About
204
Publications
42,686
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
4,304
Citations
Publications
Publications (204)
The Iberian harbour porpoise (Phocoena phocoena) reaches a larger body size than most other harbour porpoise populations and is genetically distinct, albeit closely related to the population in Northwest Africa. Currently comprising an estimated 3000–4000 individuals, genetic evidence and strandings data suggest that the population has declined in...
Mitochondrial DNA has been a popular marker in phylogeography, phylogeny, and molecular ecology, but its complex evolution is increasingly recognized. Here, we investigated mitochondrial DNA variation in Anopheles gambiae and Anopheles coluzzii, in relation to other species in the Anopheles gambiae complex, by assembling the mitogenomes of 1,219 mo...
In migratory animals, high mobility may reduce population structure through increased dispersal and enable adaptive responses to environmental change, whereas rigid migratory routines predict low dispersal, increased structure, and limited flexibility to respond to change. We explore the global population structure and phylogeographic history of th...
Species distributed across heterogeneous environments often evolve locally adapted populations, but understanding how these persist in the presence of homogenizing gene flow remains puzzling. In Gabon, Anopheles coluzzii, a major African malaria mosquito is found along an ecological gradient, including a sylvatic population, away of any human prese...
Plasmodium vivax , the predominant malaria parasite in Latin America, has a rich and complex colonization history in the region, with debated hypotheses about its origin. Our study employed cutting-edge population genomic techniques, to collect whole genome sequencing data from 620 P. vivax isolates, including 107 newly sequenced samples, thus repr...
In migratory birds, high mobility may reduce population structure through increased dispersal and enable adaptive responses to environmental change, whereas rigid migratory routines predict low dispersal, increased geographic structure, and limited flexibility to respond to change. We used nextRAD sequencing of 14,318 single-nucleotide polymorphism...
Background
Although whole-genome sequencing (WGS) is the preferred genotyping method for most genomic analyses, limitations are often experienced when studying genomes characterized by a high percentage of repetitive elements, high linkage, and recombination deserts. The Asian tiger mosquito (Aedes albopictus), for example, has a genome comprising...
Impact of climate change is expected to be especially noticeable at the edges of a species' distribution, where they meet suboptimal habitat conditions. In Mauritania and Iberia, two genetically differentiated populations of harbor porpoises ( Phocoena phocoena ) form an ecotype adapted to local upwelling conditions and distinct from other ecotypes...
Background
Although whole genome sequencing (WGS) is the preferred genotyping method for most genomic analyses, limitations are often experienced when studying genomes characterized by a high percentage of repetitive elements, high linkage, and recombination deserts. The Asian tiger mosquito (Aedes albopictus), for example, has a genome comprised o...
Right whales (genus Eubalaena) were among the first, and most extensively pursued, targets of commercial whaling. However, understanding the impacts of this persecution requires knowledge of the demographic histories of these species prior to exploitation. We used deep whole genome sequencing (~40×) of 12 North Atlantic (E. glacialis) and 10 Southw...
Mitochondrial DNA (mtDNA) has been a popular neutral marker in phylogeography, phylogeny, and molecular ecology, but its complex evolution is increasingly recognized. Here, we investigated mtDNA variation in An. gambiae and An. coluzzii , in perspective with other species in the Anopheles gambiae complex (AGC), by assembling the mitogenomes of 1219...
Parallel evolution provides strong evidence of adaptation by natural selection due to local environmental variation. Yet, the chronology, and mode of the process of parallel evolution remains debated. Here, we harness the temporal resolution of paleogenomics to address these long-standing questions, by comparing genomes originating from the mid-Hol...
Plasmodium falciparum, the most virulent agent of human malaria, spread from Africa to all continents following the out-of-Africa human migrations. During the transatlantic slave trade between the 16th and 19th centuries, it was introduced twice independently to the Americas where it adapted to new environmental conditions (new human populations an...
Species distributed across heterogeneous environments often evolve locally adapted ecotypes, but understanding of the genetic mechanisms involved in their formation and maintenance in the face of gene flow is incomplete. In Burkina Faso, the major African malaria mosquito Anopheles funestus comprises two strictly sympatric and morphologically indis...
Whilst genetic studies can address a large number of issues related to cetaceans, the primary focus of these Best practices is on matters related to understanding population structure, abundance and movements in order for ACCOBAMS to meet its conservation and management objectives.
Species distributed across heterogeneous environments often evolve locally adapted ecotypes, but understanding of the genetic mechanisms involved in their formation and maintenance in the face of gene flow is incomplete. In Burkina Faso, the major African malaria mosquito Anopheles funestus comprises two strictly sympatric and morphologically indis...
Parallel evolution provides among the strongest evidence of the role of natural selection in shaping adaptation to the local environment. Yet, the chronology, mode and tempo of the process of parallel evolution remains broadly debated and discussed in the field of evolutionary biology. In this study, we harness the temporal resolution of paleogenom...
Plasmodium falciparum , the most virulent agent of human malaria, spread from Africa to all continents following the out-of-Africa human migrations. During the transatlantic slave trade between the 16th and 19th centuries, it was introduced twice independently to the Americas where it adapted to new environmental conditions (new human populations a...
Abstract The microbial community composition is crucial for diverse life‐history traits in many organisms. However, we still lack a sufficient understanding of how the host microbiome is acquired and maintained, a pressing issue in times of global environmental change. Here we investigated to what extent host genotype, environmental conditions, and...
In cases of severe wildlife population decline, a key question is whether recovery efforts will be impeded by genetic factors, such as inbreeding depression. Decades of excess mortality from gillnet fishing have driven Mexico’s vaquita porpoise ( Phocoena sinus ) to ~10 remaining individuals. We analyzed whole-genome sequences from 20 vaquitas and...
Malaria is a vector-borne disease caused by protozoan parasites of the genus Plasmodium. Plasmodium vivax is the most prevalent human-infecting species in the Americas. However, the origins of this parasite in this continent are still debated. Similarly, it is now accepted that the existence of Plasmodium simium is explained by a P. vivax transfer...
Present‐day ecology and population structure are the legacies of past climate and habitat perturbations, and this is particularly true for species that are widely distributed at high latitudes. The red knot, Calidris canutus, is an arctic‐breeding, long‐distance migratory shorebird with six recognized subspecies defined by differences in morphology...
Studying repeated adaptation can provide insights into the mechanisms allowing species to adapt to novel environments. Here, we investigate repeated evolution driven by habitat specialization in the common bottlenose dolphin. Parapatric pelagic and coastal ecotypes of common bottlenose dolphins have repeatedly formed across the oceans. Analyzing wh...
Impact of climate changes on species is expected to be especially visible at the extremities of the species distribution, where they meet sub-optimal conditions. In Mauritania and Iberia, two genetically isolated populations of harbor porpoises form a distinct ecotype and are presumably locally adapted to the upwelling waters. By analyzing the evol...
Intraspecific niche differentiation can contribute to population persistence in changing environments. Following declines in large predatory fish, eutrophication, and climate change, there has been a major increase in the abundance of threespine stickleback (Gasterosteus aculeatus) in the Baltic Sea. Two morphotype groups with different levels of b...
Present-day ecology and population structure are the legacies of past climate and habitat perturbations, and this is particularly true for species that are widely distributed at high latitudes. The red knot, Calidris canutus , is an arctic-breeding, long-distance migratory shorebird with six recognized subspecies defined by differences in morpholog...
Declines of large predatory fish due to overexploitation are restructuring food webs across the globe. It is now becoming evident that restoring these altered food webs requires addressing not only ecological processes, but evolutionary ones as well, because human‐induced rapid evolution may in turn affect ecological dynamics. We studied the potent...
Understanding species responses to past environmental changes can help forecast how they will cope with ongoing climate changes. Harbor porpoises are widely distributed in the North Atlantic and were deeply impacted by the Pleistocene changes with the split of three sub‐species. Despite major impacts of fisheries on natural populations, little is k...
Plasmodium vivax is the most common and widespread human malaria parasite. It was recently proposed that P. vivax originates from sub-Saharan Africa based on the circulation of its closest genetic relatives ( P. vivax-like ) among African great apes. However, the limited number of genetic markers and samples investigated questions the robustness of...
Dataset of Fontaine et al. 2021 "Europe as a bridgehead in the worldwide invasion history of grapevine downy mildew, Plasmopara viticola".
Europe is the historical cradle of viticulture, but grapevines (Vitis vinifera) have been increasingly threatened by pathogens of American origin. The invasive oomycete Plasmopara viticola causes downy mildew, one of the most devastating grapevine diseases worldwide. Despite major economic consequences, its invasion history remains poorly understoo...
Supplementary resources of Fontaine et al. 2021 "Europe as a bridgehead in the worldwide invasion history of grapevine downy mildew, Plasmopara viticola".
Identification of partial sweeps, which include both hard and soft sweeps that have not currently reached fixation, provides crucial information about ongoing evolutionary responses. To this end, we introduce partialS/HIC, a deep learning method to discover selective sweeps from population genomic data. partialS/HIC uses a convolutional neural netw...
Harbor porpoise in the North Pacific are found in coastal waters from southern California to Japan, but population structure is poorly known outside of a few local areas. We used multiplexed amplicon sequencing of 292 loci and genotyped clusters of SNPs as microhaplotypes (N=271 samples) in addition to mtDNA sequence data (N=413 samples), to examin...
Supplementary resources of Small et al. 2020 "Radiation with reticulation marks the origin of a major malaria vector".
Significance
Introgressive hybridization is prevalent in recent and rapid animal radiations, and emerging evidence suggests that it leads to the sharing of genetic variation that can facilitate adaptation to new environments and generate novel phenotypes. Here we study a recent and rapid radiation of African mosquitoes in which only one species, An...
Understanding a species response to past environmental changes can help forecast how they will cope with ongoing climate changes. Harbor porpoises are widely distributed in the North Atlantic and were deeply impacted by the Pleistocene changes with the split of three sub-species. Despite major impacts of fisheries on natural populations, little is...
What are the mechanisms that allow species to extend their ranges and adapt to the novel environmental conditions they find in the newly available habitat? The study of parallel adaptation of pairs of populations to similar environments can provide great insights into this question. Here, we test for parallel evolution driven by niche specializatio...
Mosquito control remains a central pillar of efforts to reduce malaria burden in sub-Saharan Africa. However, insecticide resistance is entrenched in malaria vector populations, and countries with a high malaria burden face a daunting challenge to sustain malaria control with a limited set of surveillance and intervention tools. Here we report on t...
Harbour porpoises in the Iberian Peninsula form a genetically distinct, small (around 2900 animals) and isolated population. Their main prey are commercially important fish, hence overlap between porpoise occurrence and fishing activity is almost inevitable. We compile information on bycatch mortality, mainly collected over the last 15 years, based...
Europe is the historical cradle of viticulture, but grapevines have been increasingly threatened by pathogens of American origin. The invasive oomycete Plasmopara viticola causes downy mildew, one of the most devastating grapevine diseases worldwide. Despite major economic consequences, its invasion history remains poorly understood. Comprehensive...
Historical variation in food resources is expected to be a major driver of cetacean evolution, especially for the smallest species like porpoises. Despite major conservation issues among porpoise species (e.g., vaquita and finless), their evolutionary history remains understudied. Here, we reconstructed their evolutionary history across the speciat...
Declines of large predatory fish due to overexploitation are restructuring food webs across the globe. It is now becoming evident that restoring these altered food webs requires addressing not only ecological processes, but evolutionary ones as well, because human-induced rapid evolution may in turn affect ecological dynamics. In the central Baltic...
Plasmodium vivax is the most prevalent and widespread human malaria parasite, with almost three billion people living at risk of infection. With the discovery of its closest genetic relatives in African great apes (Plasmodium vivax-like), the origin of P. vivax has been proposed to be located in the sub-Saharan African area. However, the limited nu...
Mosquito control remains a central pillar of efforts to reduce malaria burden in sub-Saharan Africa. However, insecticide resistance is entrenched in malaria vector populations, and countries with high malaria burden face a daunting challenge to sustain malaria control with a limited set of surveillance and intervention tools. Here we report on the...
Absence of genetic differentiation is usually taken as an evidence of panmixia, but can also reflect other situations, including even nearly complete demographic independence among large-sized populations. Deciphering which situation applies has major practical implications (e.g., in conservation biology). The endangered harbor porpoises in the Bla...
Historical changes affecting food resources are a major driver of cetacean evolution. Small cetaceans like porpoises (Phocoenidae) are among the most metabolically challenged marine mammals and are particularly sensitive to changes in their food resources. The seven species of this family inhabit mostly temperate waters and constitute a textbook ex...
Documenting isolation is notoriously difficult for species with vast polymorphic populations. High proportions of shared variation impede estimation of connectivity, even despite leveraging information from many genetic markers. We overcome these impediments by combining classical analysis of neutral variation with assays of the structure of select...
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 l...
Polymorphisms in genetic copy number can influence gene expression, coding sequence, and zygosity, making them powerful actors in the evolutionary process. Copy number variants (CNVs) are however understudied, being more difficult to detect than single-nucleotide polymorphisms. We take advantage of the intense selective pressures on the major malar...
Isolated from North Atlantic populations, the Black Sea harbor porpoise ( Phocoena phocoena relicta ) is listed as Endangered due to the massive population decline triggered by historical hunting, and subsequently through fisheries bycatch, and other human activities. Of paramount importance for its conservation, is the characterization of the popu...
Symbiosis between microbial associates and a host is a ubiquitous feature of life on earth, modulating host phenotypes. In addition to endosymbionts, organisms harbour a collection of host-associated microbes, the microbiome that can impact important host traits. In this opinion article we argue that the mutual influ- ences of the microbiome and en...
Modeling and cage experiments suggest that mosquito gene drive systems will enable malaria eradication, but establishing safety and efficacy requires field-testing in isolated populations. Documenting genetic isolation is notoriously difficult for species with vast polymorphic populations like the principal African malaria vector Anopheles gambiae...
The sustainability of malaria control in Africa is threatened by rising levels of insecticide resistance, and new tools to prevent malaria transmission are urgently needed. To gain a better understanding of the mosquito populations that transmit malaria, we sequenced the genomes of 765 wild specimens of Anopheles gambiae and Anopheles coluzzii samp...
The sustainability of malaria control in Africa is threatened by the rise of insecticide resistance in Anopheles mosquitoes, which transmit the disease. To gain a deeper understanding of how mosquito populations are evolving, here we sequenced the genomes of 765 specimens of Anopheles gambiae and Anopheles coluzzii sampled from 15 locations across...
Understanding demographic trends and patterns of gene flow in an endangered species, occupying a fragmented habitat, is crucial for devising conservation strategies. Here, we examined the extent of population structure and recent evolution of the critically endangered Yangtze finless porpoise (YFP, Neophocaena asiaeorientalis asiaeorientalis). By a...
Supplementary resources of Chen et al. 2017 "Genetic footprint of Population Fragmentation and Contemporaneous Decline in the endangered Yangtze Finless Porpoise".
Dataset of Chen et al. 2017 "Genetic footprint of Population Fragmentation and Contemporaneous Decline in the endangered Yangtze Finless Porpoise".
Understanding demographic trends and patterns of gene flow in an endangered species is crucial for devising conservation strategies. Here, we examined the extent of population structure and recent evolution of the critically endangered Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis). By analysing genetic variation at the mito...
Historical fluctuations in forests’ distribution driven by past climate changes and anthropogenic activities can have large impacts on the demographic history of pathogens that have a long co-evolution history with these host trees. Using a population genetic approach, we investigated that hypothesis by reconstructing the demographic history of Arm...
Supplementary resources of Labbé et al. 2017 "Genetic signatures of variation in population size in a native fungal pathogen after the recent massive plantation of its host tree".
The data set included 206 Armillaria ostoyae individuals collected in the Landes de Gascogne forest (south-western France) between 2012 and 2014. Each individual was genotyped at 29 markers: 7 microsatellites and 22 single nucleotide polymorphism (SNP) markers.
Hybrid zones are a valuable tool for studying the process of speciation and for identifying the genomic regions undergoing divergence and the ecological (extrinsic) and non-ecological (intrinsic) factors involved. Here, we explored the genomic and geographic landscape of divergence in a hybrid zone between Papilio glaucus and Papilio canadensis. Us...
Hybrid zones are a valuable tool for studying the process of speciation and for identifying the genomic regions undergoing divergence and the ecological (extrinsic) and non-ecological (intrinsic) factors involved. Here, we explored the genomic and geographic landscape of divergence in a hybrid zone between Papilio glaucus and Papilio canadensis . U...
