References of "Michaux, Johan"
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See detailA new method to identify the endangered Pyrenean desman (Galemys pyrenaicus) and to study its diet, using next generation sequencing from faeces
Gillet, François ULg; Tiouchichine, Marie-Laure; Galan, Maxime et al

in Mammalian Biology (2015)

the Pyrenean Mountains and to the northern half of the Iberian Peninsula whose ecology and biology are still poorly known. The aim of this study was to identify Pyrenean desman faeces and to analyze its ... [more ▼]

the Pyrenean Mountains and to the northern half of the Iberian Peninsula whose ecology and biology are still poorly known. The aim of this study was to identify Pyrenean desman faeces and to analyze its diet from this material using next-generation sequencing methods. We amplified and sequenced a small DNA minibarcode (133 bp) of the COI gene in twenty-four putative faeces samples of Pyrenean desman and successfully identified the species in 16 samples. Other identified species were mammals, birds and amphibians, evidencing the potential application of our methods to a larger panel of taxa. In the Pyrenean desman faeces, we were able to identify nineteen prey species with a positive match (more than 98% of identity with a reference sequence) and eleven putative prey species with lower identity scores (90–96%). The nineteen species belonged to four orders and eleven families among which Trichoptera and Hydropsychidae were the most frequent, respectively. Future improvements could be obtained by extending the reference DNA sequence collection to reach precise identifications over the Desman’s range and by increasing the sampling to gain a better knowledge of the local diet of this endangered species. Such information is of great importance to propose the best management measures for its conservation. [less ▲]

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See detailGenetic variations of Turkish bank vole, Myodes glareolus (Mammalia: Rodentia) inferred from mtDNA
Colak, Ercument; Karacan, GO; Kandemir, I. et al

in Mitochondrial DNA: The Journal of DNA Mapping, Sequencing, and Analysis (2015)

The bank vole, Myodes glareolus, lives in deciduous forests throughout the Palearctic region. In Turkey, this species is distributed only in northern Anatolia (the Black Sea region) where these forests ... [more ▼]

The bank vole, Myodes glareolus, lives in deciduous forests throughout the Palearctic region. In Turkey, this species is distributed only in northern Anatolia (the Black Sea region) where these forests exist. This study reveals genetic differentiation among bank vole populations based on two regions of mitochondrial DNA (cytochrome b and D-loop). Populations in northern Anatolia are divided into two genetic lineages (the ‘‘eastern’’ and ‘‘western Black Sea’’ lineages) by the Kızılırmak Valley. While the western Black Sea lineage is close to the Balkan lineage, in accordance with their geographical proximities, surprisingly, the Uludag lineage, also situated in Western Turkey appears related to the eastern Black Sea population. The divergence time analyses suggest a separation between the Balkan and Turkish groups around 0.26 Mya, whereas the split between the eastern and western Black sea lineages appeared a little bit later (0.20 Mya). Our results suggest that regional refuges existed for this species in Turkey and that small-scale habitat fragmentations led to genetic differentiations between Myodes populations. [less ▲]

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See detailNew molecular data favour an anthropogenic introduction of the wood mouse (Apodemus sylvaticus) in North Africa
Lalis, Aude; Leblois, Raphael; Liefrid, Sohaib et al

in Journal of Zoological Systematics and Evolutionary Research (2015), 54

According to fossil data the wood mouse arrived in North Africa 7,500 ya, while it was present in Europe since early Pleistocene. Previous molecular studies suggested that its introduction in North Africa ... [more ▼]

According to fossil data the wood mouse arrived in North Africa 7,500 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 in order 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 paleontological 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 southwestern European origin and colonized the Maghreb through the Gibraltar strait probably during the Mesolithic or slightly after. They first colonized the Tingitane 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. [less ▲]

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See detailMolecular phylogeny of South-East Asian arboreal murine rodents
Pages, Marie; Fabre, Pierre-Henri; Chaval, Yannick et al

in Zoologica Scripta (2015)

Recent phylogenetic studies and taxonomic reviews have led to nearly complete resolution of the phylogenetic divisions within the old world rats and mice (Muridae, Murinae). The Micromys division and ... [more ▼]

Recent phylogenetic studies and taxonomic reviews have led to nearly complete resolution of the phylogenetic divisions within the old world rats and mice (Muridae, Murinae). The Micromys division and Pithecheir division are two notable exceptions where groupings of species into these divisions based on morphology and arboreal lifestyle have not been supported by phylogenetic evidence. Several enigmatic species from these divisions have been missing from molecular studies, preventing a rigorous revision of phylogenetic relationships. In this study, we sequenced for the first time one mitochondrial and three nuclear genes from South-East Asian keystone species of these two arboreal divisions: Hapalomys delacouri (Micromys division), Lenothrix canus and Pithecheir parvus (Pithecheir division). We also complemented the molecular data already available for the two divisions with new data from Sundaic Chiropodomys, Indian Vandeleuria oleracea and the recently described Sulawesian Margaretamys christinae. Using this new phylogenetic framework and molecular dating methodologies, our study allows some more detailed classification of the former Micromys and Pithecheir divisions, while confirming their polyphyletic status. Specifically, the former Micromys division should now be split into four monotypic divisions: Chiropodomys, Hapalomys, Micromys and Vandeleuria divisions. The former Pithecheir division is likely to be refined and restricted to Pithecheir and probably Pithecheirops, whereas Lenothrix and Margaretamys should now be recognized as representatives of the Dacnomys division. Our findings have profound implications with regard to the systematics of Murinae, as well as to the early evolution of murine morphology and dental characters. [less ▲]

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See detailEndogenous murine leukemia retroviral variation across wild European and inbred strains of house mouse
Hartmann, Stephanie; Hasenkamp, Natasha; Mayer, Jens et al

in BMC Genomics (2015), DOI 10.1186/s12864-015-1766-z

Background: Endogenous Q1 murine leukemia retroviruses (MLVs) are high copy number proviral elements difficult to comprehensively characterize using standard low throughput sequencing approaches. However ... [more ▼]

Background: Endogenous Q1 murine leukemia retroviruses (MLVs) are high copy number proviral elements difficult to comprehensively characterize using standard low throughput sequencing approaches. However, high throughput approaches generate data that is challenging to process, interpret and present. 8 9 10 Results: Next generation sequencing (NGS) data was generated for MLVs from two wild caught Mus musculus domesticus (from mainland France and Corsica) and for inbred laboratory mouse strains C3H, LP/J and SJL. Sequence reads were grouped using a novel sequence clustering approach as applied to retroviral sequences. A Markov cluster algorithm was employed, and the sequence reads were queried for matches to specific xenotropic (Xmv), polytropic (Pmv) and modified polytropic (Mpmv) viral reference sequences. 11 12 13 14 15 Conclusions: Various MLV subtypes were more widespread than expected among the mice, which may be due to the higher coverage of NGS, or to the presence of similar sequence across many different proviral loci. The results did not correlate with variation in the major MLV receptor Xpr1, which can restrict exogenous MLVs, suggesting that endogenous MLV distribution may reflect gene flow more than past resistance to infection. [less ▲]

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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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