François Pompanon

Ecology, Evolutionary Biology, Molecular Biology

PhD
36.38

Publications

  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Background: The current extensive use of the domestic goat (Capra hircus) is the result of its medium size and high adaptability as multiple breeds. The extent to which its genetic variability was influenced by early domestication practices is largely unknown. A common standard by which to analyze maternally-inherited variability of livestock species is through complete sequencing of the entire mitogenome (mitochondrial DNA, mtDNA). Results: We present the first extensive survey of goat mitogenomic variability based on 84 complete sequences selected from an initial collection of 758 samples that represent 60 different breeds of C. hircus, as well as its wild sister species, bezoar (Capra aegagrus) from Iran. Our phylogenetic analyses dated the most recent common ancestor of C. hircus to ∼460,000 years (ka) ago and identified five distinctive domestic haplogroups (A, B1, C1a, D1 and G). More than 90 % of goats examined were in haplogroup A. These domestic lineages are predominantly nested within C. aegagrus branches, diverged concomitantly at the interface between the Epipaleolithic and early Neolithic periods, and underwent a dramatic expansion starting from ∼12-10 ka ago. Conclusions: Domestic goat mitogenomes descended from a small number of founding haplotypes that underwent domestication after surviving the last glacial maximum in the Near Eastern refuges. All modern haplotypes A probably descended from a single (or at most a few closely related) female C. aegagrus. Zooarchaelogical data indicate that domestication first occurred in Southeastern Anatolia. Goats accompanying the first Neolithic migration waves into the Mediterranean were already characterized by two ancestral A and C variants. The ancient separation of the C branch (∼130 ka ago) suggests a genetically distinct population that could have been involved in a second event of domestication. The novel diagnostic mutational motifs defined here, which distinguish wild and domestic haplogroups, could be used to understand phylogenetic relationships among modern breeds and ancient remains and to evaluate whether selection differentially affected mitochondrial genome variants during the development of economically important breeds.
    Full-text · Article · Dec 2015 · BMC Genomics
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Livestock conservation practice is changing rapidly in light of policy developments, climate change and diversifying market demands. The last decade has seen a step change in technology and analytical approaches available to define, manage and conserve Farm Animal Genomic Resources (FAnGR). However, these rapid changes pose challenges for FAnGR conservation in terms of technological continuity, analytical capacity and integrative methodologies needed to fully exploit new, multidimensional data. The final conference of the ESF Genomic Resources program aimed to address
    Full-text · Article · Nov 2015 · Frontiers in Genetics
  • Source

    Full-text · Book · Nov 2015
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Since the time of their domestication, goats (Capra hircus) have evolved in a large variety of locally adapted populations in response to different human and environmental pressures. In the present era, many indigenous populations are threatened with extinction due to their substitution by cosmopolitan breeds, while they might represent highly valuable genomic resources. It is thus crucial to characterize the neutral and adaptive genetic diversity of indigenous populations. A fine characterization of whole genome variation in farm animals is now possible by using new sequencing technologies. We sequenced the complete genome at 12× coverage of 44 goats geographically representative of the three phenotypically distinct indigenous populations in Morocco. The study of mitochondrial genomes showed a high diversity exclusively restricted to the haplogroup A. The 44 nuclear genomes showed a very high diversity (24 million variants) associated with low linkage disequilibrium. The overall genetic diversity was weakly structured according to geography and phenotypes. When looking for signals of positive selection in each population we identified many candidate genes, several of which gave insights into the metabolic pathways or biological processes involved in the adaptation to local conditions (e.g., panting in warm/desert conditions). This study highlights the interest of WGS data to characterize livestock genomic diversity. It illustrates the valuable genetic richness present in indigenous populations that have to be sustainably managed and may represent valuable genetic resources for the long-term preservation of the species.
    Full-text · Article · Apr 2015 · Frontiers in Genetics
  • Source
    François Pompanon · Sarah Samadi
    [Show abstract] [Hide abstract]
    ABSTRACT: DNA barcoding approaches are used to describe biodiversity by analysing specimens or environmental samples in taxonomic, phylogenetic and ecological studies. While sharing data among these disciplines would be highly valuable, this remains difficult because of contradictory requirements. The properties making a DNA barcode efficient for specimen identification or species delimitation are hardly reconcilable with those required for a powerful analysis of degraded DNA from environmental samples. The use of next generation sequencing methods open up the way towards the development of new markers (e.g., multilocus barcodes) that would overcome such limitations. However, several challenges should be taken up for coordinating actions at the interface between taxonomy, ecology, molecular biology and bioinformatics in order to develop methods and protocols compatible with both taxonomic and ecological studies.
    Full-text · Article · Jan 2015 · Genetica
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Environmental DNA (eDNA) metabarcoding is increasingly used to study present and past biodiversity. eDNA analyses often rely on amplification of very small quantities or degraded DNA. To avoid missing detection of taxa that are actually present (false negatives), multiple extractions and amplifications of the same samples are often performed. However, the level of replication needed for reliable estimates of presence / absence patterns remains an unaddressed topic. Furthermore, degraded DNA and PCR/sequencing errors might produce false positives. We used simulations and empirical data to evaluate the level of replication required for accurate detection of targeted taxa in different contexts, and to assess the performance of methods used to reduce the risk of false detections. Furthermore, we evaluated whether statistical approaches developed to estimate occupancy in presence of observational errors can successfully estimate true prevalence, detection probability, and false positive rates. Replications reduced the rate of false negatives; the optimal level of replication was strongly dependent on the detection probability of taxa. Occupancy models successfully estimated true prevalence, detection probability, and false positive rates, but their performance increased with the number of replicates. At least eight PCR replicates should be performed if detection probability is not high, such as in ancient DNA studies. Multiple DNA extractions from the same sample yielded consistent results; in some cases collecting multiple samples from the same locality allowed detecting more species. The optimal level of replication for accurate species detection strongly varies among studies, and could be explicitly estimated to improve the reliability of results.This article is protected by copyright. All rights reserved.
    Full-text · Article · Oct 2014 · Molecular Ecology Resources
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: DNA metabarcoding enables efficient characterization of species composition in environmental DNA or bulk biodiversity samples, and this approach is making significant and unique contributions in the field of ecology. In metabarcoding of animals, the cytochrome c oxidase subunit I (COI) gene is frequently used as the marker of choice because no other genetic region can be found in taxonomically verified databases with sequences covering so many taxa. However, the accuracy of metabarcoding datasets is dependent on recovery of the targeted taxa using conserved amplification primers. We argue that COI does not contain suitably conserved regions for most amplicon-based metabarcoding applications. Marker selection deserves increased scrutiny and available marker choices should be broadened in order to maximize potential in this exciting field of research.
    Full-text · Article · Sep 2014 · Biology letters

  • No preview · Conference Paper · Jun 2014
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Human–carnivore conflict is one of the major challenges in the management of populations of large carnivores. Concerns include the increasing human population; habitat loss as a result of degradation and fragmentation of forest; and livestock predation as a result of a lack of natural prey, leading to retaliatory killings of wild carnivores. Conflicts may be further aggravated by occasional attacks that result in injury and loss of human life. The level of consumption of prey species by a predator is a benchmark to evaluate the scale of this conflict. We used a newly developed DNA-based diet analysis to study the prey profile of common leopards Panthera pardus in Ayubia National Park, Pakistan. The results suggest that the common leopard is a generalist predator, subsisting mainly on domestic animals. Based on the frequency of occurrence of prey items in 57 faecal samples, the diet of the leopard is dominated by domestic goat Capra hircus (64.9%), followed by domestic dog Canis lupus familiaris (17.5%) and cow Bos taurus (12.3%). Domestic animals (goat, dog, cow, water buffalo Bubalus bubalis, horse Equus caballus and sheep Ovis aries) occurred in 54 (95%) of the 57 samples. We recommend a two-step strategy to mitigate this conflict: (1) introducing incentives for increased acceptance of leopards among local communities in the vicinity of the protected area and (2) increasing the availability of wild prey. We hope that the results of this study will contribute to the survival of the leopard in Pakistan.
    Full-text · Article · Apr 2014 · Oryx
  • Source
    MA Qablan · F Boyer · C Miquel · G D'Amico · AD Mihalca · F Pompanon · D Modrý

    Full-text · Article · Apr 2014 · Parasites & Vectors
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The interactions between botanical composition of pasture, quality of herbage grazed, performances of dairy cows and sensory and nutritional properties of dairy products were investigated using an integrated system approach. Two contrasting grazing systems were evaluated from May to September in two years. The treatments included a continuous grazing system (DIV) managed at a lenient stocking rate (1.0LUha-1) on a botanically-rich permanent pasture, and a rotational grazing system (PROD) set up at a higher stocking rate (1.7LUha-1) on a former temporary grassland presenting moderate biodiversity. DIV aimed to maximize biodiversity and obtain high sensory and nutritional quality cheese, whereas PROD was oriented towards milk production and herbage quality. In each system, 12 non-feed-supplemented Montbéliarde cows were used. The DIV system led to higher milk production per cow in the early grazing season than the PROD system (22.2 vs. 19.9kgd-1). At the beginning of summer, this milk production pattern was inverted following a decrease in grass nutritive value in the DIV system. In parallel, DIV cows showed a more marked loss of body condition than PROD cows over the season. In terms of milk fatty acid profile, the DIV system proved very interesting early in the grazing season but lost its value over time as the herbage matured. Cheese sensory properties differed between systems only after a long ripening period (6 months). Regarding the ecological performances, the DIV plot showed greater botanical and entomological biodiversity than the PROD plot. This study provides evidence that the balance between animal performances, dairy product quality and biodiversity in dairy systems is more complex than previously thought, since the expected benefits of each system vary markedly over periods. The evolution of herbage vegetation stage during the grazing season combined with the botanical composition of the pasture is a key component for understanding these variations.
    Full-text · Article · Mar 2014 · Agriculture Ecosystems & Environment
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Although it is generally agreed that the Arctic flora is among the youngest and least diverse on Earth, the processes that shaped it are poorly understood. Here we present 50 thousand years (kyr) of Arctic vegetation history, derived from the first large-scale ancient DNA metabarcoding study of circumpolar plant diversity. For this interval we also explore nematode diversity as a proxy for modelling vegetation cover and soil quality, and diets of herbivorous megafaunal mammals, many of which became extinct around 10 kyr bp (before present). For much of the period investigated, Arctic vegetation consisted of dry steppe-tundra dominated by forbs (non-graminoid herbaceous vascular plants). During the Last Glacial Maximum (25-15 kyr bp), diversity declined markedly, although forbs remained dominant. Much changed after 10 kyr bp, with the appearance of moist tundra dominated by woody plants and graminoids. Our analyses indicate that both graminoids and forbs would have featured in megafaunal diets. As such, our findings question the predominance of a Late Quaternary graminoid-dominated Arctic mammoth steppe.
    Full-text · Article · Feb 2014 · Nature
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: NEXTGEN is an on-going project based on a comparative analysis of Whole Genome Sequences (WGS at 10X coverage) at the intraspecific level to optimise genetic management of livestock diversity. Adaptation is investigated in sheep and goats by studying for each species 162 individuals sampled in places representative of the contrasted environmental conditions found all over Morocco. Evaluation of the potential of wild ancestors and traditional breeds to act as reservoirs of neutral and adaptive genetic diversity is conducted by analysing the genomes of 80 individuals (asiatic mouflons, bezoars and local Iranian domestic sheep and goats). This dataset was used to address the key question of the optimal sample size and genotyping strategy to choose for optimizing the time and money dedicated to a population genomic study. We showed how the sample size (10-30 individuals) and the number of SNPs (1000 - 5 Millions and WGS) affected the estimation of population genomic parameters and the detection of signature of selection in small ruminants (O. aries, C. hircus and their wild ancestors O. orientalis and C. aegagrus). We found that 1K SNPs was not sufficient for such estimation but random 10K SNPs allowed a good estimation of heterozygosity, inbreeding coefficient and nucleotide diversity. We showed also that a reliable estimation of LD required at least 500K SNPs. We demonstrated that the Ovis exome capture and commercial 50K-SNP Chips (Ovine and Caprine Illumina® SNP50 Beadchips designed to describe the diversity of industrial breeds) biased the estimations when studying traditional breeds and wild animals.
    Full-text · Conference Paper · Jan 2014
  • François Pompanon

    No preview · Chapter · Jan 2014
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Roads are of major concern in conservation biology, as they are known to restrict animal movements through landscape fragmentation, and may therefore impact genetic patterns in native terrestrial organisms. We assessed the effect of two large-scale transportation infrastructures (LTIs), a 40-year-old highway and a 30 year-old high-speed railway, on the spatial genetic structure of the alpine newt Ichthyosaura alpestris, a highly nomadic amphibian. Genetic data were gathered following a targeted individual-based sampling scheme and analysed using both overlay and correlative methods. While simulations suggested that the highway may be old enough for a significant barrier effect to be detected, LTIs were never detected as barriers to gene flow: inferred genetic boundaries rather coincided with transition zones between major landscape entities. Further-more, spatial principal component analysis, a method designed to reveal cryptic genetic spatial patterns in high gene flow species, counter-intuitively suggested that the highway may act as a potential dispersal corridor in low-quality habitats, thus challenging traditional hypotheses on road impacts in amphibians. Our study showed that con-sidering local interactions between species, infrastructures and landscape-specific characteristics is essential for better understanding the potential impacts of roads on movement patterns in terrestrial organisms.
    Full-text · Article · Nov 2013 · Conservation Genetics
  • [Show abstract] [Hide abstract]
    ABSTRACT: Les écosystèmes aquatiques continentaux sont des milieux où la biodiversité est forte à l'échelle locale. Ils sont aussi le siège d'invasions biologiques nombreuses dont les effets sur les communautés natives sont parfois spectaculaires. Accidentellement introduite au début des années 1980 dans le marais de Brière, l'écrevisse de Louisiane (Procambarus clarkii) s'est développée au sein d'un cortège d'autres espèces exotiques. L'objectif de ce travail est de mieux comprendre les mécanismes trophiques associés au succès de cette invasion, et d'identifier les espèces aquatiques pouvant réguler l'invasion. Pour cela, nous étudions l'écologie trophique de l'écrevisse et son rôle dans le fonctionnement de l'écosystème, en combinant deux approches : (i) la caractérisation du régime alimentaire de l'écrevisse et de ses prédateurs potentiels (bio-contrôle) par metabarcoding alimentaire, et (ii) l'étude fonctionnelle des réseaux trophiques par analyse des isotopes stables sur les mêmes échantillons.
    No preview · Conference Paper · Nov 2013
  • [Show abstract] [Hide abstract]
    ABSTRACT: La caractérisation du régime alimentaire des ruminants au pâturage en milieu diversifié (prairies d’association et permanentes) est un verrou méthodologique important dans les études portant sur les relations animal-plantes dans ce type de milieu. Le développement récent de techniques permettant l’identification des végétaux dans des substrats complexes ou dégradés (DNA metabarcoding), basées sur l’analyse de fragments résiduels d’ADN des plantes dans les produits de la digestion, pourrait permettre une innovation méthodologique complémentaire aux méthodes actuelles basées sur les examens micro-histologiques, l’extraction et le dosage des alcanes à longue chaîne contenus dans les cuticules des plantes, ou les méthodes spectrales (spectroscopie en proche Infrarouge), ces méthodes étant fastidieuses, peu précises et mal adaptées aux couverts végétaux complexes. L’objectif de ce travail était de tester l’aspect quantitatif de cette méthodologie, déjà sensible pour apprécier qualitativement la composition d’une ration (Farruggia et al., 2012). Des échantillons de produits de la digestion (contenus ruminaux et fèces) ont été prélevés lors d’expérimentations au cours desquelles des espèces fourragères ont été distribuées à des moutons à l’auge en différentes proportions bien définies (mélanges binaires ray-grass anglais (RGA)-légumineuses à l’INRA de Theix, en 2010 et 2011) ou à des vaches laitières au pâturage dans des proportions mesurées par la méthode des alcanes (mélanges de une à cinq espèces à l’INRA de Rennes en 2012). Ces échantillons ont été analysés par le LECA en utilisant un couple d’amorces universelles ciblant une région variable de l’intron du gène chloroplastique trnL(UAA) des végétaux, un fragment adéquat pour l’identification de l’ADN résiduel dans les produits de la digestion car la région amplifiée est à la fois très courte et très variable selon les espèces. Puis, après séquençage massif de ces fragments, le nombre relatif de séquences obtenues dans le produit PCR pour chaque espèce végétale a été comparé à la proportion relative de ces espèces dans l’alimentation des animaux. Les résultats obtenus à partir des mélanges binaires contrôlés montrent une très bonne quantification des proportions de RGA et de légumineuses ingérées (en %, 0:100, 25:75, 50:50, 75:25 et 100:0) lorsque les analyses de DNA metabarcoding ont été réalisées sur contenus ruminaux, et ceci lors des deux années d’étude (mélanges RGA-luzerne et RGA-trèfle blanc, respectivement) (Fig. 1). Les résultats étaient plus mitigés lorsque les analyses de DNA metabarcoding ont été réalisées sur les fèces, avec une quantification correcte avec le mélange RGA-luzerne, bien que la variabilité soit élevée, mais moins bonne avec le mélange RGA-trèfle blanc pour lequel les proportions de RGA étaient sous-estimées (Fig. 1). Il est encore difficile, à ce stade, de déterminer pourquoi la quantification est de moins bonne qualité avec les fèces qu’avec les contenus ruminaux, mais il semble que l’ADN des fèces soit moins efficacement récupéré. Ceci pourrait s’expliquer par un différentiel dans la digestibilité post-ruminale des espèces ingérées, produisant un biais en raison de la méthode d’extraction de l’ADN utilisée qui tend à favoriser la récupération de l’ADN intracellulaire. Une autre explication pourrait résider dans l'assignation des séquences aux espèces : un certain niveau d'erreur est toléré dans l'assignation pour prendre en compte les erreurs de PCR et séquençage. Les ADN étant plus dégradés dans les fèces, un biais d'assignation pourrait être présent qui n'existe pas avec le contenu ruminal. Les échantillons prélevés en 2012 sur vaches laitières sont en cours d’analyse et complèteront les résultats déjà acquis.
    No preview · Article · Oct 2013
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The Podismini are melanopline grasshoppers with a Holarctic distribution and well represented in the Eurasian fauna. To investigate their controversial taxonomy and evolutionary history, we studied 86%, 78% and 33% respectively of the Eurasian, European and Asian Palaearctic genera (Otte, 1995; Eades et al., 2013). We reconstructed parsimony, maximum likelihood and Bayesian phylogenies using fragments of four genes (ITS1, 16S, 12S, CO2). We applied a Bayesian molecular clock to estimate the times of species divergence, and the event-based parsimony method to depict the biogeographic framework of the diversification. Our results suggest that the selected Eurasian Podismini constitute a monophyletic group inside the Melanoplinae, provided it includes the North American genus Phaulotettix. The clades proposed by the present study inside the Podismini do not fit the older morphological or cytological classifications, but are in agreement with more recent proposals. Furthermore, our results can be explained by a plausible biogeographic history in which the present geographical distribution of the Eurasian Podismini resulted from known changes, to the Cenozoic climate and vegetation, induced by major geological events including the genesis of high mountain chains (e.g., Himalayas, Altay, Alps) and large deserts (e.g., Gobi, Karakoum, Taklamakan), and the opening of marginal seas (e.g., Bering, Japanese and Yellow Seas).
    Full-text · Article · Sep 2013 · Molecular Phylogenetics and Evolution
  • Source
    J G Prunier · Bernard Kaufmann · Serge Fenet · D Picard · Francois Pompanon · P Joly · J P Lena
    [Show abstract] [Hide abstract]
    ABSTRACT: Genetic data are increasingly used in landscape ecology for the indirect assessment of functional connectivity, that is, the permeability of landscape to movements of organisms. Among available tools, matrix correlation analyses (e.g. Mantel tests or mixed models) are commonly used to test for the relationship between pairwise genetic distances and movement costs incurred by dispersing individuals. When organisms are spatially clustered, a population-based sampling scheme (PSS) is usually performed, so that a large number of genotypes can be used to compute pairwise genetic distances on the basis of allelic frequencies. Because of financial constraints, this kind of sampling scheme implies a drastic reduction in the number of sampled aggregates, thereby reducing sampling coverage at the landscape level. We used matrix correlation analyses on simulated and empirical genetic data sets to investigate the efficiency of an individual-based sampling scheme (ISS) in detecting isolation-by-distance and isolation-by-barrier patterns. Provided that pseudo-replication issues are taken into account (e.g. through restricted permutations in Mantel tests), we showed that the use of interindividual measures of genotypic dissimilarity may efficiently replace interpopulation measures of genetic differentiation: the sampling of only three or four individuals per aggregate may be sufficient to efficiently detect specific genetic patterns in most situations. The ISS proved to be a promising methodological alternative to the more conventional PSS, offering much flexibility in the spatial design of sampling schemes and ensuring an optimal representativeness of landscape heterogeneity in data, with few aggregates left unsampled. Each strategy offering specific advantages, a combined use of both sampling schemes is discussed.
    Full-text · Article · Aug 2013 · Molecular Ecology
  • Source
    François Pompanon · Emeline Pettex · Laurence Després
    [Show abstract] [Hide abstract]
    ABSTRACT: Life history and spatio-temporal patterns of resource utilisation were characterised in four Chiastocheta (Diptera: Anthomyiidae) species, whose larvae compete as seed predators on Trollius europaeus fruits. Interspecific co-occurrence was observed in 80% of the resource patches (= Trollius fruits) in the two communities studied. Isolated larvae from all species had a similar food intake, but differed in development time and size at emergence. Different species exhibit contrasting resource exploitation strategies with specific mining patterns and a partial temporal shift. Two species exhibited particularly singular strategies. C. rotundiventris escaped from strong interactions with other species because it was the first species to develop and the only one to exploit the central pith of Trollius fruits. The key role of this species as the main pollinator of the host-plant appears to be a by-product of constraints imposed by occupying a restricted niche. Although the resource is ephemeral due to seed dispersal, C. dentifera, the last species to oviposit, is not disadvantaged because it has a short development time and rapid food intake. The different patterns can partly explain the stability of Chiastocheta communities, but do not prevent competition to occur at high larval densities.
    Full-text · Article · Jun 2013 · Acta Oecologica

77 Following View all

245 Followers View all