References of "Michaux, Johan"
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See detailBiogeographic variations in wood mice: Testing for the role of morphological variation as a line of least resistance to evolution
Renaud, Sabrina; Quere, Jean Pierre; Michaux, Johan ULiege

in Cox, Philippe; Hautier, Lionel (Eds.) Cambridge Studies in Morphology and Molecules: New Paradigms in Evolutionary Biology ‘Evolution of the Rodents: Advances in Phylogeny, Paleontology and Functional Morphology’ (2015)

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See detailThe microbiome from the Lyme disease principal reservoir host in southern Quebec (Peromyscus leucopus)
André, Adrien ULiege; Mouton, Alice ULiege; Millien, Virginie et al

Poster (2015, June 25)

The emergence of the Lyme disease in Southern Quebec appears directly linked to the recent arrival in the region of the rodent Peromyscus leucopus. Indeed, this species is considered to be the principal ... [more ▼]

The emergence of the Lyme disease in Southern Quebec appears directly linked to the recent arrival in the region of the rodent Peromyscus leucopus. Indeed, this species is considered to be the principal reservoir of the bacteria Borrelia Burgdorferei, responsible of the Lyme disease and the recent climatic warming has allowed the mice to colonize higher latitude territories. Other factors, like the regulation made by pathogens might as well play an important role in the dynamic of expansion of P. leucopus. In our project, we sampled several populations of P. leucopus from the North American border, where the species is thought to be present for 30 years, to the most recently colonized zones, situated approximatively 150km inside of the Quebec province. A characterisation of their microbiome was then performed from their liver, spleen and lungs. Our objectives are threefold: First, we settled a protocol based on NGS methods for the detection of Borrelia Burgdorferei in micro-mammal internal organs. Second, we plan to identify the Borreliosis infection zones and to study their spatio-temporal evolution. Third, we aim to test which of the central-marginal hypothesis or the enemy release hypothesis is best describing the scenario presently happening in southern Quebec concerning the distribution’s expansion of P. leucopus. These information will be of great interest to understand the dynamic of emergence of the Borreliosis and to predict the current and future distribution of this disease in order to inform the Canadian health authorities. [less ▲]

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See detailGlobal parasite and Rattus rodent invasions: The consequences for rodent-borne diseases
Morand, Serge; Bordes, Frédéric; Chen, Hsuan-Wien et al

in Integrative Zoology (2015)

We summarize the current knowledge on parasitism-related invasion processes of the globally invasive Rattus lineages, originating from Asia, and how these invasions have impacted the local epidemiology of ... [more ▼]

We summarize the current knowledge on parasitism-related invasion processes of the globally invasive Rattus lineages, originating from Asia, and how these invasions have impacted the local epidemiology of rodent-borne diseases. Parasites play an important role in the invasion processes and successes of their hosts through multiple biological mechanisms such as "parasite release", "immunocompetence advantage", “biotic resistance” and "novel weapon". Parasites may also greatly increase the impact of invasions by spillover of parasites and other pathogens, introduced with invasive hosts, into new hosts potentially leading to novel emerging diseases. Another potential impact is the ability of the invader to amplify local parasites by spill-back. In both cases, local fauna and humans may be exposed to new health risks, which may decrease biodiversity and may potentially cause increases in human morbidity and mortality. Here we review the current knowledge on these processes and propose some research priorities. [less ▲]

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See detailOut of Himalaya: the impact of past Asian environmental changes on the evolutionary and biogeographical history of Dipodoidea (Rodentia)
Pisano, Julie ULiege; Condamine, Fabien L.; Lebedev, Vladimir et al

in Journal of Biogeography (2015), 42(5), 856-870

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See detailInfluence of past and future climate changes on the distribution of three Southeast Asian murine rodents
Latinne, Alice ULiege; Meynard, Christine; Herbreteau, Vincent et al

in Journal of Biogeography (2015), 42(9), 1714-1726

Aim: We tested the influence of Pleistocene climatic fluctuations and the potential effect of future climate change on Southeast Asian small mammal distributions using two forest-dwelling (Leopoldamys ... [more ▼]

Aim: We tested the influence of Pleistocene climatic fluctuations and the potential effect of future climate change on Southeast Asian small mammal distributions using two forest-dwelling (Leopoldamys herberti and Leopoldamys sabanus) and one karst (Leopoldamys neilli) endemic rodent species as models. Location: Southeast Asia. Methods: We used presence–absence data of genetically identified individuals, bioclimatic variables and species distribution modelling techniques to predict potential distributions of the three studied species under current, past [Last Interglacial (LIG) and Last Glacial Maximum (LGM)] and future conditions. We applied a variety of modelling techniques and then used consensus techniques to draw up robust maps of potential distribution ranges at all stages. Results: According to our models, these three Leopoldamys species did not experience significant range contraction during the LGM. Our models revealed substantial range contraction during the LIG for L. herberti in northern Indochina, while its distribution expanded in southern Indochina. Evidence of a southward range expansion during that period was also obtained for L. neilli, whereas L. sabanus remained widely distributed in insular Southeast Asia but experienced a range contraction on the Thai-Malay Peninsula. The two future climate change scenarios used predicted that large climatically suitable areas would still be available in the future for the three species. Main conclusions: Our model predictions contradict the well-established hypothesis that Southeast Asian forest-dwelling species were confined to small refugia during the LGM. Moreover, our results suggest that some Southeast Asian taxa may have been distributed in their refugial state during the LIG rather than the LGM. This could be because of vegetation changes that may have occurred at that time as a result of the increased seasonality observed during the LIG. These Pleistocene refugia may have been localized in northern Indochina but our study also revealed that southern Indochina could provide major potential refugia. [less ▲]

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See detailTesting the presence of a barrier to nuclear gene flow between two distant mitochondrial lineages of the bank vole (Myodes glareolus) in central finland
Pisano, Julie ULiege; Leblois, Raphael; Charbonnel, Nathalie et al

Poster (2015, April 22)

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See detailProgress on research on rodents and rodent-borne zoonoses in Southeast Asia
Blasdell, Kim; Bordes, Frédéric; Chaisiri, Kittipong et al

in Wildlife Research (2015), 42(2), 98-107

This review aims to synthesize the knowledge on the taxonomy of Southeast Asian murine rodents and the challenges associated with the identification of habitat preferences and associated rodent-borne ... [more ▼]

This review aims to synthesize the knowledge on the taxonomy of Southeast Asian murine rodents and the challenges associated with the identification of habitat preferences and associated rodent-borne diseases. Recent studies concerning the Rattini tribe have identified unclear species boundaries that would benefit from further investigation. The development of barcoding may allow more accurate identification of rodents, specifically for complex species. However, knowledge on the distribution and habitat specializations of many common murine rodents is still scarce, particularly regarding the specific habitat preferences of most synanthropic rodent species (Rattus tanezumi or Rattus exulans). Several studies have analyzed the prevalence of major rodent-borne diseases in Southeast Asia and it appears that the greatest risk of rodent zoonoses are in the lowland rainfed and irrigated landscapes, generally in and around rice fields. [less ▲]

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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)

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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 detailA new method to identify the endangered Pyrenean desman and to study its diet, using next generation sequencing from faeces
Gillet, François; Tiouchichine, Marie laure; Galan, Maxime et al

in Mammalian Biology (2015), 80

The Pyrenean desman (Galemys pyrenaicus) is a small endangered semi-aquatic mammal endemic to the Pyrenean Mountains and to the northern half of the Iberian Peninsula whose ecology and biology are still ... [more ▼]

The Pyrenean desman (Galemys pyrenaicus) is a small endangered semi-aquatic mammal endemic to 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 detailA new method to identify the endangered Pyrenean desman (Galemys pyrenaicus) and to study its diet, using next generation sequencing from faeces
Gillet, François ULiege; 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 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 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 ULiege 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 ULiege; 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 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 ULiege; Michaux, Johan ULiege

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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