42 Works

Data from: Integration and harmonization of trait data from plant individuals across heterogeneous sources

Tim P. Lenters, Andrew Henderson, Caroline M. Dracxler, Guilherme A. Elias, Suzanne Mogue Kamga, Thomas L. P. Couvreur & W. Daniel Kissling
Trait data represent the basis for ecological and evolutionary research and have relevance for biodiversity conservation, ecosystem management and earth system modelling. The collection and mobilization of trait data has strongly increased over the last decade, but many trait databases still provide only species-level, aggregated trait values (e.g. ranges, means) and lack the direct observations on which those data are based. Thus, the vast majority of trait data measured directly from individuals remains hidden and...

Georeferenced semi-quantitative data of the jellyfish Rhizostoma pulmo (Cnidaria: Scyphozoa) from 1810 to 2019 in the Mediterranean and Black Seas

Valentina Leoni, Delphine Bonnet, Eduardo Ramírez Romero & Juan Carlos Molinero
This dataset is a gathering of historical and contemporaneous records of the medusae stage of Rhizostoma pulmo on its distributional range. The information was compilated to analyze biogeographical patterns and temporal changes of the species population dynamics. This compilation includes data available in websites and peer-review papers. All references are indicated. Data are individualized by month and year from 1810 to 2019, totalizing 7373 records. Longitude and latitude data are reported, as well as the...

Data from Soil chemistry turned upside down: a meta-analysis of invasive earthworm effects on soil chemical properties

Olga Ferlian, Madhav P. Thakur, Alejandra Castañeda González, Layla M. San Emeterio, Susanne Marr, Barbbara Da Silva Rocha & Nico Eisenhauer
Recent studies have shown that invasive earthworms can dramatically reduce native biodiversity, both above and below the ground. However, we still lack a synthetic understanding of the underlying mechanisms behind these changes, such as whether earthworm effects on soil chemical properties drive such relationships. Here, we investigated the effects of invasive earthworms on soil chemical properties (pH, water content, and the stocks and fluxes of carbon, nitrogen, and phosphorus) by conducting a meta-analysis. Invasive earthworms...

Data from: Mitochondrial haplotypes indicate parapatric-like phylogeographic structure in blue-spotted maskray (Neotrygon kuhlii) from the Coral Triangle region

Irma S. Arlyza, Kang-Ning Shen, Jean-Dominique Durand & Philippe Borsa
Phylogeographic structure was investigated in the blue-spotted maskray, Neotrygon kuhlii, focusing on the Coral Triangle region. We used as genetic marker a 519-bp fragment of the cytochrome c-oxidase subunit I (COI) gene, sequenced in a total of 147 individuals from 26 sampling locations. The parsimony network of COI haplotypes was split into seven distinct clades within the Coral Triangle region. Different clades had exclusive but contiguous geographic distributions, indicating parapatric-like phylogeographic structure. Strong genetic differences...

Data from: Isolation and no-entry marine reserves mitigate anthropogenic impacts on grey reef shark behavior

Jean-Baptiste Juhel, Laurent Vigliola, Laurent Wantiez, Tom B. Letessier, Jessica J. Meeuwig & David Mouillot
Reef sharks are vulnerable predators experiencing severe population declines mainly due to overexploitation. However, beyond direct exploitation, human activities can produce indirect or sub-lethal effects such as behavioral alterations. Such alterations are well known for terrestrial fauna but poorly documented for marine species. Using an extensive sampling of 367 stereo baited underwater videos systems, we show modifications in grey reef shark (Carcharhinus amblyrhynchos) occurrence and feeding behavior along a marked gradient of isolation from humans...

Data from: Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies

Cédric Mariac, Nora Scarcelli, Juliette Pouzadou, Adeline Barnaud, Claire Billot, Adama Faye, Vincent Maillol, Sylvain Santoni, Yves Vigouroux, Thomas L. P. Couvreur, Ayite Kougbeadjo, François Sabot & Guillaume Martin
Biodiversity, phylogeography and population genetic studies will be revolutionized by access to large datasets thanks to next generation sequencing methods. In this study, we develop an easy and cost-effective protocol for in-solution enrichment hybridization capture of complete chloroplast genomes applicable at deep multiplexed levels. The protocol uses cheap in-house species-specific probes developed via long range PCR of the entire chloroplast. Barcoded libraries are constructed and in-solution enrichment of the chloroplasts is done using the probes....

Data from: Phylogeography and niche modelling of the relict plant Amborella trichopoda (Amborellaceae) reveal multiple Pleistocene refugia in New Caledonia

Valérie Poncet, François Munoz, Jérôme Munzinger, Yohan Pillon, Céline Gomez, Marie Couderc, Christine Tranchant-Dubreuil, Serge Hamon & Alexandre De Kochko
Amborella trichopoda Baill. (Amborellaceae, Amborellales), the sole living member of the sister group to all other extant Angiosperms, is endemic to New Caledonia. We addressed the intraspecific phylogeography of Amborella by investigating whether its present population genetic structure could be related to its current and past habitats. We found moderate range-wide genetic diversity based on nuclear microsatellite data, and detected four well-differentiated, geographically distinct genetic groups using Bayesian clustering analyses. We modeled the ecological niche...

Data from: Trait evolution and historical biogeography shape assemblages of annual killifish

Andrew Helmstetter, Alexander Papadopulos, Javier Igea & Tom Van Dooren
Aim: Different species assemblages of annual killifish possess replicated body size distributions yet have unique sets of species in each area of endemism. Here, we use models of trait evolution and historical biogeography to discover how size variation originated and has been restructured. Location: South America. Taxon: Austrolebias (Cyprinodontiformes). Methods: We sampled 63 individuals from 26 Austrolebias species. Using phylogenetic trees (BEAST2), data on environmental variables at sampling locations and size data we compare different...

Data from: Individualistic evolutionary responses of central African rain forest plants to Pleistocene climatic fluctuations

Andrew Helmstetter, Kevin Bethune, Narcisse Kamdem, Bonaventure Sonke & Thomas Couvreur
Understanding the evolutionary dynamics of genetic diversity is fundamental for species conservation in the face of climate change, particularly in hyper-diverse biomes. Species in a region may respond similarly to climate change, leading to comparable evolutionary dynamics, or individualistically, resulting in dissimilar patterns. The second largest expanse of continuous tropical rain forest (TRF) in the world is found in Central Africa. Here, present-day patterns of genetic structure are thought to be dictated by repeated expansion...

Model output for: Attributing causes of future climate change in the California Current System with multi-model downscaling

Evan Howard, Hartmut Frenzel, Fayçal Kessouri, Lionel Renault, Daniele Bianchi, James McWilliams & Curtis Deutsch
Regional Ocean Modeling System outputs from dynamic downscaling of Coupled Model Intercomparison Project climate forcings in the California Current system, including projections with full climate forcings, as well as attribution experiments with only changes in wind, heat fluxes and other properties changing stratification, and boundary biogeochemical forcings. Output variables include euphotic zone integrated net primary productivity, and incident photosytnehtically available radiation, and ocean temperature, salinity, vertical velocity, and dissolved oxygen and nitrate concentrations at select...

Data from: Recommendations for assessing earthworm populations in Brazilian ecosystems

Herlon Nadolny, Alessandra Santos, Wilian Demetrio, Talita Ferreira, Lilianne Dos Santos Maia, Ana Caroline Conrado, Marie Bartz, Marilice Garrastazu, Elodie Da Silva, Dilmar Baretta, Amarildo Pasini, Fabiane Vezzani, José Paulo Sousa, Luis Cunha, Jerome Mathieu, Patrick Lavelle, Jörg Römbke & George Brown
Earthworms are often related to fertile soils and frequently used as environmental quality indicators. However, to optimize their use as bioindicators, their populations must be evaluated together with environmental and anthropogenic variables regulating earthworm communities. In this review we identify the earthworm, soil chemical, physical, environmental and management-related variables evaluated in 124 published studies that quantified earthworm abundance (>7300 samples) in 765 sites with different types of climate, soils, land use and management systems in...

Cocoa agroforest multifunctionality and soil fertility explained by shade tree litter traits

Marie Sauvadet, Stéphane Saj, Grégoire Freschet, Jean-Daniel Essobo, Séguy Enock, Thierry Becquer, Philippe Tixier & Jean-Michel Harmand
Manipulating plant functional diversity to improve agroecosystem multifunctionality is a central challenge of agricultural systems worldwide. In cocoa agroforestry systems (cAFS), shade trees are used to supply many services to farmers, yet their impact on soil functioning and cocoa yields is likely to vary substantially among tree species. Here, we compared the impact of five shade tree species (Canarium schweinfurthii (Canarium), Dacryoides edulis (Safou), Milicia excelsa (Iroko), Ceiba pentandra (Kapok tree), Albizia adianthifolia (Albizia)) and...

Data from: Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection

Jorge Duitama, Alexander Silva, Yamid Sanabria, Daniel Felipe Cruz, Constanza Quintero, Carolina Ballen, Mathias Lorieux, Brian Scheffler, Andrew Farmer, Edgar Torres, James Oard & Joe Tohme
Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the development of rice varieties through marker assisted selection or genomic selection. In this work we...

A local and global sensitivity analysis of a mathematical model of coagulation and platelet deposition under flow

Kathryn Link, Michael Stobb, Jorge Di Paola, Keith Neeves, Aaron Fogelson, Suzanne Sindi & Karin Leiderman
The hemostatic response involves blood coagulation and platelet aggregation to stop blood loss from an injured blood vessel. The complexity of these processes make it difficult to intuit the overall hemostatic response without quantitative methods. Mathematical models aim to address this challenge but are often accompanied by numerous parameters choices and thus need to be analyzed for sensitivity to such choices. Here we use local and global sensitivity analyses to study a model of coagulation...

COMOKIT: the COVID-19 Modeling Kit

Patrick Taillandier, Alexis Drogoul, Benoit Gaudou, Kevin Chapuis, Nghi Huyng Quang, Doanh Nguyen Ngoc, Arthur Brugière, Pierre Larmande, Marc Choisy & Damien Philippon
In the face of the COVID-19 pandemic, public health authorities around the world have experimented, in a short period of time, with various combinations of interventions at different scales. However, as the pandemic continues to progress, there is a growing need for tools and methodologies to quickly analyze the impact of these interventions and answer concrete questions regarding their effectiveness, range and temporality. COMOKIT, the COVID-19 modeling kit, is such a tool. It is a...

Aquaculture at the crossroads of global warming and antimicrobial resistance

Miriam Reverter, Samira Sarter, Domenico Caruso, Jean-Christophe Avarre, Marine Combe, Elodie Pepey, Laurent Pouyaud, Hugues De Verdal, Sarahi Vega-Heredía & Rodolphe Gozlan
In many developing countries, aquaculture is key to ensuring food security for millions of people. It is thus important to measure the full implications of environmental changes on the sustainability of aquaculture. We conducted a double meta-analysis (460 articles) to explore how global warming and antimicrobial resistance (AMR) impacts aquaculture. We calculated a Multi-Antibiotic Resistance index (MAR) of aquaculture-related bacteria (11,274 strains) for 40 countries, of which mostly low- and middle-income countries present high AMR...

Data from: Genetic structuring in a Neotropical palm analyzed through an Andean orogenesis‐scenario

Sebastián Escobar, Jean‐Christophe Pintaud, Henrik Balslev, Rodrigo Bernal, Mónica Moraes Ramírez, Betty Millán & Rommel Montúfar
Andean orogenesis has driven the development of very high plant diversity in the Neotropics through its impact on landscape evolution and climate. The analysis of the intraspecific patterns of genetic structure in plants would permit inferring the effects of Andean uplift on the evolution and diversification of Neotropical flora. In this study, using microsatellite markers and Bayesian clustering analyses, we report the presence of four genetic clusters for the palm Oenocarpus bataua var. bataua which...

Data from: How to capture fish in a school? Effect of successive predator attacks on seabird feeding success

Andréa Thiebault, Magali Semeria, Christophe Lett & Yann Tremblay
1. Prey aggregations, such as fish schools, attract numerous predators. This typically leads to the formation of multi-specific groups of predators. These aggregations can be seen both as a place of increased competition and as a place of possible facilitation between predators. Consequently, the functional role of such predator-prey aggregation is uncertain, and its effect on individual feeding success is virtually unknown. 2. Using underwater film footages of different predators feeding on fish schools during...

Data from: Cross-species hybridization and the origin of North African date palms

Jonathan M. Flowers, Khaled M. Hazzouri, Muriel Gros-Balthazard, Ziyi Mo, Konstantina Koutroumpa, Andreas Perrakis, Sylvie Ferrand, Hussam S. M. Khierallah, Dorian Q. Fuller, Frederique Aberlenc, Christini Fournaraki & Michael D. Purugganan
Date palm (Phoenix dactylifera L.) is a major fruit crop of arid regions that were domesticated 7,000 y ago in the Near or Middle East. This species is cultivated widely in the Middle East and North Africa, and previous population genetic studies have shown genetic differentiation between these regions. We investigated the evolutionary history of P. dactylifera and its wild relatives by resequencing the genomes of date palm varieties and five of its closest relatives....

Data from: Serological evidence of lyssaviruses among bats on southwestern Indian Ocean islands

Julien Mélade, Stewart McCulloch, Beza Ramasindrazana, Erwan Lagadec, Magali Turpin, Hervé Pascalis, Steven M. Goodman, Wanda Markotter & Koussay Dellagi
We provide serological evidence of lyssavirus circulation among bats on southwestern Indian Ocean (SWIO) islands. A total of 572 bats belonging to 22 species were collected on Anjouan, Mayotte, La Réunion, Mauritius, Mahé and Madagascar and screened by the Rapid Fluorescent Focus Inhibition Test for the presence of neutralising antibodies against the two main rabies related lyssaviruses circulating on the African continent: Duvenhage lyssavirus (DUVV) and Lagos bat lyssavirus (LBV), representing phylogroups I and II,...

Global biogeography and diversification of a group of brown seaweeds (Phaeophyceae) driven by clade-specific evolutionary processes

Christophe Vieira, Frederique Steen, Sofie D'hondt, Quinten Bafort, Cindy Fernandez-García, Brian Wysor, Lennert Tyberghein, Ana Tronholm, Lydiane Mattio, Claude Payri, Gary Saunders, Frederik Leliaert, Heroen Verbruggen & Olivier De Clerck
Aim: Historical processes that shaped current diversity patterns of seaweeds remain poorly understood. Using Dictyotales, a globally distributed order of brown seaweeds as a model, we test if historical biogeographical and diversification patterns are comparable across clades. Dictyotales contain some 22 genera, three of which, Dictyota, Lobophora and Padina, are exceptionally diverse. Specifically we test if the evolutionary processes in these clades that shaped their latitudinal diversity patterns are in line with the tropical conservatism,...

Araignées de Nouvelle-Calédonie : poster

J. Roger , Hervé Jourdan & David Brouste
Ce poster une sélection de 30 portraits, représentatifs de l'extrême diversité des formes et des modes de vie, avec quelques espèces emblématiques comme une mygale, la veuve noire ou une gasteracanthe, et d'autres qui le sont beaucoup moins mais pourtant tout aussi intéressantes pour les naturalistes.

Spiders of New Caledonia : poster

Jean Roger, D. Brouste & Hervé Jourdain
In 2018, the World Spider Catalogue listed more than 47,000 species of spiders distributed within more than 4,000 genera worldwide. Some scientific studies suggest that at least twice as many species need to be discovered. New Caledonia, classified as one of the world’s biodiversity hotspots because of the incredible richness of its fauna and flora, both heavily threatened by human impacts, is not to be outdone. More than 320 species of spiders have been recorded...

Data from: Genome scan reveals selection acting on genes linked to stress response in wild pearl millet

Cécile Berthouly-Salazar, Anne-Céline Thuillet, Bénédicte Rhoné, Cédric Mariac, Issaka Salia Ousseini, Marie Couderc, Maud I. Tenaillon & Yves Vigouroux
Uncovering genomic regions involved in adaption is a major goal in evolutionary biology. High-throughput sequencing now makes it possible to tackle this challenge in nonmodel species. Yet, despite the increasing number of methods targeted to specifically detect genomic footprints of selection, the complex demography of natural populations often causes high rates of false positive in gene discoveries. The aim of this study was to identify climate adaptations in wild pearl millet populations, Cenchrus americanus ssp....

Data from: Spatial structure of above-ground biomass limits accuracy of carbon mapping in rainforest but large scale forest inventories can help to overcome

Stéphane Guitet, Bruno Hérault, Quentin Molto, Olivier Brunaux & Pierre Couteron
Precise mapping of above-ground biomass (AGB) is a major challenge for the success of REDD+ processes in tropical rainforest. The usual mapping methods are based on two hypotheses: a large and long-ranged spatial autocorrelation and a strong environment influence at the regional scale. However, there are no studies of the spatial structure of AGB at the landscapes scale to support these assumptions. We studied spatial variation in AGB at various scales using two large forest...

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