25 Works

Natural selection drives genome-wide evolution via chance genetic associations

Zachariah Gompert, Jeff Feder & Patrik Nosil
Understanding selection's impact on the genome is a major theme in biology. Functionally-neutral genetic regions can be affected indirectly by natural selection, via their statistical association with genes under direct selection. The genomic extent of such indirect selection, particularly across loci not physically linked to those under direct selection, remains poorly understood, as does the time scale at which indirect selection occurs. Here we use field experiments and genomic data in stick insects, deer mice...

Species ecology explains the various spatial components of genetic diversity in tropical reef fishes

Giulia Francesca Azzurra Donati, Niklaus Zemp, Stéphanie Manel, Maude Poirier, Thomas Claverie, Franck Ferraton, Théo Gaboriau, Rodney Govinden, Oskar Hagen, Shameel Ibrahim, David Mouillot, Julien Leblond, Pagu Julius, Laure Velez, Irthisham Zareer, Adam Ziyad, Fabien Leprieur, Camille Albouy & Loïc Pellissier
Generating genomic data for 19 tropical reef fish species of the Western Indian Ocean, we investigate how species ecology influences genetic diver- sity patterns from local to regional scales. We distinguish between the α, β and γ components of genetic diversity, which we subsequently link to six ecological traits. We find that the α and γ components of genetic diversity are strongly correlated so that species with a high total regional genetic diversity display systematically...

Contextual variations in calls of two non-oscine birds: the blue petrel and the Antarctic prion

Charlène Gémard, Víctor Planas-Bielsa, Francesco Bonadonna & Thierry Aubin
Bird vocalizations are critical cues in social interactions as they convey temporary information varying with the social context, e.g. the signaler motivation when facing a rival or a potential mate. To date, literature mainly focuses on learning birds. Burrowing petrels (Procellariidae) are non-learning birds with a limited vocal repertoire. Bachelor males communicate with conspecifics with a single call emitted in three situations: in absence of a certain auditory (spontaneous calls), towards females (female-directed calls) and...

Do ecological specialization and functional traits explain the abundance–frequency relationship? Arable weeds as a case study

Guillaume Fried, Laura Armengot, Jonathan Storkey, Bérenger Bourgeois, Sabrina Gaba, Cyrille Violle & François Munoz
Aim: The abundance-frequency relationship (AFR) is among the most-investigated pattern in biogeography, yet the relative contributions of niche-based processes related to ecological strategies, and of neutral processes related to spatial colonization-extinction dynamics, remains uncertain. Here, we tested the influences of ecological specialization and functional traits on local abundance and regional frequency, to determine the contribution of niche-based processes. Location: France and the UK. Taxon: Vascular plants. Methods: We used two arable weed surveys covering 1544...

Survival data of five artificial morphs with different transparency characteritics

Mónica Arias, Lucie Leroy, Clément Madec, Louane Matos, Cynthia Tedore, Marianne Elias & Doris Gomez
Fieldwork data of artificial prey survival of five different morphs with differences in their transparent element characteristics: O (opaque, 0 transparency), SW (small transparent windows), LW (large transparent windows), BE (large windows touching one prey edge) and B3E (large windows touching 3 prey edges). The experiment was performed in in two forests in southern France with evergreen and white oaks as predominant tree vegetation: La Rouvière forest (43.65°N, 3.64°E) and a large natural wooded area...

Linking genetic, morphological, and behavioural divergence between inland island and mainland deer mice

Joshua Miller, Dany Garant, Charles Perrier, Tristan Juette, Joël Jameson, Denis Réale, Eric Normandeau & Louis Bernatchez
The island syndrome hypothesis (ISH) stipulates that, as a result of local selection pressures and restricted gene flow, individuals from island populations should differ from individuals within mainland populations. Specifically, island populations are predicted to contain individuals that are larger, less aggressive, more sociable, and that invest more in their offspring. To date, tests of the ISH have mainly compared oceanic islands to continental sites, and rarely smaller spatial scales such as inland watersheds. Here,...

Sexual selection and sexual size dimorphism in animals

Tim Janicke & Salomé Fromonteil
Sexual selection is often considered as a critical evolutionary force promoting sexual size dimorphism (SSD) in animals. However, empirical evidence for a positive relationship between sexual selection on males and male-biased SSD received mixed support depending on the studied taxonomic group and on the method used to quantify sexual selection. Here, we present a meta-analytic approach accounting for phylogenetic non-independence to test how standardized metrics of the opportunity and strength of pre-copulatory sexual selection relate...

Data from: Adaptive niche‐based sampling to improve ability to find rare and elusive species: Simulations and field tests

Jules Chiffard, Philippe Fontanilles & Stephane Duchateau
Adaptive niche-based sampling (ANBS) is an iterative sampling strategy that relies on the predictions of species distribution models (SDMs). By predicting highly suitable areas to guide prospection, ANBS could improve the efficiency of sampling effort in terms of finding new locations for rare species. Its iterative quality could potentially mitigate the effect of small and initially biased samples on SDMs. In this study, we compared ANBS with random sampling by assessing the gain in terms...

Drivers of black grouse trends in the French Alps

Canonne Coline
This dataset is composed of three R files: One entitled "BGcounts" that contains an array named "count", composed of counts of black grouse males during lek season conducted on reference sites monitored by a french organisation called "OGM" (https://www.observatoire-galliformes-montagne.com/). The network is composed of 47 counting sites (raws of the dataset), and counts started on various dates on each site (from 1980's to 1990's). Columns (40) are years from 1979 to 2018. Finally, during the...

Environmental effects on the genetic architecture of fitness components in a simultaneous hermaphrodite

Tim Janicke
Understanding how environmental change affects genetic variances and covariances of reproductive traits is key to formulate firm predictions on evolutionary responses. This is particularly true for sex-specific variance in reproductive success, which has been argued to affect how populations can adapt to environmental change. Our current knowledge on the impact of environmental stress on sex-specific genetic architecture of fitness components is still limited and restricted to separate-sexed organisms. However, hermaphroditism is widespread across animals and...

Mutual mate choice and assortative mating in relation to a carotenoid-based color trait in blue tits

Samuel Caro, Léo Pierre, Matthieu Berges, Raldi Bakker, Claire Doutrelant & Francesco Bonadonna
Choosing an appropriate partner is a critical decision for many animal species. However, many mechanisms involved in mate choice are still poorly understood. Do both males and females choose their sexual partners, do both sexes use the same criteria for choosing, and do their own phenotype influence the choices they make, are questions that need further investigation. Over two successive experiments conducted in captivity with hand-reared blue tits (Cyanistes caeruleus), we manipulated the color of...

Environmental DNA metabarcoding reveals and unpacks a biodiversity conservation paradox in Mediterranean marine reserves

Emilie Boulanger, Nicolas Loiseau, Alice Valentini, Véronique Arnal, Pierre Boissery, Tony Dejean, Julie Deter, Nacim Guellati, Florian Holon, Jean-Baptiste Juhel, Philippe Lenfant, Stephanie Manel & David Mouillot
Although we are currently experiencing worldwide biodiversity loss, local species richness does not always decline under anthropogenic pressure. This conservation paradox may also apply in protected areas but has not yet received conclusive evidence in marine ecosystems. Here, we survey fish assemblages in six Mediterranean no-take reserves and their adjacent fishing grounds using environmental DNA (eDNA) while controlling for environmental conditions. We detect less fish species in marine reserves than in nearby fished areas. The...

Epidemiological and evolutionary consequences of periodicity in treatment coverage

Alicia Walter & Sébastien Lion
Host heterogeneity is a key driver of host-pathogen dynamics. In particular, the use of treatments against infectious diseases creates variation in quality among hosts, which can have both epidemiological and evolutionary consequences. We present a general theoretical model to highlight the consequences of different imperfect treatments on pathogen prevalence and evolution. These treatments differ by their action on host and pathogen traits. In contrast with previous studies, we assume that treatment coverage can vary in...

Data and code from: Predicting population genetic change in an autocorrelated random environment: insights from a large automated experiment

Marie Rescan, Daphné Grulois, Enrique Ortega Aboud, Pierre De Villemereuil & Luis-Miguel Chevin
Most natural environments exhibit a substantial component of random variation, with a degree of temporal autocorrelation that defines the color of environmental noise. Such environmental fluctuations cause random fluctuations in natural selection, affecting the predictability of evolution. But despite long-standing theoretical interest for population genetics in stochastic environments, there is a dearth of empirical estimation of underlying parameters of this theory. More importantly, it is still an open question whether evolution in fluctuating environments can...

Environmental DNA metabarcoding reveals and unpacks a biodiversity conservation paradox in Mediterranean marine reserves

Emilie Boulanger, Nicolas Loiseau, Alice Valentini, Véronique Arnal, Pierre Boissery, Tony Dejean, Julie Deter, Nacim Guellati, Florian Holon, Jean-Baptiste Juhel, Philippe Lenfant, Stephanie Manel & David Mouillot
Although we are currently experiencing worldwide biodiversity loss, local species richness does not always decline under anthropogenic pressure. This conservation paradox may also apply in protected areas but has not yet received conclusive evidence in marine ecosystems. Here, we survey fish assemblages in six Mediterranean no-take reserves and their adjacent fishing grounds using environmental DNA (eDNA) while controlling for environmental conditions. We detect less fish species in marine reserves than in nearby fished areas. The...

Data from: Maternal allocation in relation to weather, predation, and social factors in a colonial cooperative bird

Rita Fortuna, Matthieu Paquet, André C. Ferreira, Liliana R. Silva, Franck Theron, Claire Doutrelant & Rita Covas
Females may adjust prenatal allocation in relation to ecological conditions that affect reproductive success, such as weather conditions or predation risk. In cooperative breeders, helpers might also influence reproductive success and previous studies suggest that females can lay smaller eggs or larger clutches when breeding with more helpers. Although recent work suggests that helper effects can vary according to climatic variables, how social and ecological factors interact to shape prenatal allocation is poorly understood. Here,...

Restricted dispersal in a sea of gene flow

Laura Benestan
How far do marine larvae disperse in the ocean? Decades of population genetic studies have revealed generally low levels of genetic structure at large spatial scales (hundreds of km). Yet this result, which is typically based on discrete sampling designs, does not necessarily imply extensive dispersal. Here, we adopt a continuous sampling strategy along 950 km of coast in the Northwestern Mediterranean Sea to address this question in four species. In line with expectations, we...

Land use changes threaten bird taxonomic and functional diversity across the Mediterranean basin: a spatial analysis to prioritize monitoring for conservation

Johanna Fusco, Walker Emily, Papaïx Julien, Debolini Marta, Bondeau Alberte & Barnagaud Jean-Yves
Land use changes rank among the highest threats to biodiversity, but assessment of their ecological impact is impaired by data paucity in vast regions of the world. For birds, land use changes may mean habitat loss or fragmentation, changes in resource availability and disruption of biotic interactions or dispersal pathways. As a result, avian population sizes and assemblage diversity decline in areas subjected to urbanization, agricultural intensification and land abandonment worldwide. This threat is especially...

metabarcoding data for: Benchmark of bioinformatics tools for fast and accurate species identification from environmental DNA metabarcoding

Laetitia Mathon
This dataset contains fish DNA sequences samples, simulated with Grinder, to build a mock community, as well as real fish eDNA metabarcoding data from the Mediterranean sea. These data have been used to compare the efficiency of different bioinformatic tools in retrieving the species composition of real and simulated samples.

A worldwide assessment of soil macroinvertebrate communities

Patrick Lavelle, Jerome Mathieu, Alister Spain, George Brown, Carlos Fragoso, Emmanuel Lapied, Adriana De Aquino, Isabelle Barois, Edmundo Barrios, Eleusa Barros, Juan Camilo Bedano, Eric Blanchart, Mark Caulfield, Yamileth Chagueza, Jun Dai, Thibaud Decaens, Anahi Domninquez, Yamileth Dominquez, Alex Feijoo, Patricia Folgaraiti, Steven Fonte, Norma Gorosito, Esperanza Huerta, Juan Jose Jimenez, Courtland Kelly … & Cesar Botero
Soil macroinvertebrate communities have been assessed worldwide using the standard ISO/TSBF sampling procedure. The Macrofauna database currently comprises 3694 sites distributed throughout 41 countries, from 55º S latitude to 57ºN, sea level to over 4000m in elevation, in total annual total rainfall regimes between 500 and >3000mm and 5 to 32ºC mean temperature. These communities are significantly influenced by climatic parameters, soil texture and vegetation cover. Abundance and diversity were highest in tropical rain forests...

Efficient use of harvest data: A size-class-structured integrated population model for exploited populations

Marlène Gamelon, Chloé R. Nater, Eric Baubet, Aurelien Besnard, Laura Touzot, Jean-Michel Gaillard, Jean-Dominique Lebreton & Olivier Gimenez
Many animal populations are subject to hunting or fishing in the wild. Detailed knowledge of demographic parameters (e.g. survival, reproduction) and temporal dynamics of such populations is crucial for sustainable management. Despite their relevance for management decisions, structure and size of exploited populations are often not known, and data limited. Recently, joint analysis of different types of demographic data, such as population counts, reproductive data and capture-mark-recapture data, within integrated population models (IPMs) has gained...

Multiple paths to cold tolerance: the role of environmental cues, morphological traits and the circadian clock gene vrille

Noora Poikela, Venera Tyukmaeva, Anneli Hoikkala & Maaria Kankare
Background: Tracing the association between insect cold tolerance and latitudinally and locally varying environmental conditions, as well as key morphological traits and molecular mechanisms, is essential for understanding the processes involved in adaptation. We explored these issues in two closely-related species, Drosophila montana and Drosophila flavomontana, originating from diverse climatic locations across several latitudes on the coastal and mountainous regions of North America. We also investigated the association between sequence variation in one of the...

Data from: Population genomics and history of speciation reveal fishery management gaps in two related redfish species (Sebastes mentella and Sebastes fasciatus)

Laura Benestan
Understanding the processes shaping population structure and reproductive isolation of marine organisms can improve their management and conservation. Using genomic markers combined with estimation of individual ancestries, assignment tests, spatial ecology, and demographic modelling, we (i) characterized the contemporary population structure, (ii) assessed the influence of space, fishing depth and sampling years on contemporary distribution, and (iii) reconstructed the speciation history of two cryptic redfish species, Sebastes mentella and S. fasciatus. We genotyped 860 individuals...

Climate differently influences genomic patterns of two sympatric marine fish species

Emilie Boulanger, Laura Benestan, Pierre-Edouard Guerin, Alicia Dalongeville, David Mouillot & Stéphanie Manel
1- Climate influences population genetic variation of marine species. Capturing those impacts remains challenging for marine fishes dispersing over a large geographic scale spanning steep environmental gradients. This requires an extensive spatial sampling of individuals or populations, representative of seascape heterogeneity, combined with a set of highly informative molecular markers able to reveal climatic-associated genomic variations. 2- We explored how space, dispersal and environment shape the genomic patterns of two marine fish species. We hypothesized...

Phenological data for the article: Phenotypic plasticity drives phenological changes in a Mediterranean blue tit population

Juliette Biquet, Suzanne Bonamour, Pierre De Villemereuil, Christophe De Franceschi & Céline Teplitsky
Earlier phenology induced by climate change, such as the passerines' breeding time, is observed in many natural populations. Understanding the nature of such changes is key to predict the responses of wild populations to climate change. Genetic changes have been rarely investigated for laying date, though it has been shown to be heritable and under directional selection, suggesting that the trait could evolve. In a Corsican blue tit population, the birds' laying date has significantly...

Registration Year

  • 2021

Resource Types

  • Dataset


  • Centre d'Ecologie Fonctionnelle et Evolutive
  • Marine Biodiversity Exploitation and Conservation
  • National Research Institute for Agriculture, Food and Environment
  • University of Perpignan
  • Université Laval
  • National University of Río Cuarto
  • University of Quebec at Montreal
  • Paris-Saclay Institute of Neuroscience
  • MacEwan University
  • Universität Hamburg