François Pompanon

Ecology, Evolutionary Biology, Molecular Biology
PhD
36.02

Publications

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    François Pompanon, Sarah Samadi
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    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.
    Genetica 01/2015; 143(2). DOI:10.1007/s10709-015-9816-7 · 1.75 Impact Factor
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    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.
    Frontiers in Genetics 01/2015; 6:107. DOI:10.3389/fgene.2015.00107
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    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.
    Molecular Ecology Resources 10/2014; DOI:10.1111/1755-0998.12338 · 5.63 Impact Factor
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    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.
    Biology letters 09/2014; 10(9). DOI:10.1098/rsbl.2014.0562 · 3.43 Impact Factor
  • 1st Joint meeting of FAO-CIHEAM Mountain Pastures and Mediterranean Forages Resources networks and Mountain Cheese network, Clermont-Ferrand; 06/2014
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    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.
    Oryx 04/2014; 49(02):1-6. DOI:10.1017/S0030605313001026 · 1.91 Impact Factor
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    Parasites & Vectors 04/2014; 7(Suppl 1):O13. DOI:10.1186/1756-3305-7-S1-O13 · 3.25 Impact Factor
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    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 (1.0 LU ha−1) on a botanically-rich permanent pasture, and a rotational grazing system (PROD) set up at a higher stocking rate (1.7 LU ha−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. 19.9 kg d−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.
    Agriculture Ecosystems & Environment 03/2014; 185:231–244. DOI:10.1016/j.agee.2014.01.001 · 3.20 Impact Factor
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    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.
    Nature 02/2014; 506(7486):47-51. DOI:10.1038/nature12921 · 42.35 Impact Factor
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    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.
    International Plant and Animal Genome XXII, San Diego - USA; 01/2014
  • François Pompanon
    Encyclopedia of global archaeology, Edited by C. Smith, 01/2014: pages 3061-3064; Springer.
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    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.
    Conservation Genetics 11/2013; 15(2). DOI:10.1007/s10592-013-0553-0 · 1.85 Impact Factor
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    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).
    Molecular Phylogenetics and Evolution 09/2013; DOI:10.1016/j.ympev.2013.09.009 · 4.02 Impact Factor
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    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.
    Molecular Ecology 08/2013; 22(22). DOI:10.1111/mec.12499 · 5.84 Impact Factor
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    François Pompanon, Emeline Pettex, Laurence Després
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    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.
    Acta Oecologica 06/2013; DOI:10.1016/j.actao.2005.11.003 · 1.84 Impact Factor
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    ABSTRACT: Wildlife is considered to be mainly exposed to environmental contaminants via oral route. Food web analysis is therefore crucial in environmental risk assessment and management. In this context, diet information is commonly obtained from literature and little attention has been given to site-specific considerations (habitat, season…), which might considerably affect diet composition and thus wildlife exposure assessment. By associating next-generation sequencing and DNA barcoding techniques, the metabarcoding molecular approach of diet analysis could achieve a better taxonomic identification of food items with lower time investment than traditional micro- and macro-histological observations of food remains. In this context, the aim of this study is to evaluate the use of this new molecular method to investigate the diet of wild small mammals exposed to arsenic (As) and eventually to better understand and model its transfers. On a partially remediated former gold mine in southern France, small mammals were captured in spring and autumn in zones differing by their remediation treatment and in a control site. Botanical surveys were also performed on the polluted site. DNA was extracted from stomach content (n=96) and faeces (n=19) and then amplified with 3 primers sets, allowing to get plants and invertebrates (molluscs, arthropods and earthworms) DNA. Finally, amplified DNA was sequenced on next-generation sequencer. Preliminary results on plant DNA showed that 95% of the sequences were at least identified to family level and among them 13% were identified up to species level. This attests the possibility to reach a precise taxonomic level with this molecular method. Stomach contents and faeces from a given small mammal specimen gave complementary information, probably because they correspond to different meals. The results also suggested different food patterns among small mammal species, probably related to their foraging ecology. Comparisons between plant taxa identified in the diet and local botanical survey showed some mismatches, which may be related to small mammal mobility during their foraging activity. As a conclusion, the recent DNA metabarcoding is a promising approach to relate local food web structure to resource availability and thus to better understand pollutant trophic transfer in ecosystems.
    SETAC Europe, Glasgow, UK; 05/2013
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    Oryx 01/2013; · 1.91 Impact Factor
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    ABSTRACT: Ecosystems across the globe are threatened by climate change and human activities. New rapid survey approaches for monitoring biodiversity would greatly advance assessment and understanding of these threats. Taking advantage of next-generation DNA sequencing, we tested an approach we call metabarcoding: high-throughput and simultaneous taxa identification based on a very short (usually <100 base pairs) but informative DNA fragment. Short DNA fragments allow the use of degraded DNA from environmental samples. All analyses included amplification using plant-specific versatile primers, sequencing and estimation of taxonomic diversity. We tested in three steps whether degraded DNA from dead material in soil has the potential of efficiently assessing biodiversity in different biomes. First, soil DNA from eight boreal plant communities located in two different vegetation types (meadow and heath) was amplified. Plant diversity detected from boreal soil was highly consistent with plant taxonomic and growth form diversity estimated from conventional above-ground surveys. Second, we assessed DNA persistence using samples from formerly cultivated soils in temperate environments. We found that the number of crop DNA sequences retrieved strongly varied with years since last cultivation, and crop sequences were absent from nearby, uncultivated plots. Third, we assessed the universal applicability of DNA metabarcoding using soil samples from tropical environments: a large proportion of species and families from the study site were efficiently recovered. The results open unprecedented opportunities for large-scale DNA-based biodiversity studies across a range of taxonomic groups using standardized metabarcoding approaches.
    Molecular Ecology 04/2012; 21(15):3647-55. DOI:10.1111/j.1365-294X.2012.05545.x · 5.84 Impact Factor
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    ABSTRACT: Virtually all empirical ecological studies require species identification during data collection. DNA metabarcoding refers to the automated identification of multiple species from a single bulk sample containing entire organisms or from a single environmental sample containing degraded DNA (soil, water, faeces, etc.). It can be implemented for both modern and ancient environmental samples. The availability of next-generation sequencing platforms and the ecologists' need for high-throughput taxon identification have facilitated the emergence of DNA metabarcoding. The potential power of DNA metabarcoding as it is implemented today is limited mainly by its dependency on PCR and by the considerable investment needed to build comprehensive taxonomic reference libraries. Further developments associated with the impressive progress in DNA sequencing will eliminate the currently required DNA amplification step, and comprehensive taxonomic reference libraries composed of whole organellar genomes and repetitive ribosomal nuclear DNA can be built based on the well-curated DNA extract collections maintained by standardized barcoding initiatives. The near-term future of DNA metabarcoding has an enormous potential to boost data acquisition in biodiversity research.
    Molecular Ecology 04/2012; 21(8):2045-50. DOI:10.1111/j.1365-294X.2012.05470.x · 5.84 Impact Factor
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    ABSTRACT: Accurate information about the diet of large carnivores that are elusive and inhabit inaccessible terrain, is required to properly design conservation strategies. Predation on livestock and retaliatory killing of predators have become serious issues throughout the range of the snow leopard. Several feeding ecology studies of snow leopards have been conducted using classical approaches. These techniques have inherent limitations in their ability to properly identify both snow leopard feces and prey taxa. To examine the frequency of livestock prey and nearly-threatened argali in the diet of the snow leopard, we employed the recently developed DNA-based diet approach to study a snow leopard population located in the Tost Mountains, South Gobi, Mongolia. After DNA was extracted from the feces, a region of ∼100 bp long from mitochondrial 12S rRNA gene was amplified, making use of universal primers for vertebrates and a blocking oligonucleotide specific to snow leopard DNA. The amplicons were then sequenced using a next-generation sequencing platform. We observed a total of five different prey items from 81 fecal samples. Siberian ibex predominated the diet (in 70.4% of the feces), followed by domestic goat (17.3%) and argali sheep (8.6%). The major part of the diet was comprised of large ungulates (in 98.8% of the feces) including wild ungulates (79%) and domestic livestock (19.7%). The findings of the present study will help to understand the feeding ecology of the snow leopard, as well as to address the conservation and management issues pertaining to this wild cat.
    PLoS ONE 02/2012; 7(2):e32104. DOI:10.1371/journal.pone.0032104 · 3.53 Impact Factor

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