Raphael Leblois

Université de Montpellier, Montpelhièr, Languedoc-Roussillon, France

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Publications (44)227.38 Total impact


  • No preview · Article · Mar 2016 · Biological Conservation

  • No preview · Article · Dec 2015 · Biological Journal of the Linnean Society
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    ABSTRACT: According to fossil data, the wood mouse arrived in North Africa 7500 ya, while it was present in Europe since Early Pleistocene. Previous molecular studies suggested that its introduction in North Africa probably occurred via the Strait of Gibraltar more than 0.4 Mya ago. In this study, we widely sampled wood mice to get a better understanding of the geographic and demographic history of this species in North Africa and possibly to help resolving the discrepancy between genetic and palaeontological data. Specifically, we wanted to answer the following questions: (1) When and how did the wood mouse arrive in North Africa? and (2) What is its demographic and geographic history in North Africa since its colonization? We collected in the field 438 new individuals and used both mtDNA and six microsatellite markers to answer these questions. Our results confirm that North African wood mice have a south-western European origin and colonized the Maghreb through the Strait of Gibraltar probably during the Mesolithic or slightly after. They first colonized the Tingitana Peninsula and then expanded throughout North Africa. Our genetic data suggest that the ancestral population size comprised numerous individuals reinforcing the idea that wood mice did not colonize Morocco accidentally through rafting of a few individuals, but via recurrent/multiple anthropogenic translocations. No spatial structuring of the genetic variability was recorded in North Africa, from Morocco to Tunisia.
    No preview · Article · Sep 2015 · Journal of Zoological Systematics and Evolutionary Research
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    Full-text · Conference Paper · Aug 2015
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    ABSTRACT: The freshwater blenny (Salaria fluviatilis), an endemic fish to the tributaries of the Mediterranean and Black seas, is considered endangered in five of the nine Mediterranean-European countries. Substantial effort has recently been made to improve our understanding of its biology (i.e., habitat modelling, morphology, behaviour), but developing a conservation program for a species is less effective without a thorough knowledge of its genetic heterogeneity. The goal of this study was to assess the existence and boundaries of freshwater blenny genetic clusters in the occidental basin of the Mediterranean Sea. Our results suggest a genetic structure at two levels. The first is a range-wide product of two different glacial refuges, potentially the Iberian Peninsula (South of Spain; the origin of the “western” group) and Corsica (the “eastern” group). Subsequent northward migration likely took place along the Mediterranean coasts from these two glacial refuges to the southern part of mainland France, where a second contact zone potentially occurred. The second level is a fine-scale genetic structure corresponding to eight genetic groups—four to the west from the “western” refuge and four to the east from the “eastern” refuge. Furthermore, we demonstrate that population differentiation between the western and eastern groups had occurred far enough in the past that new mutations and not solely drift effects were detectable. These results provide a foundation on which to design future conservation efforts of the freshwater blenny in the occidental basin of the Mediterranean Sea.
    Full-text · Article · Jun 2015 · Conservation Genetics
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    ABSTRACT: Dispersal may be strongly influenced by landscape and habitat characteristics that could either enhance or restrict movements of organisms. Therefore, spatial heterogeneity in landscape structure could influence gene flow and the spatial structure of populations. In the past decades, agricultural intensification has led to the reduction of grassland surfaces, their fragmentation and intensification. Since these changes are not homogeneously distributed in landscapes, they have resulted in spatial heterogeneity with generally less intensified hedged farmland areas remaining alongside streams and rivers. In this study, we assessed spatial pattern of abundance and population genetic structure of a flightless grasshopper species, Pezotettix giornae, based on the surveys of 363 grasslands in a 430 km² agricultural landscape of Western France. Data was analyzed using geostatistics and landscape genetics based on microsatellites markers and computer simulations. Results suggested that small scale intense dispersal allows this species to survive in intensive agricultural landscapes. A complex spatial genetic structure related to landscape and habitat characteristics was also detected. Two P. giornae genetic clusters bisected by a linear hedged farmland were inferred from clustering analyses. This linear hedged farmland was characterized by high hedgerow and grassland density as well as higher grassland temporal stability which were suspected to slow down dispersal. Computer simulations demonstrated that a linear{\hyphen}shaped landscape feature limiting dispersal could be detected as a barrier to gene flow and generate the observed genetic pattern. This study illustrates the relevance of using computer simulations to test hypotheses in landscape genetics studies. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
    Full-text · Article · Mar 2015 · Molecular Ecology
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    ABSTRACT: Historical factors, current popul ation size, population connectivity and selective processes at linked loci contribute to shaping contemporary patterns of neutral genetic diversity. It is now widely acknowledged that nuclear and mitochondrial markers react differently to current demography as well as to past history, so the use of both types of markers is often advocated to gain insight on both historical and contempor ary processes. We used 12 microsatellite loci genotyped in 13 populations of a mountain lizard ( Iberolacerta bonnali ) to test if the historical scenario favoured by a previous mitochondrial study was also supported by nuclear markers and thereby evaluated the consequences of post-glacial range movements on nuclear diversity. Congruent signals of recent histor y were revealed by nuclear and mitochondrial markers using an Approximate Bayesian Comput ation approach but cont emporary patterns of mtDNA and nuclear DNA diversity were radically different. Although dispersal in this species is probably highly restricted at all spatial scales, colonisation abilities have been historically good, suggesting capability for reestablishment of locally extinct populations except in fully disconnected habitats.
    Full-text · Article · Nov 2014 · Molecular Ecology
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    ABSTRACT: sampling includes 4 widely separated locations in the Indo-Pacific and 11 islands in French Polynesia with different levels of coastal development. 14 microsatellite loci were analysed for samples from all locations and 2 mitochondrial DNA fragments, the control region and cytochrome b, were examined for 10 locations. For microsatellites, genetic diversity is higher for the locations in the large open systems of the Red Sea and Australia than for the fragmented habitat of the smaller islands of French Polynesia. Strong significant structure was found for distant locations with FST values as high as ~0.3, and a smaller but still significant structure is found within French Polynesia. Both mitochondrial genes show only a few mutations across the sequences with a dominant shared haplotype in French Polynesia and New Caledonia suggesting a common lineage different to that of East Australia. Demographic history analyses indicate population expansions in the Red Sea and Australia that may coincide with sea level changes after climatic events. Expansions and flat signals are indicated for French Polynesia as well as a significant recent bottleneck for Moorea, the most human-impacted lagoon of the locations in French Polynesia.
    Full-text · Article · Sep 2014 · Molecular Ecology
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    ABSTRACT: Understanding the demographic history of populations and species is a central issue in evolutionary biology and molecular ecology. In this work, we develop a maximum-likelihood method for the inference of past changes in population size from microsatellite allelic data. Our method is based on importance sampling of gene genealogies, extended for new mutation models, notably the generalized stepwise mutation model (GSM). Using simulations, we test its performance to detect and characterize past reductions in population size. First, we test the estimation precision and confidence intervals coverage properties under ideal conditions, then we compare the accuracy of the estimation with another available method (MSVAR) and we finally test its robustness to misspecification of the mutational model and population structure. We show that our method is very competitive compared with alternative ones. Moreover, our implementation of a GSM allows more accurate analysis of microsatellite data, as we show that the violations of a single step mutation assumption induce very high bias toward false contraction detection rates. However, our simulation tests also showed some limits, which most importantly are large computation times for strong disequilibrium scenarios and a strong influence of some form of unaccounted population structure. This inference method is available in the latest implementation of the MIGRAINE software package.
    Full-text · Article · Jul 2014 · Molecular Biology and Evolution
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    ABSTRACT: This study presents genetic evidence that whale sharks, Rhincodon typus, are comprised of at least two populations that rarely mix and is the first to document a population expansion. Relatively high genetic structure is found when comparing sharks from the Gulf of Mexico with sharks from the Indo-Pacific. If mixing occurs between the Indian and Atlantic Oceans, it is not sufficient to counter genetic drift. This suggests whale sharks are not all part of a single global meta-population. The significant population expansion we found was indicated by both microsatellite and mitochondrial DNA. The expansion may have happened during the Holocene, when tropical species could expand their range due to sea level rise eliminating dispersal barriers and increasing plankton productivity. However, the historic trend of population increase may have reversed recently. Declines in genetic diversity are found for 6 consecutive years at Ningaloo Reef in Australia. The declines in genetic diversity being seen now may be due to commercial-scale harvesting of whale sharks and collision with boats in past decades in other countries in the Indo-Pacific. The study findings have implications for models of population connectivity for whale sharks and advocate for continued focus on effective protection of the world's largest fish at multiple spatial scales.This article is protected by copyright. All rights reserved.
    Full-text · Article · Apr 2014 · Molecular Ecology
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    ABSTRACT: DIYABC is a software package for a comprehensive analysis of population history using approximate Bayesian computation (ABC) on DNA polymorphism data. Version 2.0 implements a number of new features and analytical methods. It allows: (i) the analysis of single nucleotide polymorphism (SNP) data at large number of loci, apart from microsatellite and DNA sequence data; (ii) efficient Bayesian model choice using linear discriminant analysis on summary statistics; and (iii) the serial launching of multiple post-processing analyses. DIYABC v2.0 also includes a user-friendly graphical interface with various new options. It can be run on three operating systems: GNU/Linux, Microsoft Windows and Apple Os X. Availability: Freely available with a detailed notice document and example projects to academic users from: http://www1.montpellier.inra.fr/CBGP/diyabc CONTACT: estoup@supagro.inra.fr.
    Full-text · Article · Jan 2014 · Bioinformatics
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    ABSTRACT: Environmental changes have been shown to play an important role in the emergence of new human diseases of zoonotic origin. The contribution of social factors to their spread, especially conflicts followed by mass movement of populations, has not been extensively investigated. Here we reveal the effects of civil war on the phylogeography of a zoonotic emerging infectious disease by concomitantly studying the population structure, evolution and demography of Lassa virus and its natural reservoir, the rodent Mastomys natalensis, in Guinea, West Africa. Analysis of nucleoprotein gene sequences enabled us to reconstruct the evolutionary history of Lassa virus, which appeared 750 to 900 years ago in Nigeria and only recently spread across western Africa (170 years ago). Bayesian demographic inferences revealed that both the host and the virus populations have gone recently through severe genetic bottlenecks. The timing of these events matches civil war-related mass movements of refugees and accompanying environmental degradation. Forest and habitat destruction and human predation of the natural reservoir are likely explanations for the sharp decline observed in the rodent populations, the consequent virus population decline, and the coincident increased incidence of Lassa fever in these regions. Interestingly, we were also able to detect a similar pattern in Nigeria coinciding with the Biafra war. Our findings show that anthropogenic factors may profoundly impact the population genetics of a virus and its reservoir within the context of an emerging infectious disease.
    Full-text · Article · May 2012 · PLoS ONE
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    ABSTRACT: DNA barcoding is the assignment of individuals to species using standardized mitochondrial sequences. Nuclear data are sometimes added to the mitochondrial data to increase power. A barcoding method for analysing mitochondrial and nuclear data is developed. It is a Bayesian method based on the coalescent model. Then this method is assessed using simulated and real data. It is found that adding nuclear data can reduce the number of ambiguous assignments. Finally, the robustness of coalescent-based barcoding to departures from model assumptions is studied using simulations. This method is found to be robust to past population size variations, to within-species population structures, and to designs that poorly sample populations within species. Supplementary Material is available online at www.liebertonline.com/cmb.
    Preview · Article · Mar 2012 · Journal of computational biology: a journal of computational molecular cell biology
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    François Rousset · Raphaël Leblois
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    ABSTRACT: Likelihood-based methods of inference of population parameters from genetic data in structured populations have been implemented but still little tested in large networks of populations. In this work, a previous software implementation of inference in linear habitats is extended to two-dimensional habitats, and the coverage properties of confidence intervals are analyzed in both cases. Both standard likelihood and an efficient approximation are considered. The effects of misspecification of mutation model and dispersal distribution, and of spatial binning of samples, are considered. In the absence of model misspecification, the estimators have low bias, low mean square error, and the coverage properties of confidence intervals are consistent with theoretical expectations. Inferences of dispersal parameters and of the mutation rate are sensitive to misspecification or to approximations inherent to the coalescent algorithms used. In particular, coalescent approximations are not appropriate to infer the shape of the dispersal distribution. However, inferences of the neighborhood parameter (or of the product of population density and mean square dispersal rate) are generally robust with respect to complicating factors, such as misspecification of the mutation process and of the shape of the dispersal distribution, and with respect to spatial binning of samples. Likelihood inferences appear feasible in moderately sized networks of populations (up to 400 populations in this work), and they are more efficient than previous moment-based spatial regression method in realistic conditions.
    Preview · Article · Mar 2012 · Molecular Biology and Evolution
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    ABSTRACT: Testudo marginata, the largest European land tortoise, is suffering habitat degradation and destruction. Some populations, in markedly degraded habitats, are characterized by divergent morphotypes. However, the evolutionary significance of these morphotypes is of debate. Using 11 polymorphic microsatellites, we studied: (1) marginated tortoises from Sardinia that display a divergent morphotype – this population was potentially introduced from Greece; and (2) an area in the southern Peloponnese that includes a small and degraded zone in which marginated tortoises are dwarf. Genetic analyses run without any a priori assignment clearly acknowledge the specimens sampled in the territory of the dwarf form as a single group whilst Sardinian specimens are clustered with other specimens from the northern part of the area sampled in Greece. Demographic analyses suggest that Sardinian tortoises originated recently from some of the populations sampled in the northern part of the area sampled in Greece. Over locations sampled in Greece, a landscape-genetic analysis allowed us to detect potential landscape features that may reduce gene flow between the dwarf form territory and surrounding areas. Our results suggest that the territory of the dwarf form is particularly propitious for marginated tortoises and that conservation regulations in Greece should be reinforced to protect this area from increasing impact of human activities changing from traditional agriculture to mechanization and extensive use of chemicals. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105, 591–606.
    No preview · Article · Dec 2011 · Biological Journal of the Linnean Society
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    ABSTRACT: Gene flow between domesticated plants and their wild relatives is one of the major evolutionary processes acting to shape their structure of genetic diversity. Earlier literature, in the 1970s, reported on the interfertility and the sympatry of wild, weedy and cultivated sorghum belonging to the species Sorghum bicolor in most regions of sub-Saharan Africa. However, only a few recent surveys have addressed the geographical and ecological distribution of sorghum wild relatives and their genetic structure. These features are poorly documented, especially in western Africa, a centre of diversity for this crop. We report here on an exhaustive in situ collection of wild, weedy and cultivated sorghum assembled in Mali and in Guinea. The extent and pattern of genetic diversity were assessed with 15 SSRs within the cultivated pool (455 accessions), the wild pool (91 wild and weedy forms) and between them. F ST and R ST statistics, distance-based trees, Bayesian clustering methods, as well as isolation by distance models, were used to infer evolutionary relationships within the wild–weedy–crop complex. Firstly, our analyses highlighted a strong racial structure of genetic diversity within cultivated sorghum (F ST = 0.40). Secondly, clustering analyses highlighted the introgressed nature of most of the wild and weedy sorghum and grouped them into two eco-geographical groups. Such closeness between wild and crop sorghum could be the result of both sorghum’s domestication history and preferential post-domestication crop-to-wild gene flow enhanced by farmers’ practices. Finally, isolation by distance analyses showed strong spatial genetic structure within each pool, due to spatially limited dispersal, and suggested consequent gene flow between the wild and the crop pools, also supported by R ST analyses. Our findings thus revealed important features for the collection, conservation and biosafety of domesticated and wild sorghum in their centre of diversity.
    Full-text · Article · Aug 2011 · Theoretical and Applied Genetics
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    ABSTRACT: The evolutionary history of Leishmania chagasi, the aetiological agent of visceral leishmaniasis in South America has been widely debated. This study addresses the problem of the origin of L. chagasi, its timing and demography with fast evolving genetic markers, a suite of Bayesian clustering algorithms and coalescent modelling. Here, using 14 microsatellite markers, 450 strains from the Leishmania donovani complex, we show that the vast majority of the Central and South American L. chagasi were nested within the Portuguese Leishmania infantum clade. Moreover, L. chagasi allelic richness was half that of their Old World counterparts. The bottleneck signature was estimated to be about 500 years old and the settlement of L. chagasi in the New World, probably via infected dogs, was accompanied by a thousand-fold population decrease. Visceral leishmaniasis, lethal if untreated, is therefore one more disease that the Conquistadores brought to the New World.
    Full-text · Article · Jul 2011 · Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases
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    ABSTRACT: Reconstructing the demographic history of populations is a central issue in evolutionary biology. Using likelihood-based methods coupled with Monte Carlo simulations, it is now possible to reconstruct past changes in population size from genetic data. Using simulated data sets under various demographic scenarios, we evaluate the statistical performance of Msvar, a full-likelihood Bayesian method that infers past demographic change from microsatellite data. Our simulation tests show that Msvar is very efficient at detecting population declines and expansions, provided the event is neither too weak nor too recent. We further show that Msvar outperforms two moment-based methods (the M-ratio test and Bottleneck) for detecting population size changes, whatever the time and the severity of the event. The same trend emerges from a compilation of empirical studies. The latest version of Msvar provides estimates of the current and the ancestral population size and the time since the population started changing in size. We show that, in the absence of prior knowledge, Msvar provides little information on the mutation rate, which results in biased estimates and/or wide credibility intervals for each of the demographic parameters. However, scaling the population size parameters with the mutation rate and scaling the time with current population size, as coalescent theory requires, significantly improves the quality of the estimates for contraction but not for expansion scenarios. Finally, our results suggest that Msvar is robust to moderate departures from a strict stepwise mutation model.
    Full-text · Article · Mar 2011 · Genetics
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    ABSTRACT: Hunter-gatherer Pygmies from Central Africa are described as being extremely mobile. Using neutral genetic markers and population genetics theory, we explored the dispersal behaviour of the Baka Pygmies from Cameroon, one of the largest Pygmy populations in Central Africa. We found a strong correlation between genetic and geographical distances: a pattern of isolation by distance arising from limited parent-offspring dispersal. Our study suggests that mobile hunter-gatherers do not necessarily disperse over wide geographical areas.
    Full-text · Article · Dec 2010 · Biology letters
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    ABSTRACT: This article documents the addition of 396 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Anthocidaris crassispina, Aphis glycines, Argyrosomus regius, Astrocaryum sciophilum, Dasypus novemcinctus, Delomys sublineatus, Dermatemys mawii, Fundulus heteroclitus, Homalaspis plana, Jumellea rossii, Khaya senegalensis, Mugil cephalus, Neoceratitis cyanescens, Phalacrocorax aristotelis, Phytophthora infestans, Piper cordulatum, Pterocarpus indicus, Rana dalmatina, Rosa pulverulenta, Saxifraga oppositifolia, Scomber colias, Semecarpus kathalekanensis, Stichopus monotuberculatus, Striga hermonthica, Tarentola boettgeri and Thermophis baileyi. These loci were cross-tested on the following species: Aphis gossypii, Sooretamys angouya, Euryoryzomys russatus, Fundulus notatus, Fundulus olivaceus, Fundulus catenatus, Fundulus majalis, Jumellea fragrans, Jumellea triquetra Jumellea recta, Jumellea stenophylla, Liza richardsonii, Piper marginatum, Piper aequale, Piper darienensis, Piper dilatatum, Rana temporaria, Rana iberica, Rana pyrenaica, Semecarpus anacardium, Semecarpus auriculata, Semecarpus travancorica, Spondias acuminata, Holigarna grahamii, Holigarna beddomii, Mangifera indica, Anacardium occidentale, Tarentola delalandii, Tarentola caboverdianus and Thermophis zhaoermii. A supplementary dataset for Delomys is available.
    Full-text · Article · Nov 2010 · Molecular Ecology Resources

Publication Stats

2k Citations
227.38 Total Impact Points

Institutions

  • 2014
    • Université de Montpellier
      Montpelhièr, Languedoc-Roussillon, France
  • 2003-2014
    • French National Centre for Scientific Research
      • Laboratoire Statistique et Génome
      Lutetia Parisorum, Île-de-France, France
    • Uppsala University
      Uppsala, Uppsala, Sweden
  • 2009-2012
    • Muséum National d'Histoire Naturelle
      Lutetia Parisorum, Île-de-France, France
  • 2011
    • French National Institute for Agricultural Research
      • Centre de Biologie pour la Gestion des Populations (CBGP)
      Lutetia Parisorum, Île-de-France, France
  • 2007
    • University of California, Berkeley
      • Department of Integrative Biology
      Berkeley, California, United States
  • 2000
    • University of Queensland
      • School of Biological Sciences
      Brisbane, Queensland, Australia