References of "Michaux, Johan"
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See detailAlphacoronaviruses Detected in French Bats Are Phylogeographically Linked to Coronaviruses of European Bats
Goffard, Anne; Demanche, Christine; Arthur, Laurent et al

in Viruses (2015), 7

Bats are a reservoir for a diverse range of viruses, including coronaviruses (CoVs). To determine the presence of CoVs in French bats, fecal samples were collected between July and August of 2014 from ... [more ▼]

Bats are a reservoir for a diverse range of viruses, including coronaviruses (CoVs). To determine the presence of CoVs in French bats, fecal samples were collected between July and August of 2014 from four bat species in seven different locations around the city of Bourges in France. We present for the first time the presence of alpha-CoVs in French Pipistrellus pipistrellus bat species with an estimated prevalence of 4.2%. Based on the analysis of a fragment of the RNA-dependent RNA polymerase (RdRp) gene, phylogenetic analyses show that alpha-CoVs sequences detected in French bats are closely related to other European bat alpha-CoVs. Phylogeographic analyses of RdRp sequences show that several CoVs strains circulate in European bats: (i) old strains detected that have probably diverged a long time ago and are detected in different bat subspecies; (ii) strains detected in Myotis and Pipistrellus bat species that have more recently diverged. Our findings support previous observations describing the complexity of the detected CoVs in bats worldwide. [less ▲]

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See detailPatterns of genetic variation in the endangered European mink ( Mustela lutreola L., 1761)
Cabria, Maite; Gonzalez, Elena; Gomez-Moliner, Benjamin et al

in BMC Evolutionary Biology (2015), 15

Background: The European mink ( Mustela lutreola , L. 1761) is a critically endangered mustelid, which inhabits several main river drainages in Europe. Here, we assess the genetic variation of existing ... [more ▼]

Background: The European mink ( Mustela lutreola , L. 1761) is a critically endangered mustelid, which inhabits several main river drainages in Europe. Here, we assess the genetic variation of existing populations of this species, including new sampling sites and additional molecular markers (newly developed microsatellite loci specific to European mink) as compared to previous studies. Probabilistic analyses were used to examine genetic structure within and between existing populations, and to infer phylogeographic processes and past demography. Results: According to both mitochondrial and nuclear microsatellite markers, Northeastern (Russia, Estonia and Belarus) and Southeastern (Romania) European populations showed the highest intraspecific diversity. In contrast, Western European (France and Spain) populations were the least polymorphic, featuring a unique mitochondrial DNA haplotype. The high differentiation values detected between Eastern and Western European populations could be the result of genetic drift in the latter due to population isolation and reduction. Genetic differences among populations were further supported by Bayesian clustering and two main groups were confirmed (Eastern vs. Western Europe) along with two contained subgroups at a more local scale (Northeastern vs. Southeastern Europe; France vs. Spain). Conclusions: Genetic data and performed analyses support a historical scenario of stable European mink populations, not affected by Quaternary climate oscillations in the Late Pleistocene, and posterior expansion events following river connections in both North- and Southeastern European populations. This suggests an eastern refuge during glacial maxima (as already proposed for boreal and continental species). In contrast, Western Europe was colonised more recently following either natural expansions or putative human introductions. Low levels of genetic diversity observed within each studied population suggest recent bottleneck events and stress the urgent need for conservation measures to counteract the demographic decline experienced by the European mink. [less ▲]

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See detailWhat do Pneumocystis organisms tell us about the phylogeography of their hosts? The case of the woodmouse Apodemus sylvaticus in continental Europe and western Mediterranean islands
Demanche, christine; Deville, Manjula; Michaux, Johan ULg et al

in PLoS ONE (2015), DOI:10.1371

Pneumocystis fungi represent a highly diversified biological group with numerous species, which display a strong host-specificity suggesting a long co-speciation process. In the present study, the ... [more ▼]

Pneumocystis fungi represent a highly diversified biological group with numerous species, which display a strong host-specificity suggesting a long co-speciation process. In the present study, the presence and genetic diversity of Pneumocystis organisms was investigated in 203 lung samples from woodmice (Apodemus sylvaticus) collected on western continental Europe and Mediterranean islands. The presence of Pneumocystis DNA was assessed by nested PCR at both large and small mitochondrial subunit (mtLSU and mtSSU) rRNA loci. Direct sequencing of nested PCR products demonstrated a very high variability among woodmouse-derived Pneumocystis organisms with a total number of 30 distinct combined mtLSU and mtSSU sequence types. However, the genetic divergence among these sequence types was very low (up to 3.87%) and the presence of several Pneumocystis species within Apodemus sylvaticus was considered unlikely. The analysis of the genetic structure of woodmouse-derived Pneumocystis revealed two distinct groups. The first one comprised Pneumocystis from woodmice collected in continental Spain, France and Balearic islands. The second one included Pneumocystis from woodmice collected in continental Italy, Corsica and Sicily. These two genetic groups were in accordance with the two lineages currently described within the host species Apodemus sylvaticus. Pneumocystis organisms are emerging as powerful tools for phylogeographic studies in mammals [less ▲]

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See detailPCR-RFLP identification of the endangered Pyrenean desman, Galemys pyrenaicus (Soricomorpha, Talpidae), based on faecal DNA
Gillet, François ULg; Cabria Garrido, Maria Teresa; Némoz, Mélanie et al

in Mammalia (2015)

The Pyrenean desman is a vulnerable mammal species endemic to Pyrenees and the northern Iberian Peninsula. The presence of this elusive species can be most easily detected by sampling its faeces. However ... [more ▼]

The Pyrenean desman is a vulnerable mammal species endemic to Pyrenees and the northern Iberian Peninsula. The presence of this elusive species can be most easily detected by sampling its faeces. However, these faecal samples can be confused with those of other vertebrate species living in the same habitats. This study provides two easy and reliable methods for the identification of the Pyrenean desman faeces based on genetic analyses. The first one consists of a nested PCR and sequencing of a mitochondrial cytochrome b fragment, and the second one is an enzymatic digestion with endonucleases Alu I and Sau 3AI. The restriction patterns given by the two enzymes were found suitable for the successful discrimination of the Pyrenean desman from the other species based on species-specific sequence variations. [less ▲]

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See detailPhylogeography analysis and molecular evolution patterns of the nematode parasite Heligmosomum mixtum based on mitochondrial DNA sequences
Sakka, Hela; Henttonen, Heikki; Baraket, Ghada et al

in Acta Parasitologica (2015), 60(1), 85-98

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See detailIntegrating hydrological features and 1 genetically validated occurrence data in occupancy 2 modeling of an endemic and endangered semi‐aquatic mammal species, Galemys pyrenaicus. 3 4
Charbonnel, Anaïs; Buisson, Laetitia; Biffi, Marjorie et al

in Biological Conservation (2015), Sous Presse

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See detailEvolutionary history of the wood mouse (Apodemus sylvaticus) in the Palearctic region, with emphasis on the colonization of the Orkney Islands and Iceland
Durieu, Benoit ULg; Michaux, Johan ULg

Poster (2014, December 12)

To improve our knowledge concerning the hypothesis of northern refugia during the last glaciation for European species, we have focused our study on the evolutionary history of the wood mouse (Apodemus ... [more ▼]

To improve our knowledge concerning the hypothesis of northern refugia during the last glaciation for European species, we have focused our study on the evolutionary history of the wood mouse (Apodemus sylvaticus) throughout its Palearctic distribution. In addition, we also studied the wood mice populations from Orkney Islands and Iceland in order to understand their ways of colonization in the Atlantic islands. We used different molecular markers (cytb mitochondrial gene and a mitochondrial pseudogene). A geometric morphometric analysis using a morphological marker (mandible) was also used. This work highlights the potential existence of new wood mice lineages in Western Europe. These would be genetically differentiated, probably due to a geographical separation of an ancestral population in different refugia situated in the Iberian Peninsula during the last glacial maximum. Morphological differences also exist between the wood mice lineages. However, the study did not bring any evidence concerning the existence of Nordic refugia for this species. Concerning the insular populations, our results seem to show that populations from Orkney Islands and Iceland are genetically close to the Great Britain populations. They would have been introduced in these islands by Vikings or by earlier human populations. Additional sampling in Western Europe and in the Atlantic islands will clarify the origins of these populations. [less ▲]

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See detailGenetic structure of fragmented southern populations of African Cape Buffalo (Syncerus caffer caffer) based on microsatellite analysis
Smitz, Nathalie ULg; Cornélis, Daniel; Chardonnet, Philippe et al

Poster (2014, December 12)

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See detailGenetic structure of nase, Chondrostoma nasus, and common barbel, Barbus barbus (Teleostei, Cyprinidae) populations in South Belgium rivers: toward a rational management of conservation restocking
Gennotte, Vincent ULg; Michaux, Johan ULg; Prignon, Christian ULg et al

Poster (2014, December)

Nase (Chondrostoma nasus) and common barbel (Barbus barbus) are two rheophilic cyprinid fish naturally present in the Belgian Meuse and Rhine basins. During the last decades, the construction of dams ... [more ▼]

Nase (Chondrostoma nasus) and common barbel (Barbus barbus) are two rheophilic cyprinid fish naturally present in the Belgian Meuse and Rhine basins. During the last decades, the construction of dams together with changes in hydrological regimes, modifications of riverbed morphology and water pollution have caused some local dramatic declines in their populations. However, recent improvements in terms of water quality and habitat fragmentation allow considering as realistic a rational restocking plan of locally endangered patrimonial fish species such as nase and common barbel. Restocking operations for a conservation purpose have to be based on the knowledge and the use of wild type genetic strains. Therefore, the aim of this study was to characterize the genetic structure and diversity of nase and common barbel populations in South Belgium rivers. Wild common barbels (n = 313) and nases (n = 271) were sampled by electrofishing in respectively 10 and 6 different tributaries from the Meuse and Rhine rivers. Genotyping was performed on 24 microsatellite markers for each species. Preliminary results showed, for both species, a differential genetic clustering between fish originating from the Meuse basin and those originating from the Rhine basin. Detailed analysis describing the genetic structure and diversity of South Belgium populations will be presented and will serve as a management tool to set up a breeding plan for conservation restocking. [less ▲]

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See detailEvidence of a fine-scale genetic structure for the endangered Pyrenean desman (Galemys pyrenaicus) in the French Pyrenees
Gillet, François ULg; Cabria Garrido, Maria Teresa; Blanc, Frédéric et al

Poster (2014, December)

The Pyrenean desman (Galemys pyrenaicus) is a small semi-aquatic mammal endemic to the Pyrenean Mountains and the northern half of the Iberian Peninsula where it lives in mountain streams of cold and well ... [more ▼]

The Pyrenean desman (Galemys pyrenaicus) is a small semi-aquatic mammal endemic to the Pyrenean Mountains and the northern half of the Iberian Peninsula where it lives in mountain streams of cold and well-oxygenated flowing waters (Nores et al. 2007). This species is currently considered as vulnerable in the IUCN Red List (Fernandes et al. 2008) and has been suffering from habitat loss and fragmentation for decades, inevitably impacting its distribution. The ecology and biology of this species are poorly known, notably because of its elusive behavior and its primarily nocturnal activity (Stone 1987, Bertrand 1994). Its distribution area is even not definitively established. Furthermore, a recent genetic study, based on mitochondrial and intronic sequences (Igea et al. 2013), showed that the genetic variability of the Pyrenean desman is very low in the Pyrenees. In this study we investigated the potential existence of a genetic structure and gene flow at a smaller scale using 24 polymorphic microsatellites loci. As the Pyrenean desman is a very elusive species, we completed our sample collection of tissues with faeces samples coming from the French distribution area of this species. Doing so, we successfully identify 70 individuals out of 355 faeces samples. Bayesian analyses revealed a cryptic genetic structure in our data set. Three clusters were evidenced (one western, one central and one eastern) and gene flow appears to be limited between these clusters (min. Fst value of 0.2). [less ▲]

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See detailWhen morphometrics meets genetics: the case of the hazel dormouse, Muscardinus avellanarius
Mouton, Alice ULg; Renaud, Sabrina; Michaux, Johan ULg

Conference (2014, September 19)

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See detailBiological characteristics of a rodent species in expansion
André, Adrien ULg; millien, Virginie; Michaux, Johan ULg

Conference (2014, May)

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See detailÉtude du stress à long terme chez un rongeur (Peromyscus leucopus)
André, Adrien ULg; gaitan, Jorge; Millien, Virginie et al

Poster (2014)

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See detailPhylogenetic and morphometrics assessment of the evolutionary history of the hazel dormouse: Muscardinus avellanarius
Mouton, Alice ULg; Mortelliti, Alessio; Grill, Andrea et al

Conference (2014)

The hazel dormouse, Muscardinus avellanarius is a hibernating rodent, member of the Gliridae family. At the European level, the hazel dormouse is a strictly protected species listed in Annex IV of the ... [more ▼]

The hazel dormouse, Muscardinus avellanarius is a hibernating rodent, member of the Gliridae family. At the European level, the hazel dormouse is a strictly protected species listed in Annex IV of the " Fauna-Flora -Habitat Directive" ( Directive 92/43/EEC ) and Annex II of the Bern Convention. Concrete conservation measures must be implemented to maintain long-term viable populations of this species. To develop appropriate tools for conservation, it is essential to understand the origin and the evolution of this species whose ancestor appeared 17 million years ago. To this aim, it is fundamental to analyze the evolutionary history of the species in both a geographic dimension (spatial) and a temporal scale. Both mitochondrial and nuclear markers revealed a complex phylogeographic pattern for the hazel dormouse with the presence of two highly divergent and allopatric genetic lineages, respectively distributed in South-Western and Central-Eastern Europe. The presence of two highly differentiated phylogenetic lineages might question the taxonomic status of the hazel dormouse. Our work has highlighted the difficulty of delineating species boundaries and stressed the importance of integrating complementary approaches to achieve further taxonomic work. We used a quantitative analysis of intra- specific phenotypic variation as a complementary tool of the molecular approach by studying the upper first molar (UM1) in hazel dormouse populations. The analysis of phenotypic feature appears as a valuable complement to genetic analyses, providing a complementary insight into evolutionary processes, such as differentiation by vicariance or adaptation to different environments. A geographic structure emerges from the morphometric pattern of differentiation, partially corresponding to the expectations based on the genetic results. The knowledge acquired through this study might add a significant piece of the puzzle for the understanding of the evolutionary history of the common dormouse and might have important implications for its conservation. [less ▲]

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See detailPostglacial climate changes and rise of three ecotypes of harbour porpoises, Phocoena phocoena, in western Palearctic waters
Fontaine, Michaël; Roland, K.; Calves, I. et al

in Molecular Ecology (2014)

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See detailLa loutre en France et Navarre
Pigneur, Lise-Marie; Marc, Daniel; Fournier, Pascal et al

in Bulletin de liaison des Mammalogistes de Midi-Pyrénées (2014)

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See detailGenetic structure of fragmented southern populations of African Cape buffalo (Syncerus caffer caffer)
Smitz, Nathalie ULg; Cornelis, Daniel; Chardonnet, Philippe et al

in BMC Evolutionary Biology (2014), 14

Background African wildlife experienced a reduction in population size and geographical distribution over the last millennium, particularly since the 19th century as a result of human demographic ... [more ▼]

Background African wildlife experienced a reduction in population size and geographical distribution over the last millennium, particularly since the 19th century as a result of human demographic expansion, wildlife overexploitation, habitat degradation and cattle-borne diseases. In many areas, ungulate populations are now largely confined within a network of loosely connected protected areas. These metapopulations face gene flow restriction and run the risk of genetic diversity erosion. In this context, we assessed the “genetic health” of free ranging southern African Cape buffalo populations (S.c. caffer) and investigated the origins of their current genetic structure. The analyses were based on 264 samples from 6 southern African countries that were genotyped for 14 autosomal and 3 Y-chromosomal microsatellites. Results The analyses differentiated three significant genetic clusters, hereafter referred to as Northern (N), Central (C) and Southern (S) clusters. The results suggest that splitting of the N and C clusters occurred around 6000 to 8400 years ago. Both N and C clusters displayed high genetic diversity (mean allelic richness (Ar) of 7.217, average genetic diversity over loci of 0.594, mean private alleles (Pa) of 11), low differentiation, and an absence of an inbreeding depression signal (mean FIS = 0.037). The third (S) cluster, a tiny population enclosed within a small isolated protected area, likely originated from a more recent isolation and experienced genetic drift (FIS = 0.062, mean Ar = 6.160, Pa = 2). This study also highlighted the impact of translocations between clusters on the genetic structure of several African buffalo populations. Lower differentiation estimates were observed between C and N sampling localities that experienced translocation over the last century. Conclusions We showed that the current genetic structure of southern African Cape buffalo populations results from both ancient and recent processes. The splitting time of N and C clusters suggests that the current pattern results from human-induced factors and/or from the aridification process that occurred during the Holocene period. The more recent S cluster genetic drift probably results of processes that occurred over the last centuries (habitat fragmentation, diseases). Management practices of African buffalo populations should consider the micro-evolutionary changes highlighted in the present study. [less ▲]

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See detailNegative purifying selection drives prion and doppel protein evolution
Tsangaras, K.; Kolokotronis, S.-O.; Ulrich, R. G. et al

in Journal of Molecular Evolution (2014), 79(1-2), 12-20

The prion protein (PrP) when misfolded into the pathogenic conformer PrPSc is the major causative agent of several lethal transmissible spongiform encephalopathies in mammals. Studies of evolutionary ... [more ▼]

The prion protein (PrP) when misfolded into the pathogenic conformer PrPSc is the major causative agent of several lethal transmissible spongiform encephalopathies in mammals. Studies of evolutionary pressure on the corresponding gene using different datasets have yielded conflicting results. In addition, putative PrP or PrP interacting partners with strong similarity to PrP such as the doppel protein have not been examined to determine if the same evolutionary mechanisms apply to prion paralogs or if there are coselected sites that might indicate how and where the proteins interact. We examined several taxonomic groups that contain model organisms of prion diseases focusing on primates, bovids, and an expanded dataset of rodents for selection pressure on the prion gene (PRNP) and doppel gene (PRND) individually and for coevolving sites within. Overall, the results clearly indicate that both proteins are under strong selective constraints with relaxed selection on amino acid residues connecting α-helices 1 and 2. © 2014 Springer Science+Business Media New York. [less ▲]

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See detailNuclear and mitochondrial genetic structure in the Eurasian beaver (Castor fiber) - implications for future reintroductions
Senn, H.; Ogden, R.; Frosch, C. et al

in Evolutionary Applications (2014), 7(6), 645-662

Many reintroduction projects for conservation fail, and there are a large number of factors that may contribute to failure. Genetic analysis can be used to help stack the odds of a reintroduction in ... [more ▼]

Many reintroduction projects for conservation fail, and there are a large number of factors that may contribute to failure. Genetic analysis can be used to help stack the odds of a reintroduction in favour of success, by conducting assessment of source populations to evaluate the possibility of inbreeding and outbreeding depression and by conducting postrelease monitoring. In this study, we use a panel of 306 SNP (single nucleotide polymorphism) markers and 487-489 base pairs of mitochondrial DNA control region sequence data to examine 321 individuals from possible source populations of the Eurasian beaver for a reintroduction to Scotland. We use this information to reassess the phylogenetic history of the Eurasian beavers, to examine the genetic legacy of past reintroductions on the Eurasian landmass and to assess the future power of the genetic markers to conduct ongoing monitoring via parentage analysis and individual identification. We demonstrate the capacity of medium density genetic data (hundreds of SNPs) to provide information suitable for applied conservation and discuss the difficulty of balancing the need for high genetic diversity against phylogenetic best fit when choosing source population(s) for reintroduction. © 2014 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd. [less ▲]

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See detailThe genetic legacy of multiple beaver reintroductions in central Europe
Frosch, C.; Kraus, R. H. S.; Angst, C. et al

in PLoS ONE (2014), 9(5),

The comeback of the Eurasian beaver (Castor fiber) throughout western and central Europe is considered a major conservation success. Traditionally, several subspecies are recognised by morphology and ... [more ▼]

The comeback of the Eurasian beaver (Castor fiber) throughout western and central Europe is considered a major conservation success. Traditionally, several subspecies are recognised by morphology and mitochondrial haplotype, each linked to a relict population. During various reintroduction programs in the 20th century, beavers from multiple source localities were released and now form viable populations. These programs differed in their reintroduction strategies, i.e., using pure subspecies vs. mixed source populations. This inhomogeneity in management actions generated ongoing debates regarding the origin of present beaver populations and appropriate management plans for the future. By sequencing of the mitochondrial control region and microsatellite genotyping of 235 beaver individuals from five selected regions in Germany, Switzerland, Luxembourg, and Belgium we show that beavers from at least four source origins currently form admixed, genetically diverse populations that spread across the study region. While regional occurrences of invasive North American beavers (n = 20) were found, all but one C. fiber bore the mitochondrial haplotype of the autochthonous western Evolutionary Significant Unit (ESU). Considering this, as well as the viability of admixed populations and the fact that the fusion of different lineages is already progressing in all studied regions, we argue that admixture between different beaver source populations should be generally accepted. © 2014 Frosch et al. [less ▲]

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