantly associated to environmental variables in B. vulgaris subsp. maritima. These associations are interpreted as results of natural selection. The variable most often involved in the associations was annual mean temperature. Therefore, these markers can be useful for the development of frost-tolerant winter beets and drought-tolerant rain-fed beets. [ABSTRACT FROM AUTHOR]

Population genetics simulation models are useful tools to study the effects of demography and environmental factors on genetic variation and genetic differentiation. They allow for studying species and populations with complex life histories, spatial distribution and many other complicating factors that make analytical treatment impracticable. Most simulation models are individual-based: this poses a limitation to simulation of very large populations because of the limits in computer memory and long computation times. To overcome these limitations, we propose an intermediate approach that allows modelling of very complex demographic scenarios, which would be intractable with analytical models, and removes the limitations imposed by large population size, which affect individual-based simulation models. We implement this approach in a software package for the r environment, MetaPopGen. The innovative concept of this approach with respect to the other population genetic simulators is that it focuses on genotype numbers rather than on individuals. Genotype numbers are iterated through time by using random number generators for appropriate probabilistic distributions to reproduce the stochasticity inherent to Mendelian segregation, survival, dispersal and reproduction. Features included in the model are age structure, monoecious and dioecious (or separate sexes) life cycles, mutation, dispersal and selection. The model simulates only one locus at a time. All demographic parameters can be genotype-, sex-, age-, deme- and time-dependent. MetaPopGen is therefore indicated to study large populations and very complex demographic scenarios. We illustrate the capabilities of MetaPopGen by applying it to the case of a marine fish metapopulation in the Mediterranean Sea. [ABSTRACT FROM AUTHOR]

Protected areas (PAs) are recognized as the flagship tool to offset biodiversity loss on Earth. Spatial conservation planning seeks optimal designs of PAs that meet multiple targets such as biodiversity representation and population persistence. Since connectivity between PAs is a fundamental requirement for population persistence, several methods have been developed to include connectivity into PA design algorithms. Among these, the eigenvalue decomposition of the connectivity matrix allows for identifying clusters of strongly connected sites and selecting the sites contributing the most to population persistence. So far, this method was only suited to optimize an entire network of PAs without considering existing PAs in the new design. However, a more cost-effective and realistic approach is to optimize the design of an extended network to improve its connectivity and thus population persistence. Here, we develop a flexible algorithm based on eigenvalue decomposition of connectivity matrices to extend existing networks of PAs while optimizing connectivity and population growth rate. We also include a splitting algorithm to improve cluster identification. The new algorithm accounts for the change in connectivity due to the increased biological productivity often observed in existing PAs. We illustrate the potential of our algorithm by proposing an extension of the network of ∼100 Mediterranean marine PAs to reach the targeted 10% surface area protection from the current 1.8%. We identify differences between the clean slate scenario, where all sites are available for protection, irrespective of their current protection status, and the scenario where existing PAs are forced to be included into the optimized solution. By integrating this algorithm to existing multi-objective and multi-specific algorithms of PA selection, the demographic effects of connectivity can be explicitly included into conservation planning. [ABSTRACT FROM AUTHOR]

Aim To study the combined effects of climate change on connectivity between marine protected areas ( MPAs) and larval supply to the continental shelf. Location The Mediterranean Sea, where sea surface temperatures are expected to strongly increase by the end of the 21st century, represents an archetypal situation with a dense MPA network but resource overexploitation outside. Methods Using an individual-based mechanistic model of larval transport, forced with an emission-driven regional climate change scenario for the Mediterranean Sea, we explored the combined effects of changes in hydrodynamics, adult reproductive timing and larval dispersal on the connectivity among MPAs and their ability to seed fished areas with larvae. Results We show that, over the period 1970-2099, larval dispersal distances would decrease by 10%, the continental shelf area seeded with larvae would decrease by 3% and the larval retention fraction would increase by 5%, resulting in higher concentration of larvae in smaller areas of the continental shelf. However, connectance within the MPA network would increase by 5% as more northern MPAs would become suitable for reproduction with increasing temperatures. We also show that the effects of changes in adult reproductive timing and larval dispersal on connectivity patterns are additive. Main conclusions Climate change will influence connectivity and the effectiveness of MPA networks, and should receive more attention in future conservation planning and large-scale population dynamics. [ABSTRACT FROM AUTHOR]

Marine protected areas (MPAs) are major tools to protect biodiversity and sustain fisheries. For species with a sedentary adult phase and a dispersive larval phase, the effectiveness of MPA networks for population persistence depends on connectivity through larval dispersal. However, connectivity patterns between MPAs remain largely unknown at large spatial scales. Here, we used a biophysical model to evaluate connectivity between MPAs in the Mediterranean Sea, a region of extremely rich biodiversity that is currently protected by a system of approximately a hundred MPAs. The model was parameterized according to the dispersal capacity of the dusky grouper Epinephelus marginatus, an archetypal conservation-dependent species, with high economic importance and emblematic in the Mediterranean. Using various connectivity metrics and graph theory, we showed that Mediterranean MPAs are far from constituting a true, well-connected network. On average, each MPA was directly connected to four others and MPAs were clustered into several groups. Two MPAs (one in the Balearic Islands and one in Sardinia) emerged as crucial nodes for ensuring multi-generational connectivity. The high heterogeneity of MPA distribution, with low density in the South-Eastern Mediterranean, coupled with a mean dispersal distance of 120 km, leaves about 20% of the continental shelf without any larval supply. This low connectivity, here demonstrated for a major Mediterranean species, poses new challenges for the creation of a future Mediterranean network of well-connected MPAs providing recruitment to the whole continental shelf. This issue is even more critical given that the expected reduction of pelagic larval duration following sea temperature rise will likely decrease connectivity even more. [ABSTRACT FROM AUTHOR]

Effective population size (N e ) determines the strength of genetic drift and can influence the level of genetic diversity a population can maintain. Assessing how changes in demographic rates associated with environmental variables and management actions affect N e thus can be crucial to the conservation of endangered species. Calculation of N e through demographic models makes it possible to use elasticity analyses to study this issue. The elasticity of N e to a given vital rate is the proportional change in N e associated with a proportional increase in that vital rate. In addition, demographic models can be used to study N e and population growth rate (λ) simultaneously. Simultaneous examination is important because some vital rates differ diametrically in their associations with λ and N e . For example, in some cases increasing these vital rates increases λ and decreases N e . We used elasticity analysis to study the effect of stage-specific survival and flowering rates on N e, annual effective population size (Na), and λ in seven populations of the endangered plant Austrian dragonhead (Dracocephalum austriacum). In populations with λ≥ 1, the elasticities of Ne and Na were similar to those of λ. Survival rates of adults were associated with greater elasticities than survival rates of juveniles, flowering rates, or fecundity. In populations with λ < 1, Ne and Na exhibited greater elasticities to juvenile than to adult vital rates. These patterns are similar to those observed in other species with similar life histories. We did not observe contrasting effects of any vital rate on λ and Ne; thus, management actions that increase the λ of populations of Austrian dragonhead will not increase genetic drift. Our results show that elasticity analyses of Ne and Na can complement elasticity analysis of λ. Moreover, such analyses do not require more data than standard matrix models of population dynamics. [ABSTRACT FROM AUTHOR]

Abstract: Extreme climatic events like the 2003 summer heatwave and inappropriate land management can threaten the existence of rare plants. We studied the response of Eryngium alpinum, a vulnerable species, to this extreme climatic event and different agricultural practices. A demographic study was conducted in seven field sites between 2001 and 2010. Stage-specific vital rates were used to parameterize matrix population models and perform stochastic projections to calculate population growth rates and estimate extinction probabilities. Among management regimes, spring grazing and land abandonment decreased vital rates and population growth, while autumn grazing and late mowing had positive effects on population viability. The 2003 heatwave reduced fecundity rates and survival rates. Only spring grazed sites presented considerable extinction risk. Stochastic projections showed that an increased frequency of 2003-like events may exacerbate extinction risk, but extinction probability depends mainly on land management regimes. To better conserve E. alpinum populations, we recommend conversion of presently spring grazed and abandoned sites to late mowing or autumn grazing. [Copyright &y& Elsevier]

The evolutionary enlightened management of species with complex life cycles often requires the development of mathematical models integrating demographic and genetic data. The genetic structure of the endangered European eel ( Anguilla anguilla L.) has been thoroughly analyzed in several studies in the past years. However, the interpretation of the key demographic and biologic processes that determine the observed spatio-temporal genetic structure has been very challenging owing to the complex life cycle of this catadromous species. Here, we present the first integrated demographic-genetic model applied to the European eel that explicitly accounts for different levels of larval and adult mixing during oceanic migrations and allows us to explore alternative hypotheses on genetic differentiation. Our analyses show that (i) very low levels of mixing occurring during larval dispersal or adult migration are sufficient to erase entirely any genetic differences among sub-populations; (ii) small-scale temporal differentiation in recruitment can arise if the spawning stock is subdivided in distinct reproductive groups; and (iii) the geographic differentiation component might be overestimated if a limited number of temporal recruits are analyzed. Our study can inspire the scientific debate on the interpretation of genetic structure in other species characterized by complex life cycle and long-range migrations. [ABSTRACT FROM AUTHOR]

Aim: Coralligenous reefs are the main marine bioconstructions in terms of spatial distribution within the Mediterranean basin. Two distinct reef morphologies can be distinguished based on the surface and topographical features of the seafloor: cliffs developing vertical slopes and banks found on gently steep or horizontal bottoms. Despite their importance for monitoring and conservation efforts, observations regarding the variability of biogeographical patterns are scarce. Here, we aimed to assess the differences in the composition and structure of these cliffs across ecoregions and estimate the relative role of abiotic environmental features, geographic location, and connectivity in shaping diversity patterns. Location: The study was carried out in the Central‐Western Mediterranean Sea. Samples were collected at 65 sites across the Algero‐Provençal Basin, the Ionian Sea and the Tyrrhenian Sea. Methods: We assessed the composition and structure of coralligenous cliffs through photographic samplings collected by scuba divers. Patterns in α‐ and β‐diversity were associated with 9 abiotic environmental variables, latitudinal and longitudinal gradients, and connectivity measures using Generalized Additive (GAM) and Conditional Autoregressive (CAR) models. Results: Coralligenous cliffs were primarily composed of algae and displayed a high degree of variability. The Partition Around Medoids (PAM) clustering method successfully delineated seven distinct clusters with a non‐uniform distribution within the studied ecoregions. The α‐diversity increased in eastern and northern sites and with phosphate concentration, while decreased with temperature, chlorophyll and nitrates concentration. β‐diversity at the site level increased with temperature, while it was negatively affected by northward current speed and chlorophyll concentration. Moveover, β‐diversity increased within connected sites. Main Conclusions: Coralligenous cliff diversity responds both to the physico‐chemical features of the habitat and between‐habitats connectivity. However, our findings suggest that small‐scale abiotic and biotic processes could contribute to explaining the variability observed. These findings can significantly enhance the monitoring and conservation efforts of this Mediterranean endemic ecosystem. [ABSTRACT FROM AUTHOR]

The availability of genomic data for an increasing number of species makes it possible to incorporate evolutionary processes into conservation plans. Recent studies show how genetic data can inform spatial conservation prioritization (SCP), but they focus on metrics of diversity and distinctness derived primarily from neutral genetic data sets. Identifying adaptive genetic markers can provide important information regarding the capacity for populations to adapt to environmental change. Yet, the effect of including metrics based on adaptive genomic data into SCP in comparison to more widely used neutral genetic metrics has not been explored. We used existing genomic data on a commercially exploited species, the giant California sea cucumber (Parastichopus californicus), to perform SCP for the coastal region of British Columbia (BC), Canada. Using a RAD‐seq data set for 717 P. californicus individuals across 24 sampling locations, we identified putatively adaptive (i.e., candidate) single nucleotide polymorphisms (SNPs) based on genotype–environment associations with seafloor temperature. We calculated various metrics for both neutral and candidate SNPs and compared SCP outcomes with independent metrics and combinations of metrics. Priority areas varied depending on whether neutral or candidate SNPs were used and on the specific metric used. For example, targeting sites with a high frequency of warm‐temperature‐associated alleles to support persistence under future warming prioritized areas in the southern coastal region. In contrast, targeting sites with high expected heterozygosity at candidate loci to support persistence under future environmental uncertainty prioritized areas in the north. When combining metrics, all scenarios generated intermediate solutions, protecting sites that span latitudinal and thermal gradients. Our results demonstrate that distinguishing between neutral and adaptive markers can affect conservation solutions and emphasize the importance of defining objectives when choosing among various genomic metrics for SCP. Article impact statement: Genomic metrics derived from neutral and adaptive genomic data result in different spatial conservation prioritization solutions. [ABSTRACT FROM AUTHOR]

Islands have been used as model systems to study ecological and evolutionary processes, and they provide an ideal set‐up for validating new biodiversity monitoring methods. The application of environmental DNA metabarcoding for monitoring marine biodiversity requires an understanding of the spatial scale of the eDNA signal, which is best tested in island systems. Here, we investigated the variation in Actinopterygii and Elasmobranchii species composition recovered from eDNA metabarcoding along a gradient of distance‐to‐reef in four of the five French Scattered Islands in the Western Indian Ocean. We collected surface water samples at an increasing distance from reefs (0 m, 250 m, 500 m, 750 m). We used a metabarcoding protocol based on the 'teleo' primers to target marine reef fishes and classified taxa according to their habitat types (benthic or pelagic). We investigated the effect of distance‐to‐reef on β diversity variation using generalised linear mixed models and estimated species‐specific distance‐to‐reef effects using a model‐based approach for community data. Environmental DNA metabarcoding analyses recovered distinct fish species compositions across the four inventoried islands and variations along the distance‐to‐reef gradient. The analysis of β‐diversity variation showed significant taxa turnover between the eDNA samples on and away from the reefs. In agreement with a spatially localised signal from eDNA, benthic species were distributed closer to the reef than pelagic ones. Our findings demonstrate that the combination of eDNA inventories and spatial modelling can provide insights into species habitat preferences related to distance‐to‐reef gradients at a small scale. As such, eDNA can not only recover large compositional differences among islands but also help understand habitat selection and distribution of marine species at a finer spatial scale. [ABSTRACT FROM AUTHOR]

Current approaches that compare spatial genetic structure of a given species and the dispersal of its mobile phase can detect a mismatch between both patterns mainly due to processes acting at different temporal scales. Genetic structure result from gene flow and other evolutionary and demographic processes over many generations, while dispersal predicted from the mobile phase often represents solely one generation on a single time‐step. In this study, we present a spatial graph approach to landscape genetics that extends connectivity networks with a stepping‐stone model to represent dispersal between suitable habitat patches over multiple generations. We illustrate the approach with the case of the striped red mullet Mullus surmuletus in the Mediterranean Sea. The genetic connectivity of M. surmuletus was not correlate with the estimated dispersal probability over one generation, but with the stepping‐stone estimate of larval dispersal, revealing the temporal scale of connectivity across the Mediterranean Sea. Our results highlight the importance of considering multiple generations and different time scales when relating demographic and genetic connectivity. The spatial graph of genetic distances further untangles intra‐population genetic structure revealing the Siculo‐Tunisian Strait as an important corridor rather than a barrier for gene flow between the Western‐ and Eastern Mediterranean basins, and identifying Mediterranean islands as important stepping‐stones for gene flow between continental populations. Our approach can be easily extended to other systems and environments. [ABSTRACT FROM AUTHOR]

Long-distance (>40-km) dispersal from marine reserves is poorly documented; yet, it can provide essential benefits such as seeding fished areas or connecting marine reserves into networks. From a meta-analysis, we suggest that the spatial scale of marine connectivity is underestimated due to the limited geographic extent of sampling designs. We also found that the largest marine reserves (>1000 km2) are the most isolated. These findings have important implications for the assessment of evolutionary, ecological, and socio-economic long-distance benefits of marine reserves. We conclude that existing methods to infer dispersal should consider the up-to-date genomic advances and also expand the spatial scale of sampling designs. Incorporating long-distance connectivity in conservation planning will contribute to increase the benefits of marine reserve networks. Highlights Marine dispersal distance estimates are limited by the spatial scale of sampling design and therefore biased downwards. Active larval behavior, oceanographic eddies and fronts, tsunamis, marine debris, and translocations are potentially important, but overlooked, dispersal vectors over long distances. The largest marine reserves have the highest potential for massive and long-distance benefits but are the most isolated reserves. Long-distance dispersal has important consequences for the design of marine reserve networks. [ABSTRACT FROM AUTHOR]

Studying demographic and genetic connectivity can help assess marine metapopulation structure. Rays and skates have no larval phase; hence, population connectivity can only result from active movement of individuals. Using thornback ray (Raja clavata) in European waters as a case study, demographic and genetic connectivity were studied for 11 putative populations with unequal population abundances and two hypotheses of dispersal rates. Genetic simulation results highlighted three large metapopulations: in the Mediterranean, around the Azores, and on the Northeast Atlantic shelf. Demographic results highlighted a finer population structure indicating that several pairs of putative populations might be demographically linked. Results were highly sensitive to dispersal assumptions and relative population abundances, which provided insights into the potential magnitude of genetic and demographic connectivity differences. Accounting for demographic connectivity appears to be crucial for managing and conserving rays and skates, while genetic connectivity provides a longer-term perspective and less subtle spatial structures. Moreover, accounting for heterogeneity in population abundances is a key factor for determining or interpreting metapopulation connectivity. [ABSTRACT FROM AUTHOR]

Aim: Coastal fishes have a fundamental role in marine ecosystem functioning and contributions to people, but face increasing threats due to climate change, habitat degradation and overexploitation. The extent to which human pressures are impacting coastal fish biodiversity in comparison with geographic and environmental factors at large spatial scale is still under scrutiny. Here, we took advantage of environmental DNA (eDNA) metabarcoding to investigate the relationship between fish biodiversity, including taxonomic and genetic components, and environmental but also socio‐economic factors. Location: Tropical, temperate and polar coastal areas. Time period: Present day. Major taxa studied: Marine fishes. Methods: We analysed fish eDNA in 263 stations (samples) in 68 sites distributed across polar, temperate and tropical regions. We modelled the effect of environmental, geographic and socio‐economic factors on α‐ and β‐diversity. We then computed the partial effect of each factor on several fish biodiversity components using taxonomic molecular units (MOTU) and genetic sequences. We also investigated the relationship between fish genetic α‐ and β‐diversity measured from our barcodes, and phylogenetic but also functional diversity. Results: We show that fish eDNA MOTU and sequence α‐ and β‐diversity have the strongest correlation with environmental factors on coastal ecosystems worldwide. However, our models also reveal a negative correlation between biodiversity and human dependence on marine ecosystems. In areas with high dependence, diversity of all fish, cryptobenthic fish and large fish MOTUs declined steeply. Finally, we show that a sequence diversity index, accounting for genetic distance between pairs of MOTUs, within and between communities, is a reliable proxy of phylogenetic and functional diversity. Main conclusions: Together, our results demonstrate that short eDNA sequences can be used to assess climate and direct human impacts on marine biodiversity at large scale in the Anthropocene and can further be extended to investigate biodiversity in its phylogenetic and functional dimensions. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Abstract: Disentangling the demographic processes that determine the genetic structure of a given species is a fundamental question in conservation and management. In the present study, the population structure of the European eel was examined with a multidisciplinary approach combining the fields of molecular genetics and population dynamics modelling. First, we analyzed a total of 346 adult specimens of known age collected in three separate sample sites using a large panel of 22 EST-linked microsatellite loci. Second, we developed a European eel-specific model to unravel the demographic mechanisms that can produce the level of genetic differentiation estimated by molecular markers. This is the first study that reveals a pattern of genetic patchiness in maturing adults of the European eel. A highly significant genetic differentiation was observed among samples that did not follow an Isolation-by-Distance or Isolation-by-Time pattern. The observation of genetic patchiness in adults is likely to result from a limited parental contribution to each spawning event as suggested by our modelling approach. The value of genetic differentiation found is predicted by the model when reproduction occurs in a limited number of spawning events isolated from each other in time or space, with an average of 130–375 breeders in each spawning event. Unpredictability in spawning success may have important consequences for the life-history evolution of the European eel, including a bet-hedging strategy (distributing reproductive efforts over time) which could in turn guarantee successful reproduction of some adults. [Copyright &y& Elsevier]

Natural floating objects (FOBs) have always been a major component of the habitat of pelagic species. Since the 1990s, the number of FOBs in the open ocean has increased greatly as a result of the introduction of fish aggregating devices (FADs) by the industrial tropical tuna purse seine vessels. These changes, and their potential impacts on the species that associate with FOBs, remain poorly understood. Using fisheries observer data, data from satellite-linked tracking buoys attached to FOBs and Lagrangian simulations, this study quantifies the temporal changes in the density and spatial distribution of FOBs due to the use of FADs in the Indian Ocean (IO) between 2006 and 2018. From 2012 to 2018, the entire western IO is impacted, with FADs representing more than 85% of the overall FOBs, natural FOBs less than 10%, and objects originating from pollution 5%. Results also suggest that both FADs and natural FOBs densities are lower in the eastern IO, but this initial investigation highlights the need for further studies. Our study confirms that FADs have greatly modified the density and spatial distribution of FOBs, which highlights the need to investigate potential consequences on the ecology of associated species. [ABSTRACT FROM AUTHOR]

Quantifying fish species diversity in rich tropical marine environments remains challenging. Environmental DNA (eDNA) metabarcoding is a promising tool to face this challenge through the filtering, amplification, and sequencing of DNA traces from water samples. However, because eDNA concentration is low in marine environments, the reliability of eDNA to detect species diversity can be limited. Using an eDNA metabarcoding approach to identify fish Molecular Taxonomic Units (MOTUs) with a single 12S marker, we aimed to assess how the number of sampling replicates and filtered water volume affect biodiversity estimates. We used a paired sampling design of 30 L per replicate on 68 reef transects from 8 sites in 3 tropical regions. We quantified local and regional sampling variability by comparing MOTU richness, compositional turnover, and compositional nestedness. We found strong turnover of MOTUs between replicated pairs of samples undertaken in the same location, time, and conditions. Paired samples contained non‐overlapping assemblages rather than subsets of one another. As a result, non‐saturated localized diversity accumulation curves suggest that even 6 replicates (180 L) in the same location can underestimate local diversity (for an area <1 km). However, sampling regional diversity using ~25 replicates in variable locations (often covering 10 s of km) often saturated biodiversity accumulation curves. Our results demonstrate variability of diversity estimates possibly arising from heterogeneous distribution of eDNA in seawater, highly skewed frequencies of eDNA traces per MOTU, in addition to variability in eDNA processing. This high compositional variability has consequences for using eDNA to monitor temporal and spatial biodiversity changes in local assemblages. Avoiding false‐negative detections in future biomonitoring efforts requires increasing replicates or sampled water volume to better inform management of marine biodiversity using eDNA. [ABSTRACT FROM AUTHOR]

Understanding larval connectivity patterns is critical for marine spatial planning, particularly for designing marine protected areas and managing fisheries. Patterns of larval dispersal and connectivity can be inferred from numerical transport models at large spatial and temporal scales. We assess model-based connectivity patterns between seamounts of the Southwestern Indian Ocean (SWIO) and the coastal ecosystems of Mauritius, La Réunion, Madagascar, Mozambique and South Africa, with emphasis on three shallow seamounts (La Pérouse [LP], MAD-Ridge [MR] and Walters Shoal [WS]). Using drifter trajectory and a Lagrangian model of ichthyoplankton dispersal, we show that larvae can undertake very long dispersion, with larval distances increasing with pelagic larval duration (PLD). There are three groups of greater connectivity: the region between the eastern coast of Madagascar, Mauritius and La Réunion islands; the seamounts of the South West Indian Ridge; and the pair formed by WS and a nearby un-named seamount. Connectivity between these three groups is evident only for the longest PLD examined (360 d). Connectivity from seamounts to coastal ecosystems is weak, with a maximum of 2% of larvae originating from seamounts reaching coastal ecosystems. Local retention at the three focal seamounts (LP, MR and WS) peaks at about 11% for the shortest PLD considered (15 d) at the most retentive seamount (WS) and decreases sharply with increasing PLD. Information on PLD and age of larvae collected at MR and LP are used to assess their putative origin. These larvae are likely self-recruits but it is also plausible that they immigrate from nearby coastal sites, i.e. the southern coast of Madagascar for MR and the islands of La Réunion and Mauritius for LP. [ABSTRACT FROM AUTHOR]