Soil environment is a key driver of adaptation in Medicago truncatula: new insights from Landscape genomics. P0301

Legumes have great economic importance in global agriculture as they are a major source of protein for humans, and their ability to fixate nitrogen through endosymbiosis is unique. Nevertheless, they have not been studied as extensively as other crops. ln this sense, the barrel medic (Medicago truncatula) is an invaluable model for studying local adaptation in legumes. Previous studies on M.truncatula have identified loci potentially responsible for adaptation to climatic variables. However, environ mental characteristics other than climate can pose selective pressures on adaptive genomic variation of barrel medic. ln the present study, we used Latent-Factor-Mixed-Models (LFMM) and Maran spectral outlier detection/ randomization (MSOD-MSR) to identify candidate loci for adaptation to 10 environ mental variables (climatic, soil and atmospheric) among 43,515 SNPs from 202 accessions of the model legume Medicago truncatula. We found that most candidate loci were associated with soil variables, highlighting the importance of soil environment as driver of local adaptation. Candidate SNPs associated with drought and soil salinity tagged genes with known functions in response to abiotic and biotic stress, while candidates associated with atmospheric and soil nitrogen tagged genes involved in different stages of the legume-rhizobia symbiosis. Candidate SNPs identified by bath LFMM and MSOD-MSR explained up to 56% of variance in phenotypic traits such as growth and flowering time, which supports their adaptive relevance in M.truncatula. Our findings highlight the importance of variables other than climate in promoting local adaptation in the system, and suggest that global climate change and anthropogenic disruption of the nitrogen cycle cou Id disrupt local adaptation

Geographic distance, water circulation and environmental conditions shape the biodiversity of Mediterranean rocky coasts

11 páginas, 2 tablas, 3 figuras.Ecological connectivity is important for effective marine planning and biodiversity conservation. Our aim was to identify factors important in influencing variation in benthic community structure on shallow rocky reefs in 2 regions of the Mediterranean Sea with contrasting oceanographic regimes. We assessed beta (β) diversity at 146 sites in the littoral and shallow sublittoral from the Adriatic/Ionian Seas (eastern region) and Ligurian/Tyrrhenian Seas (western region) using a null modelling approach to account for variation in species richness. The distance decay relationship between species turnover within each region and geographic distance by sea was determined using generalised linear models. Mantel tests were used to examine correlations between β diversity and connectivity by ocean currents, estimated from Lagrangian dispersal simulations. Variation in β diversity between sites was partitioned according to environmental and spatial components using a distance-based redundancy approach. Species turnover along a gradient of geographic distance was greater by a factor of 3 to 5 in the western region than the eastern region, suggesting lower connectivity between sites. β diversity was correlated with connectivity by ocean currents at both depths in the eastern region but not in the western region. The influOPEN ACCESS ence of spatial and environmental predictors of β diversity varied considerably between regions, but was similar between depths. Our results highlight the interaction of oceanographic, spatial and environmental processes influencing benthic marine β diversity. Persistent currents in the eastern region may be responsible for lower observed β diversity compared to the western region, where patterns of water circulation are more variable.This work was supported by the European Community’s 7th Framework Programme (FP7/ 2007−2013) under Grant Agreement No. 287844 for the project ‘Towards COast to COast NETworks of marine protected areas (from the shore to the high and deep sea), coupled with sea-based wind energy potential (CoCoNet)’.Peer reviewe

Biologically representative and well-connected marine reserves enhance biodiversity persistence in conservation planning

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

New insights on the population genetic structure of the great scallop (Pecten maximus) in the English Channel coupling microsatellite data and demogenetic simulations.

International audienceThe great scallop (Pecten maximus) is a commercially important bivalve in Europe, particularly in the English Channel, where fisheries are managed at regional and local scales through the regulation of fishing effort. In the long term, knowledge about larval dispersal and gene flow between populations is essential to ensure proper stock management. Yet, previous population genetic studies have reported contradictory results. In this study, scallop samples collected across the main fishing grounds along the French and English coasts of the English Channel (20 samples with temporal replicates for three sites,n= 1059 individuals), and the population genetic structure was analysed using 13 microsatellite loci. Coupling empirical genetic data with demogenetic modelling based on a biophysical model simulating larval exchanges among scallop beds revealed a subtle genetic differentiation between south-west English populations and the rest of the English Channel, which was consistent with larval dispersal simulations. The present study provides a step forward in the understanding of great scallop population biology in the English Channel, underlining the fact that even in a context of potentially high gene flow and recent divergence times since the end of the last glacial maximum, weak but significant spatial genetic structure can be identified at a regional scale

Structure and diversity patterns of coralligenous cliffs across three ecoregions in the Central‐Western Mediterranean Sea

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.The authors did not receive financial support from any organization for the submitted work.Peer reviewe

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

Advances in systematic conservation planning to meet global biodiversity goals

Systematic conservation planning (SCP) involves the cost-effective placement and application of management actions to achieve biodiversity conservation objectives. Given the political momentum for greater global nature protection, restoration, and improved management of natural resources articulated in the targets of the Global Biodiversity Framework, assessing the state-of-the-art of SCP is timely. Recent advances in SCP include faster and more exact algorithms and software, inclusion of ecosystem services and multiple facets of biodiversity (e.g., genetic diversity, functional diversity), climate-smart approaches, prioritizing multiple actions, and increased SCP accessibility through online tools. To promote the adoption of SCP by decision-makers, we provide recommendations for bridging the gap between SCP science and practice, such as standardizing the communication of planning uncertainty and capacity-building training courses

Estimation et analyse de la taille efficace de populations structurées en classes d'âge ou en stades

Effective population size Ne is a central parameter in evolutionary and conservation biology and can be estimated with demographic- and genetic-based methods. The objective of this thesis was to analyze the effects of life-history on Ne in species with overlapping generations using demographic models. One demographic and two genetic estimators were used to derive Ne in the endangered perennial plant Eryngium alpinum. The three methods gave considerably different estimates. The differences could be attributed to the difficulty in obtaining al the necessary data needed in the demographic model, but also to the reduced precision of genetic estimators when dealing with small genetic sample sizes. Demographic models nonetheless permitted identifying the effect of lifehistory on Ne through elasticity and sensitivity analyses. Numerical elasticity was employed to study the effect of stage-specific vital rates on Ne in E. alpinum and the endangered perennial plant Dracocephalum austriacum. The derived elasticity patterns were often, but not always, similar in populations with comparable demography. One demographic model was then analysed in detail to derive analytically an expression for the sensitivity of Ne/N to age-specific vital rates. This expression was used to study Ne/N in three species differing in their survivorship curves (humans, sparrows and barnacles). In this way, the differences in the sensitivity patterns among the three species could be attributed to specific components of the life-cycle. This thesis demonstrates that demographic models are powerful methods to understand the effects of the life-history on Ne and could be useful tools to complement genetic estimators when sufficient ecological and demographic data are available. The next step will be to generalize the observed elasticity and sensitivity patterns using a comparative approach on a large number of populations, which will be possible thanks to the quick accumulation of large amounts of demographic and genetic data on a great number of species.La taille efficace des populations, Ne, est un paramètre central en biologie de la conservation et en biologie évolutive et peut être estimée avec des méthodes démographiques et génétiques. L'objectif de cette thèse a été l'analyse des effets de l'histoire de vie sur Ne dans des espèces à générations chevauchantes en utilisant des modèles démographiques. Un modèle démographique et deux estimateurs génétiques ont été utilisés pour dériver Ne dans des population d' Eryngium alpinum, une plante pérenne et menacée. Les trois méthodes ont donné des estimations considérablement différentes. Les différences ont pu être attribuées à la difficulté d'obtenir toutes les données nécessaires au modèle démographique, mais aussi à la faible précision des estimateurs génétiques quand ils sont appliqués à des jeux de données limités. Les modèles démographiques ont cependant permis l'identification des effets de l'histoire de vie sur Ne à travers des analyses de sensibilité et d'élasticité. L'élasticité numérique a été utilisée pour étudier les effets sur Ne de taux vitaux stadespécifiques dans E. alpinum et dans Dracocephalum austriacum, une plante alpine pérenne et menacée. Les patrons d'élasticité dérivés étaient souvent, mais pas toujours, similaires dans des populations à démographie comparable. Ensuite, un modèle démographique a été analysé en détail pour dériver analytiquement une expression pour la sensibilité de Ne/N aux taux vitaux âgespécifiques. Cette expression a été utilisée pour étudier Ne/N dans trois espèces qui diffèrent dans leur patron de courbe de survie (humains, bruants et balanes). Les différences des patrons de sensibilité entre ces trois espèces ont pu être ainsi attribuées à des composantes spécifiques du cycle de vie. Cette thèse montre que les modèles démographiques sont des méthodes utiles pour comprendre les effets de l'histoire de vie sur Ne et qu'ils pourraient être des outils puissants pour complémenter les estimateurs génétiques quand des données écologiques et démographiques sont disponibles en quantité suffisante. L'étape suivante sera la généralisation des patrons de sensibilité et d'élasticité observés en utilisant une approche comparative sur un grande nombre de populations, ce qui sera possible grâce à la rapide accumulation de grandes quantités des données démographiques et génétiques sur un grand nombre d'espèces