References of "Michaux, Johan"
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See detailAn endogenous gibbon ape leukemia virus (GALV) identified in a rodent (Melomys sp.) from Indonesia
Niccolo, Alfano; Michaux, Johan ULg; Fabre, pierre-Henri et al

in Journal of Virology (2016), sous presse

ABSTRACT Gibbon ape leukemia virus (GALV) and koala retrovirus (KoRV) most likely originated from a cross-species transmission of an ancestral retrovirus into koalas and gibbons via one or more ... [more ▼]

ABSTRACT Gibbon ape leukemia virus (GALV) and koala retrovirus (KoRV) most likely originated from a cross-species transmission of an ancestral retrovirus into koalas and gibbons via one or more intermediate as yet unknown hosts. A highly similar virus to GALV has been identified in an Australian rodent (Melomys burtoni) after extensive screening of Australian wildlife. GALV-like viruses have also been discovered in several Southeast Asian species although screening has not been extensive and viruses discovered to date are only distantly related to GALV. We therefore screened 26 Southeast Asian rodent species for KoRV- and GALV-like sequences, using hybridization capture and high-throughput sequencing, in the attempt to identify potential GALV and KoRV hosts. Only one species, an undescribed species of Melomys from Indonesia, was positive yielding an endogenous provirus very closely related to a strain of GALV. The sequence of the critical receptor domain for GALV infection in the Indonesian Melomys sp. was consistent with the susceptibility of the species to GALV infection. The discovery of a GALV in a second Melomys species provides further evidence that Melomys may play a role in the spread of GALV-like viruses, especially since the genus is found in Indonesia, Papua New Guinea and Australia, connecting the home ranges of koalas and gibbons. IMPORTANCE The gibbon ape leukemia virus (GALV) and the koala retrovirus (KoRV) are very closely related, yet their hosts are neither closely related nor overlap geographically. Direct cross-species infection between koalas and gibbons is unlikely. Therfore, GALV and KoRV may have arisen via a cross-species transfer from an intermediate host that overlaps in range with both gibbons and koalas. Using hybridization capture and high-throughput sequencing, we have screened a wide range of rodent candidate hosts from Southeast Asia for KoRV- and GALV-like sequences. Only a Melomys species from Indonesia was positive for GALV. We report the genome sequence of this newly identified GALV, the critical domain for infection of its potential cellular receptor and its phylogenetic relationships with the other previously characterized GALVs. We hypothesize that the genus Melomys may have played a key role in cross-species transmission to other taxa. [less ▲]

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See detailIs adult translocation a credible way to accelerate the recolonization process of Chondrostoma nasus in a rehabilitated river?
Ovidio, Michaël ULg; Hanzen, Céline; Gennotte, Vincent ULg et al

in Cybium (2016), 40(1), 43-49

The decline of the patrimonial rheophilic nase, Chondrostoma nasus (Linnaeus, 1758) populations was mainly caused by construction of dams and hydroelectric power-plants, together with the straightening ... [more ▼]

The decline of the patrimonial rheophilic nase, Chondrostoma nasus (Linnaeus, 1758) populations was mainly caused by construction of dams and hydroelectric power-plants, together with the straightening and artificialization of the river banks and water pollution. In this study, we tested the hypothesis whether the translocation of few adult nase individuals from a river stretch to another upstream may be a credible way to accelerate the recolonization process of the species in the Amblève River (Southern Belgium). In February and March 2011, just before their spawning period, eight adult nases (462-509 mm; 1546-2002 g; presumed males and females) were captured in the lower part of the River Amblève. Fin clip samples were stored in alcohol for further genetic analysis. They were equipped with a 14 g radio transmitter and translocated upstream in a 18 km river stretch, where the species had disappeared since decades due to river anthropization. They were manually located two to five times/week using mobile receivers until maximum June 2012 (n = 977 locations). River temperature and flow were hourly recorded during the entire tracking period. The tagged nase individuals displayed various mobility patterns, exploited different areas of the river stretch, occupied longitudinal home ranges from 3.4 to 36.1 km (one individual finally left the new river stretch) and travelled total distances from 12.2 to 186.6 km. The tagged individuals were most of the times apart from one to another, but most individuals grouped together in potential spawning areas in late March-early April 2011, suggesting an attempt to reproduce. In September 2011, electric fishing in two potential detected spawning sites allowed to capture 16 juvenile (0+) nases, demonstrating the existence of spawning activity in the newly occupied river stretch. Individual genetic characterization was performed in 2014 in order to reveal a possible direct lineage between juveniles and adults. Allelic distribution of 22 microsatellite markers unambiguously identified the 16 juveniles as full-sib progeny descending from two of the translocated adults. This demonstrated that the adult nases succeeded to find spawning areas and that progeny found raised-up from the translocated individuals. [less ▲]

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See detailFrom sample hunt to sequence processing, the journey of a biologist
André, Adrien ULg; Millien, Virginie; Michaux, Johan ULg

Conference (2015, December 08)

Metabarcoding studies are becoming more and more popular with a field of applications constantly increasing. However, the methods used are sometimes complex and might remain “obscure” for most of us. The ... [more ▼]

Metabarcoding studies are becoming more and more popular with a field of applications constantly increasing. However, the methods used are sometimes complex and might remain “obscure” for most of us. The objective of this presentation is therefore to familiarize people with this field of research by giving an overview of the different steps permitting the achievement of metabarcoding studies. Field work, lab work and bioinformatics will be subsequently detailed and accessibly explained. [less ▲]

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See detailEtude de la diversité génétique et de l’état des stocks des populations de barbeaux et de hotus en Wallonie. Amélioration des techniques d’élevage en vue de repeuplements raisonnés et de transferts de connaissances vers les pisciculteurs
Gennotte, Vincent ULg; Prignon, Christian ULg; Dierckx, Arnaud ULg et al

Report (2015)

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

Nase (Chondrostoma nasus) and common barbel (Barbus barbus) are two rheophilic cyprinid fish naturally present in South Belgian rivers. During the last decades, the construction of dams together with changes in hydrological regimes, modifications of riverbed morphology and water pollution caused some local dramatic declines in their populations. However, recent improvements in terms of water quality and habitat fragmentation allow now to implement a rational restocking plan of locally endangered patrimonial fish species such as nase and common barbel. To reach this goal, this project (co-funded by the European Fisheries Fund and the Wallonia Public Service) proposed to develop five complementary parts with specific objectives: • Review of the knowledge on nase and barbel geographical distribution and stock health in Wallonia. This section presents the distribution and recent evolution of populations in Europe, and more specifically in Wallonia. Areas where population declines were reported are identified. Even if a weak population expansion was reported in some isolated cases, the global status of Walloon populations is still concerning. • Characterization of genetic structure and diversity of South Belgium populations. Restocking operations for a conservation purpose have to be based on the knowledge and the use of wild type genetic strains. Nase and barbel populations from South Belgium were genetically characterized by use of microsatellites. Globally, nase and barbel populations are structured on a basin scale. A slight genetic differentiation exists between populations from the Rhine basin and the Meuse basin, defining two conservation units, but no finer structure was observed among populations from the Meuse basin. Genetic variation was high within populations. Genetic structure of barbel populations is more complex due to past restocking operations with different genetic lineages. An analysis of mDNA identified 6 different haplotypes but was unable to categorize them as autochtone or allochtone. • Development of fish production techniques. The complete control of fish farming is necessary to produce high quality juveniles for restocking. All the steps of the production cycle were addressed: broodstock management and reproduction, egg incubation, larval rearing and grow-out. Production systems ranging from extensive pond culture to intensive RAS were tested and the optimal farming conditions were identified (temperature, density, feeding, tank volumes, …). • Adaptation assessment of farmed fingerlings to natural conditions. Growth and survival performances of captive farmed fish were assessed in an experimental environment that mimics natural conditions. The results suggested that the more efficient practice for restocking would be based on operations performed in spring with large juveniles (3 to 50 g). • Know-how diffusion toward fish farmers. All the breeding and grow-out techniques developed for nase and barbel production are the subject of two handbooks. These documents, attached to the report, will be published and distributed to fish producers. [less ▲]

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See detailPast and future distributions of Southeast Asian murine rodents: the influence of climate changes
Latinne, Alice ULg; Meynard, Christine; Morand, Serge et al

Conference (2015, August 18)

Our study, involving species distribution modelling techniques, aimed at assessing the influence of past and future climatic fluctuations on Southeast Asian small mammal distributions using two forest ... [more ▼]

Our study, involving species distribution modelling techniques, aimed at assessing the influence of past and future climatic fluctuations on Southeast Asian small mammal distributions using two forest-dwelling (Leopoldamys herberti and Leopoldamys sabanus) and one karst endemic (Leopoldamys neilli) rodent species as models. Our model predictions contradict the well-established hypothesis that Southeast Asian forest-dwelling species were confined to small refugia during the LGM. Moreover, these results suggest that the distribution of several East and Southeast Asian taxa were in their refugial state during Pleistocene interglacial periods rather than during glacial periods. 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. The two future climate change scenarios used in this study predicted that large climatically suitable areas would still be available in the future for the three species. [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 (2015, August 05)

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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 ULg

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 ULg; Mouton, Alice ULg; 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 ULg; 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 ULg; 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 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 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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