28 Works

Data from: Worldwide patterns of genetic differentiation imply multiple \"domestications\" of Aedes aegypti, a major vector of human diseases

Julia E. Brown, Carolyn S. McBride, Petrina Johnson, Scott Ritchie, Christophe Paupy, Hervé Bossin, Joel Lutomiah, Ildefonso Fernandez-Salas, Alongkot Ponlawat, Anthony J. Cornel, William C. Black, Norma Gorrochotegui-Escalante, Ludmel Urdaneta-Marquez, Massamba Sylla, Michel Slotman, Kristy O. Murray, Christopher Walker, Jeffrey R. Powell & W. C. Black
Understanding the processes by which species colonize and adapt to human habitats is particularly important in the case of disease-vectoring arthropods. The mosquito species Aedes aegypti, a major vector of dengue and yellow fever viruses, probably originated as a wild, zoophilic species in sub-Saharan Africa, where some populations still breed in tree holes in forested habitats. Many populations of the species, however, have evolved to thrive in human habitats and to bite humans. This includes...

Data from: Global biogeography and diversification of palms sheds light on the evolution of tropical lineages. I. Historical biogeography

William J. Baker, Thomas L. P. Couvreur & Thomas L.P. Couvreur
AIM: Palms (Arecaceae/Palmae) are a model group for evolutionary studies in the tropics. Family-wide data on taxonomy, phylogenetics and distribution are now available, but a general framework of palm evolution is still lacking. The overall aim of this study, published in two companion papers, is to seek evolutionary explanations for the geographical distribution of palm lineages and species diversity patterns at global and regional levels. In this first paper we undertake a detailed analysis of...

Data from: Acute febrile illness and influenza disease burden in a rural cohort dedicated to malaria in Senegal, 2012-2013

Fatoumata Diene Sarr, Mbayame Niang, Diamilatou Thiam, Ndongo Dia, Abdoulaye Badiane, Abdoulaye B. Ndao, Cheikh Sokhna, André Spiegel & Vincent Richard
Background: African populations are considered to be particularly vulnerable to fever illnesses, including malaria, and acute respiratory disease, owing to limited resources and overcrowding. However, the overall burden of influenza in this context is poorly defined and incidence data for African countries are scarce. We therefore studied the fever syndrome incidence and more specifically influenza incidence in a cohort of inhabitants of Dielmo and Ndiop in Sokone district, Senegal. Methods: Daily febrile-illness data were prospectively...

Data from: Geographic population structure of the African malaria vector Anopheles gambiae suggests a role for the forest-savannah biome transition as a barrier to gene flow

Joao Pinto, Alexander Egyir-Yawson, José L. Vicente, Bruno Gomes, Federica Santalomazza, Marta Moreno, Jacques D. Charlwood, Frederic Simard, Nohal Elissa, David Weetman, Martin J. Donnelly, Adalgisa Caccone, Alessandra Della Torre, Caccone A, Simard F, Pinto J, Vicente JL, Gomes B, Elissa N, Weetman D & Donnelly MJ
The primary Afrotropical malaria mosquito vector Anopheles gambiae sensu stricto has a complex population structure. In western Africa, this species is split into two molecular forms and displays local and regional variation in chromosomal arrangements and behaviours. To investigate patterns of macro-geographic population substructure, 25 An. gambiae samples from 12 African countries were genotyped at 13 microsatellite loci. This analysis detected the presence of additional population structuring, with the M-form being subdivided into distinct west,...

Data from: Revisiting the ichthyodiversity of Java and Bali through DNA barcodes: taxonomic coverage, identification accuracy, cryptic diversity and identification of exotic species

Hadi Dahruddin, Aditya Hutama, Frédéric Busson, Sopian Sauri, Robert Hanner, Philippe Keith, Renny Hadiaty & Nicolas Hubert
Among the 899 species of freshwater fishes reported from Sundaland biodiversity hotspot, nearly 50% are endemics. The functional integrity of aquatic ecosystems is currently jeopardized by human activities, and landscape conversion led to the decline of fish populations in several part of Sundaland, particularly in Java. The inventory of the Javanese ichthyofauna has been discontinuous, and the taxonomic knowledge is scattered in the literature. This study provides a DNA barcode reference library for the inland...

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: 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: Morphological clines and weak drift along an urbanization gradient in the butterfly, Pieris rapae

Sean D. Schoville, Ivo Widmer, Magali Deschamps-Cottin, Marie-Hélène Lizée, Laurence Després, Delphine Rioux, Ludovic Gielly & Stéphanie Manel
Urban areas are increasing globally, providing opportunities for biodiversity researchers to study the process in which species become established in novel, highly disturbed habitats. This ecological process can be understood through analyses of morphological and genetic variation, which can shed light on patterns of neutral and adaptive evolution. Previous studies have shown that urban populations often diverge genetically from non-urban source populations. This could occur due to neutral genetic drift, but an alternative is that...

Data from: Cenozoic colonization and diversification patterns of tropical American palms: evidence from Astrocaryum (Arecaceae)

Julissa Roncal, Francis Kahn, Betty Millan, Thomas L. P. Couvreur & Jean-Christophe Pintaud
With 788 species in 67 genera in the Neotropics, Arecaceae are an important ecological and economic component of the region. We review the influence of geological events such as the Pebas system, the Andean uplift and the land connections between South and Central/North America, on the historical assembly of Neotropical palms. We present a case study of the palm genus Astrocaryum (40 species) as a model for evaluating colonization and diversification patterns of lowland Neotropical...

Data from: Investigating the genetics of Bti resistance using mRNA tag sequencing: application on laboratory strains and natural populations of the dengue vector Aedes aegypti

Margot Paris, Sebastien Marcombe, Eric Coissac, Vincent Corbel, Jean-Philippe David & Laurence Després
Mosquito control is often the main method used to reduce mosquito-transmitted diseases. In order to investigate the genetic basis of resistance to the bio-insecticide Bacillus thuringiensis subsp. israelensis (Bti), we used information on polymorphism obtained from cDNA tag sequences from pooled larvae of laboratory Bti-resistant and susceptible Aedes aegypti mosquito strains to identify and analyse 1520 single nucleotide polymorphisms (SNPs). Of the 372 SNPs tested, 99.2% were validated using DNA Illumina GoldenGate® array, with a...

Data from: Energetic and Ecological Constraints on Population Density of Reef Fishes

Diego R. Barneche, Michel Kulbicki, Sergio R. Floeter, Alan M. Friedlander & Andrew P. Allen
Population ecology has classically focused on pairwise species interactions, hindering the description of general patterns and processes of population abundance at large spatial scales. Here we use the Metabolic Theory of Ecology as a framework to formulate and test a model that yields predictions linking population density to the physiological constraints of body size and temperature on individual metabolism, and the ecological constraints of trophic structure and species richness on energy partitioning among species. Our...

Data from: Benefits and challenges of scaling up expansion of marine protected area networks in the Verde Island Passage, Central Philippines

Vera Horigue, Robert L. Pressey, Morena Mills, Jana Brotanková, Reniel Cabral & Serge Andrefouet
Locally-established marine protected areas (MPAs) have been proven to achieve local-scale fisheries and conservation objectives. However, since many of these MPAs were not designed to form ecologically-connected networks, their contributions to broader-scale goals such as complementarity and connectivity can be limited. In contrast, integrated networks of MPAs designed with systematic conservation planning are assumed to be more effective—ecologically, socially, and economically—than collections of locally-established MPAs. There is, however, little empirical evidence that clearly demonstrates the...

Map of the proportion of threatened endemic species per country in relation with environmental and socioeconomic drivers

Robin Pouteau
This dataset is a shapefile representing the proportion of threatened endemic species (both plants and animals) in 247 countries along with associated environmental and socioeconomic drivers. The geographic coordinate system is World Geodetic System 1984 (EPSG: 4326).

Data from: Habitat segregation and ecological character displacement in cryptic African malaria mosquitoes

Billy Tene Fossog, Diego Ayala, Pelayo Acevedo, Pierre Kengne, Ignacio Ngomo Abeso Mebuy, Boris Makanga, Julie Magnus, Parfait Awono-Ambene, Flobert Njiokou, Marco Pombi, Christophe Antonio-Nkondjio, Christophe Paupy, Nora J. Besansky & Carlo Costantini
Understanding how divergent selection generates adaptive phenotypic and population diversification provides a mechanistic explanation of speciation in recently separated species pairs. Toward this goal, we sought ecological gradients of divergence between the cryptic malaria vectors Anopheles coluzzii and An. gambiae, and then looked for a physiological trait that may underlie such divergence. Using a large set of occurrence records and eco-geographical information, we built a distribution model to predict the predominance of the two species...

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: 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: Phylogeography in continuous space: coupling species distribution models and circuit theory to assess the effect of contiguous migration at different climatic periods on genetic differentiation in Busseola fusca (Lepidoptera: Noctuidae)

Stéphane Dupas, Bruno Le Rü, Antoine Branca, Nathalie Faure, Guillaume Gigot, Pascal Campagne, Michel Sezonlin, Rose Ndemah, Paul-André Calatayud, Jean-François Silvain, G. Ong'amo, B. Le Ru, P.-A. Calatayud & J.-F. Silvain
Current population genetic models fail to cope with genetic differentiation for species with large, contiguous and heterogeneous distribution. We show that in such a case, genetic differentiation can be predicted at equilibrium by circuit theory, where conductance corresponds to abundance in species distribution models (SDM). Circuit-SDM approach was used for the phylogeographic study of the lepidopteran cereal stemborer Busseola fusca Füller (Noctuidae) across sub-Saharan Africa. Species abundance was surveyed across its distribution range. SDM models...

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...

Data from: Genetic diversity, clonality and connectivity in the scleractinian coral Pocillopora damicornis: a multi-scale analysis in an insular, fragmented reef system

Mehdi Adjeroud, Aurélie Guérécheau, Jeremie Vidal-Dupiol, Jean-François Flot, Sophie Arnaud-Haond & François Bonhomme
Clonality and genetic structure of the coral Pocillopora damicornis sensu lato were assessed using five microsatellites in 12 populations from four islands of the Society Archipelago (French Polynesia) sampled in June 2008. The 427 analysed specimens fell into 132 multilocus genotypes (MLGs), suggesting that asexual reproduction plays an important role in the maintenance of these populations. A haploweb analysis of ITS2 sequences of each MLG was consistent with all of them being conspecific. Genetic differentiation...

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: Diversification of an emerging pathogen in a biodiversity hotspot: Leptospira in endemic small mammals of Madagascar

Muriel Dietrich, David A. Wilkinson, Voahangy Soarimalala, Steven M. Goodman, Koussay Dellagi & Pablo Tortosa
Biodiversity hotspots and associated endemism are ideal systems for the study of parasite diversity within host communities. Here, we investigated the ecological and evolutionary forces acting on the diversification of an emerging bacterial pathogen, Leptospira spp., in communities of endemic Malagasy small mammals. We determined the infection rate with pathogenic Leptospira in 23 species of sympatric rodents (subfamily Nesomyinae) and tenrecids (family Tenrecidae) at two eastern humid forest localities. A multilocus genotyping analysis allowed the...

Data from: Deepwater Horizon oil spill impacts on sea turtles could span the Atlantic

Nathan F. Putman, F. Alberto Abreu-Grobois, Iñaky Iturbe-Darkistade, Emily M. Putman, Paul M. Richards & Philippe Verley
We investigated the extent that the 2010 Deepwater Horizon oil spill potentially affected oceanic-stage sea turtles from populations across the Atlantic. Within an ocean-circulation model, particles were backtracked from the Gulf of Mexico spill site to determine the probability of young turtles arriving in this area from major nesting beaches. The abundance of turtles in the vicinity of the oil spill was derived by forward-tracking particles from focal beaches and integrating population size, oceanic-stage duration...

Data from: Predictive modelling of habitat selection by marine predators with respect to the abundance and depth distribution of pelagic prey

Charlotte Boyd, Ramiro Castillo, , André E. Punt, Glenn R. VanBlaricom, Henri Weimerskirch, Sophie Bertrand & George L. Hunt
1. Understanding the ecological processes that underpin species distribution patterns is a fundamental goal in spatial ecology. However, developing predictive models of habitat use is challenging for species that forage in marine environments, as both predators and prey are often highly mobile and difficult to monitor. Consequently, few studies have developed resource selection functions for marine predators based directly on the abundance and distribution of their prey. 2. We analysed contemporaneous data on the diving...

Data from: Stability of the gorilla microbiome despite simian immunodeficiency virus infection

Andrew H. Moeller, Martine Peeters, Ahidjo Ayouba, Eitel Mpoudi Ngole, Amadine Esteban, Beatrice H. Hahn & Howard Ochman
Simian immunodeficiency viruses (SIVs) have been discovered in over 45 primate species; however, the pathogenic potential of most SIV strains remains unknown due to difficulties inherent in observing wild populations. Because those SIV infections that are pathogenic have been shown to induce changes in the host's gut microbiome, monitoring the microbiota present in faecal samples can provide a noninvasive means for studying the effects of SIV infection on the health of wild-living primates. Here, we...

Data from: Nurse-based restoration of degraded tropical forests with tussock grasses: experimental support from the Andean cloud forest

Fabien Anthelme, Lorena Gómez-Aparicio & Rommel Montúfar
1. The degradation of the Andean cloud forest raises strong biological conservation issues and threatens the sustainability of a crucial water resource. The idea that nurse-based restoration can accelerate the recovery of these forests is underexplored, despite its promise as a restoration technique. Recent conceptual models predict that facilitation among plants may be an important mechanism, but there is a lack of strong empirical support. We gathered experimental data to test this prediction and explore...

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