301 Works

Data from: The early spread and epidemic ignition of HIV-1 in human populations

Nuno R. Faria, Andrew Rambaut, Marc A. Suchard, Guy Baele, Trevor Bedford, Melissa J. Ward, Andrew J. Tatem, João D. Sousa, Nimalan Arinaminpathy, Jacques Pépin, David Posada, Martine Peeters, Oliver P. Pybus & Philippe Lemey
Thirty years after the discovery of HIV-1, the early transmission, dissemination and establishment of the virus in human populations remain unclear. Using statistical approaches applied to HIV-1 sequence data from central Africa, we show that from the 1920s Kinshasa was the focus of early transmission and the source of pre-1960 pandemic viruses elsewhere. Location and dating estimates were validated using the earliest HIV-1 archival sample, also from Kinshasa. The epidemic histories of HIV-1 group M...

Data from: Distinguishing contemporary hybridization from past introgression with postgenomic ancestry-informative SNPs in strongly differentiated Ciona species

Sarah Bouchemousse, Cathy Liautard-Haag, Nicolas Bierne & Frédérique Viard
Biological introductions bring into contact species that can still hybridize. The evolutionary outcomes of such secondary contacts may be diverse (e.g. adaptive introgression from or into the introduced species) but are not yet well examined in the wild. The recent secondary contact between the non-native sea squirt Ciona robusta (formerly known as C. intestinalis type A) and its native congener C. intestinalis (formerly known as C. intestinalis type B), in the Western English Channel, provides...

Data from: Relating fitness to long-term environmental variations in natura

Pascal Milesi, Thomas Lenormand, Christophe Lagneau, Mylène Weill & Pierrick Labbé
Quantifying links between ecological processes and adaptation dynamics in natura remains a crucial challenge. Many studies have documented the strength, form and direction of selection, and its variations in space and time, but only a few managed to link these variations to their proximal causes. This step is, however, crucial, if we are to understand how the variation in selective pressure affects adaptive allele dynamics in natural settings. We used data from a long-term survey...

Data from: RClone: a package to identify MultiLocus Clonal Lineages and handle clonal datasets in R

Diane Bailleul, Solenn Stoeckel & Sophie Arnaud-Haond
Partially clonal species are common in the Tree of Life. And yet, population genetics models still mostly focus on the extremes: strictly sexual versus purely asexual reproduction. Here we present an R package built upon GenClone software including new functions and several improvements. The RClone package includes functions to handle clonal datasets, allowing (i) checking for dataset reliability to discriminate multi-locus genotypes (MLG), (ii) ascertainment of MLG and semi-automatic determination of clonal lineages (MLL), (iii)...

Data from: How structured is the entangled bank? The surprisingly simple organization of multiplex ecological networks leads to increased persistence and resilience

Sonia Kéfi, Vincent Miele, Evie A. Wieters, Sergio A. Navarrete & Eric L. Berlow
Species are linked to each other by a myriad of positive and negative interactions. This complex spectrum of interactions constitutes a network of links that mediates ecological communities’ response to perturbations, such as exploitation and climate change. In the last decades, there have been great advances in the study of intricate ecological networks. We have, nonetheless, lacked both the data and the tools to more rigorously understand the patterning of multiple interaction types between species...

Data from: Phylogeography of the small Indian civet and origin of introductions to western Indian Ocean islands

Philippe Gaubert, Riddhi Patel, Geraldine Veron, Steve M. Goodman, Maraike Willsch, Raquel Vasconcelos, Andre Lourenço, Marie Sigaud, Fabienne Justy, Bheem Dutt Joshi, Joerns Fickel & Abdreas Wilting
The biogeographic dynamics affecting the Indian subcontinent, East and Southeast Asia during the Plio-Pleistocene has generated complex biodiversity patterns. We assessed the molecular biogeography of the small Indian civet (Viverricula indica) through mitogenome and cytochrome b + control region sequencing of 89 historical and modern samples to (i) establish a time-calibrated phylogeography across the species’ native range and (ii) test introduction scenarios to western Indian Ocean islands. Bayesian phylogenetic analyses identified three geographic lineages (East...

Data from: Size evolution in microorganisms masks trade-offs predicted by the growth rate hypothesis

Isabelle Gounand, Tanguy Daufresne, Dominique Gravel, Corinne Bouvier, Thierry Bouvier, Marine Combe, Claire Gougat-Barbera, Franck Poly, Clara Torres-Barceló & Nicolas Mouquet
Adaptation to local resource availability depends on responses in growth rate and nutrient acquisition. The growth rate hypothesis (GRH) suggests that growing fast should impair competitive abilities for phosphorus and nitrogen due to high demand for biosynthesis. However, in microorganisms, size influences both growth and uptake rates, which may mask trade-offs and instead generate a positive relationship between these traits (size hypothesis, SH). Here, we evolved a gradient of maximum growth rate (μmax) from a...

Data from: How the truffle got its mate: insights from genetic structure in spontaneous and planted Mediterranean populations of Tuber melanosporum

Elisa Taschen, François Rousset, Mathieu Sauve, Laure Benoit, Marie-Pierre Dubois, Franck Richard, Marc-André Selosse, M.-P. Dubois & M.-A. Selosse
The life cycles and dispersal of edible fungi are still poorly known, thus limiting our understanding of their evolution and domestication. The prized Tuber melanosporum produces fruitbodies (fleshy organs where meiospores mature) gathered in natural, spontaneously inoculated forests or harvested in plantations of nursery-inoculated trees. Yet, how fruitbodies are formed remains unclear, thus limiting yields, and how current domestication attempts affect population genetic structure is overlooked. Fruitbodies result from mating between two haploid individuals: the...

Data from: DNA metabarcoding of Amazonian ichthyoplankton swarms

Marie Eugenie Maggia, Yves Vigouroux, Jean François Renno, Fabrice Duponchelle, Erick Desmarais, Jesus Nunez, Carmen García-Dávila, Fernando M. Carvajal, Emmanuel Paradis, Jean Francois Martin & Cédric Mariac
Tropical rainforests harbor extraordinary biodiversity. The Amazon basin is thought to hold 30% of all river fish species in the world. Information about the ecology, reproduction, and recruitment of most species is still lacking, thus hampering fisheries management and successful conservation strategies. One of the key understudied issues in the study of population dynamics is recruitment. Fish larval ecology in tropical biomes is still in its infancy owing to identification difficulties. Molecular techniques are very...

Data from: Range expansion underlies historical introgressive hybridization in the Iberian hare

João P. Marques, Liliana Farelo, Joana Vilela, Dan Vanderpool, Paulo C. Alves, Jeffrey M. Good, Pierre Boursot & José Melo-Ferreira
Introgressive hybridization is an important and widespread evolutionary process, but the relative roles of neutral demography and natural selection in promoting massive introgression are difficult to assess and an important matter of debate. Hares from the Iberian Peninsula provide an appropriate system to study this question. In its northern range, the Iberian hare, Lepus granatensis, shows a northwards gradient of increasing mitochondrial DNA (mtDNA) introgression from the arctic/boreal L. timidus, which it presumably replaced after...

Data from: Evolutionary rescue and local adaptation under different rates of temperature increase: a combined analysis of changes in phenotype expression and genotype frequency in Paramecium microcosms

Joshua Killeen, Claire Gougat-Barbera, Sascha Krenek & Oliver Kaltz
Evolutionary Rescue (ER) occurs when populations, which have declined due to rapid environmental change, recover through genetic adaptation. The success of this process and the evolutionary trajectory of the population strongly depend on the rate of environmental change. Here we investigated how different rates of temperature increase (from 23°C to 32°C) affect population persistence and evolutionary change in experimental microcosms of the protozoan Paramecium caudatum. Consistent with theory on ER, we found that those populations...

Data from: Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow

Mark Ravinet, Rui Faria, Roger K. Butlin, Juan Galindo, Nicolas Bierne, Marina Rafajlović, Mohamed A. F. Noor, Bernhard Mehlig & Anja M. Westram
Speciation, the evolution of reproductive isolation amongst populations, is continuous, complex, and involves multiple, interacting barriers. Until it is complete, the effects of this process vary along the genome and can lead to a heterogeneous genomic landscape with peaks and troughs of differentiation and divergence. When gene flow occurs during speciation, barriers restricting migration locally in the genome lead to patterns of heterogeneity. However, genomic heterogeneity can also be produced or modified by variation in...

Data from: Does water shortage generate water stress? An ecohydrological approach across Mediterranean plant communities

Karim Barkaoui, Marie-Laure Navas, Catherine Roumet, Pablo Cruz & Florence Volaire
The interactions between hydrological and ecological processes are key issues to improve our predictions of ecosystem responses to increasing droughts. However, predicting the dynamics and the impacts of vegetation water stress remains challenging because of complex ecohydrological feedbacks. The ecohydrological optimality approach proposes that functional adjustments within plant communities may buffer the increase in vegetation water stress despite local water shortage. This study aimed to test whether vegetation water stress may be invariant across contrasting...

Data from: Dissecting functional components of reproductive isolation among closely related sympatric species of the Anopheles gambiae complex

Marco Pombi, Pierre Kengne, Geoffrey Gimonneau, Billy Tene-Fossog, Diego Ayala, Colince Kamdem, Federica Santalomazza, Wamdaogo Moussa Guelbeogo, N'Falé Sagnon, Vincenzo Petrarca, Didier Fontenille, Nora J. Besansky, Christophe Antonio-Nkondjio, Roch K. Dabire, Alessandra Della Torre, Frederic Simard & Carlo Costantini
Explaining how and why reproductive isolation evolves and determining which forms of reproductive isolation have the largest impact on the process of population divergence are major goals in the study of speciation. By studying recent adaptive radiations in incompletely isolated taxa, it is possible to identify barriers involved at early divergence before other confounding barriers emerge after speciation is complete. Sibling species of the Anopheles gambiae complex offer opportunities to provide insights into speciation mechanisms....

Data from: Effect of pollination strategy, phylogeny and distribution on pollination niches of Euro-Mediterranean orchids

Nina Joffard, Francois Massol, Matthias Grenié, Claudine Montgelard & Bertrand Schatz
1. Pollination niches are important components of ecological niches and have played a major role in the diversification of Angiosperms. In this study, we focused on Euro-Mediterranean orchids, which use diverse pollination strategies and interact with various functional groups of insects. In these orchids, we investigated the determinants of pollination niche breadth and overlap by analysing the orchid-pollinator network and the factors that may have shaped it. 2. We constructed a database reporting 1278 interactions...

Data from: Community-wide scan identifies fish species associated with coral reef services across the Indo-Pacific

Eva Maire, Sébastien Villéger, Nicholas A.J. Graham, Andrew S. Hoey, Joshua Cinner, Sebastian C.A. Ferse, Catherine Aliaume, David J. Booth, David A. Feary, Michel Kulbicki, Stuart A. Sandin, Laurent Vigliola, David Mouillot & Sebastian C. A. Ferse
Determining whether many functionally complementary species or only a subset of key species are necessary to maintain ecosystem functioning and services is a critical question in community ecology and biodiversity conservation. Identifying such key species remains challenging, especially in the tropics where many species co-occur and can potentially support the same or different processes. Here, we developed a new community-wide scan (CWS) approach, analogous to the genome-wide scan, to identify fish species that significantly contribute,...

Data from: Dry-season decline in tree sapflux is correlated with leaf turgor loss point in a tropical rainforest

Isabelle Maréchaux, Damien Bonal, Megan K. Bartlett, Benoît Burban, Sabrina Coste, Elodie A. Courtois, Maguy Dulormne, Jean-Yves Goret, Eléonore Mira, Ariane Mirabel, Lawren Sack, Clément Stahl & Jerome Chave
1. Water availability is a key determinant of forest ecosystem function and tree species distributions. While droughts are increasing in frequency in many ecosystems, including in the tropics, plant responses to water supply vary with species and drought intensity, and are therefore difficult to model. Based on physiological first principles, we hypothesized that trees with a lower turgor loss point (πtlp), i.e., a more negative leaf water potential at wilting, would maintain water transport for...

Data from: Population-level dynamics in experimental mixed infections: evidence for competitive exclusion among bacterial parasites of Paramecium caudatum

Alison B. Duncan, Eike Dusi, Martina Schrallhammer, Thomas Berendonk & Oliver Kaltz
Parasites frequently share their host populations with other parasites. However, little is known about how different parasites respond to competition with diverse competitor species in the within-host and between-host environments. We explored the repeatability of competition by simultaneously exposing microcosm populations of the ciliate Paramecium caudatum to pairs of parasites from the Holospora species complex (H. undulata, H. caryophila and H. obtusa) affected the persistence and prevalence of each compared to single infections, across three...

Data from: Population structure, connectivity and demographic history of an apex marine predator, the bull shark Carcharhinus leucas

Agathe Pirog, Virginie Ravigné, Michaël Fontaine, Adrien Rieux, Aude Gilabert, Geremy Cliff, Eric Clua, Ryan Daly, Michael Heithaus, Jeremy Kiszka, Philip Matich, John Nevill, Amy Smoothey, Andrew Temple, Per Berggren, Sebastien Jaquemet & Hélène Magalon
Knowledge of population structure, connectivity and effective population size remains limited for many marine apex predators, including the bull shark Carcharhinus leucas. This large-bodied coastal shark is distributed worldwide in warm temperate and tropical waters, and uses estuaries and rivers as nurseries. As an apex predator, the bull shark likely plays a vital ecological role within marine food webs, but is at risk due to inshore habitat degradation and various fishing pressures. We investigated the...

Data from: Which frugivory‐related traits facilitated historical long‐distance dispersal in the custard apple family (Annonaceae)?

Renske E. Onstein, W. Daniel Kissling, Lars W. Chatrou, Thomas L. P. Couvreur, Hélène Morlon & Hervé Sauquet
Aim Long-distance dispersal has contributed to the disjunct biogeographical distribution of rain forest plants – something that has fascinated biogeographers since Humboldt’s time. However, the dispersal ‘agent’ for these tropical plant lineages remains puzzling. Here, we investigate which frugivory-related traits may have facilitated past intercontinental long-distance dispersal in the custard apple family (Annonaceae), a major vertebrate-dispersed tropical plant family. We hypothesize that long-distance dispersal was associated with the evolution of traits related to dispersal by...

Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate

Michael Abrouk, Hanin Ibrahim Ahmed, Philippe Cubry, Denisa Šimoníková, Stéphane Cauet, Yveline Pailles, Jan Bettgenhaeuser, Liubov Gapa, Nora Scarcelli, Marie Couderc, Leila Zekraoui, Nagarajan Kathiresan, Jana Čížková, Eva Hřibová, Jaroslav Doležel, Sandrine Arribat, Hélène Bergès, Jan Wieringa, Mathieu Gueye, Ndjido Kane, Christian Leclerc, Sandrine Causse, Sylvie Vancoppenolle, Claire Billot, Thomas Wicker … & Simon Krattinger
Sustainable food production in the context of climate change necessitates diversification of agriculture and a more efficient utilization of plant genetic resources. Fonio millet (Digitaria exilis) is an orphan African cereal crop with a great potential for dryland agriculture. Here, we established high-quality genomic resources to facilitate fonio improvement through molecular breeding. These include a chromosome-scale reference assembly and deep re-sequencing of 183 cultivated and wild Digitaria accessions, enabling insights into genetic diversity, population structure,...

In situ resistance, not immigration, supports invertebrate community resilience to drought intensification in a Neotropical ecosystem

Camille Bonhomme, Régis Céréghino, Jean-François Carrias, Arthur Compin, Bruno Corbara, Vincent E.J. Jassey, Joséphine Leflaive, Vinicius F. Farjalla, Nicholas A. C. Marino, Thibaut Rota, Diane S. Srivastava & Céline Leroy
While future climate scenarios predict declines in precipitations in many regions of the world, little is known of the mechanisms underlying community resilience to prolonged dry seasons, especially in “naïve” Neotropical rainforests. Predictions of community resilience to intensifying drought are complicated by the fact that the underlying mechanisms are mediated by species’ tolerance and resistance traits, as well as rescue through dispersal from source patches. We examined the contribution of in situ tolerance-resistance and immigration...

Spatial plant-plant associations from a Mediterranean grassland and associated analyses

Alexandre Génin, Thierry Dutoit, Alain Danet, Alice Le Priol & Sonia Kéfi
This dataset contains data documenting plant spatial patterns in a Mediterranean grassland (la Crau, France) along a grazing and nutrient enrichment gradient, along with accessory data documenting soil characteristics. It has been used to compute spatial association networks for plant communties to investigate changes in plant-plant interactions with grazing. Results show that association networks become closer to random expectations as grazing pressure increases.

The legacy of recurrent introgression during the radiation of hares

Mafalda S. Ferreira, Matthew R. Jones, Colin M. Callahan, Liliana Farelo, Zelalem Tolesa, Franz Suchentrunk, Pierre Boursot, L. Scott Mills, Paulo C. Alves, Jeffrey M. Good & José Melo-Ferreira
Hybridization may often be an important source of adaptive variation, but the extent and long-term impacts of introgression have seldom been evaluated in the phylogenetic context of a radiation. Hares (Lepus) represent a widespread mammalian radiation of 32 extant species characterized by striking ecological adaptations and recurrent admixture. To understand the relevance of introgressive hybridization during the diversification of Lepus, we analyzed whole exome sequences (61.7 Mb) from 15 species of hares (1- 4 individuals...

Pre-introduction introgression contributes to parallel differentiation and contrasting hybridisation outcomes between invasive and native marine mussels

Iva Popovic, Nicolas Bierne, Federico Gaiti, Miloš Tanurdžić & Cynthia Riginos
Non-native species experience novel selection pressures in introduced environments and may interbreed with native lineages. Species introductions therefore provide opportunities to investigate repeated patterns of adaptation and introgression across replicated contact zones. Here, we investigate genetic parallelism between multiple introduced populations of the invasive marine mussel, Mytilus galloprovincialis, in the absence (South Africa and California) and presence of hybridisation with a native congener (Mytilus planulatus in Batemans Bay and Sydney Harbour, Australia). Repeatability in post-introduction...

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  • University of Montpellier
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  • Inserm
  • Centre de Coopération Internationale en Recherche Agronomique pour le Développement
  • University of Pennsylvania
  • Washington University in St. Louis
  • Lukuru Foundation
  • Sorbonne University