Johan R Michaux

Johan R Michaux
University of Liège | ulg · Department of Life Sciences

PhD

About

333
Publications
60,656
Reads
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6,063
Citations
Additional affiliations
September 2003 - September 2015
University of Liège
Position
  • Research Associate
Description
  • I'm the director of the Conservation Genetics Research Unit of the University of Liège. This unit investigates the evolutionary history and the conservation genetics of different mammal species, distributed in Europe, Asia, North America and Africa.
March 2003 - March 2014
French National Institute for Agriculture, Food, and Environment (INRAE)
Position
  • invited researcher
October 2001 - March 2014
L'institut Agro | Montpellier SupAgro
Position
  • Research Associate

Publications

Publications (333)
Article
Les informations sur la biologie de la reproduction des poissons du genre Marcusenius vivant au pool Malebo, sont peu connues. Pourtant, leur exploitation très importante actuellement se fait sans tenir compte du renouvellement de leurs stocks. Cette étude avait comme objectif de déterminer les stratégies de reproduction de quatre espèces du genre...
Article
Full-text available
The hazel dormouse Muscardinus avellanarius presents an exemplary non-model species that is both locally threatened and whose genetic status is not fully understood owing to insufficient resolution of the currently available molecular tools. We performed normalized Genotyping-by-Sequencing (nGBS) on 48 hazel dormouse samples collected across the sp...
Article
Full-text available
The current anarchic exploitation of Marcusenius fish in the Malebo Pool located in the Congo River stands as a threat of extinction to certain species, while the ecology of most of them are hardly known. This study aims at evaluating the impact of environmental factors on the distribution of Marcusenius fish caught in six fishing stations in the M...
Conference Paper
Full-text available
The Forest Dormouse, Dryomys nitedula , has a wide geographic distribution, from Switzerland in the west, through eastern and southern Europe, Asia Minor and the Caucasus, to central Russia, central Asia and Mongolia in the east. Previous phylogenetic studies revealed highly divergent lineages in some part of the distribution, suggesting that the h...
Article
Full-text available
The Forest Dormouse ( Dryomys nitedula ) is one of the most widespread species of the Gliridae family, occurring in the Eastern Mediterranean, Central Asia, Caucasus and the Arabian plateau. The populations are mostly threatened by the destruction of their forest habitats. Despite being considered as Least Concern by the International Union for Con...
Preprint
Full-text available
Host’s fitness can be affected by its genotype and gut microbiota, defined as the microbes living in the host’s intestinal tract. This study explored how the genetic diversity of the host influences its bacterial communities in the context of captive breeding programs, for the critically endangered European mink (Mustela lutreola). As stated by the...
Preprint
Full-text available
One of the threats that the critically endangered European mink (Mustela lutreola) faces throughout its relict range, including the occidental population, is the impact of the American mink (Mustela vison) invasion in its natural habitat. We aimed to explore the differences in microbiota and genetic diversity between European and American mink to t...
Article
Full-text available
Espèce protégée et en régression sur l’ensemble de son aire de répartition, le Desman des Pyrénées Galemys pyrenaicus (É. Geoffroy Saint-Hilaire, 1811) reste une espèce mal connue malgré les programmes d’actions en faveur de sa conservation mis en œuvre en France depuis 2010. Le manque de connaissance sur la densité des populations et les déplaceme...
Article
Full-text available
Ecological theory postulates that niches of co-occurring species must differ along some ecological dimensions in order to allow their stable coexistence. Yet, many biological systems challenge this competitive exclusion principle. Insectivorous bats from the Northern Hemisphere typically form local assemblages of multiple species sharing highly sim...
Article
Pneumocystis fungi are opportunistic parasites of mammalian lungs whose evolution, ecology and host specificity in natural host populations remain poorly understood and controversial. Using an extensive collection of 731 lung samples from 27 rodent species sampled in five Southeast Asian countries, and nested PCR amplification of mitochondrial and...
Chapter
The study of wildlife/livestock interfaces has long suffered from the sealing among the different agricultural - including veterinary - and environmental sectors and the lack of multidisciplinary approaches. Following the SARS and H5N1 crisis, bridges have been developed between sectors and different disciplines, especially between the fields of ep...
Article
Full-text available
Host-adapted microorganisms are generally assumed to have evolved from free-living, environmental microorganisms, as examples of the reverse process are rare. In the phylum Gammaproteobacteria, family Moraxellaceae, the genus Psychrobacter includes strains from a broad ecological distribution including animal bodies as well as sea ice and other non...
Article
For the last three decades, Nile tilapia Oreochromis niloticus (Linnaeus, 1758) is considered as one of the most productive and internationally traded food fish. Although economically important, our knowledge on the genetic structure of natural and farmed populations is scarce, especially in Africa. Sustainable aquaculture however requires integrat...
Preprint
Full-text available
Host-adapted microbiota are generally thought to have evolved from free-living ancestors. This process is in principle reversible, but examples are few. The genus Psychrobacter (family Moraxellaceae , phylum Gamma-Proteobacteria ) includes species inhabiting diverse and mostly polar environments, such as sea ice and marine animals. To probe Psychro...
Article
Water voles from the genus Arvicola display an amazing ecological versatility, with aquatic and fossorial populations. The Southern water vole (Arvicola sapidus) is largely accepted as a valid species, as well as the newly described Arvicola persicus. In contrast, the taxonomic status and evolutionary relationships within Arvicola amphibius sensu l...
Preprint
Ecological theory postulates that the niche of co-occurring species must differ along some ecological dimensions in order to allow their stable coexistence. Yet, many biological systems challenge this competitive exclusion principle. For instance, insectivorous bats from the Northern Hemisphere typically form local assemblages of multiple species s...
Article
Full-text available
To better understand the evolutionary history of oriental wildlife newcomers in Europe, we studied the phylogeography and demographic history of the striped field mouse, Apodemus agrarius, throughout its Palaearctic distribution area. Genetic datasets including cytochrome b gene sequences and microsatellite markers were analysed using a large range...
Article
Full-text available
Viruses belonging to the Dicistroviridae family have attracted a great deal of attention from scientists owing to their negative impact on agricultural economics, as well as their recent identification as potential aetiological agents of febrile illness in human patients. On the other hand, some Dicistroviruses are also studied for their potential...
Article
Full-text available
The present study investigated the natural recovery of the Eurasian otter (Lutra lutra) in France. The otter was widely distributed in France at the dawn of the 20th century, but then its range considerably shrank and became highly fragmented until the early 1970s, just before it was legally protected. However, for more than 25 years, the otter has...
Article
Full-text available
Metabarcoding of feces has revolutionized the knowledge of animal diets by providing unprecedented resolution of consumed resources. However, it is still unclear how different methodological approaches influence the ecological conclusions that can be drawn from such data. Here, we propose a critical evaluation of several data treatments on the infe...
Article
Full-text available
Background: Snow leopards, Panthera uncia, are a threatened apex predator, scattered across the mountains of Central and South Asia. Disease threats to wild snow leopards have not been investigated.Methods and Results: Between 2008 and 2015, twenty snow leopards in the South Gobi desert of Mongolia were captured and immobilised for health screening...
Article
The genetic structure of forest animal species may allow the spatial dynamics of the forests themselves to be tracked. Two scales of change are commonly discussed: changes in forest distribution during the Quaternary, due to glacial/ interglacial cycles, and current fragmentation related to habitat destruction. However, anthropogenic changes in for...
Article
Full-text available
Après un fort et rapide déclin en Europe au cours de la seconde moitié du XXe siècle, la Loutre d’Europe Lutra lutra (Linnaeus, 1758) a survécu dans une série de noyaux de populations isolés d’où elle a entrepris la recolonisation de nombreux territoires. Une série d’études a tenté de mieux comprendre les raisons de l’expansion rapide de cette espè...
Article
Full-text available
The African lion (Panthera leo), listed as a vulnerable species on the IUCN Red List of Threatened Species (Appendix II of CITES), is mainly impacted by indiscriminate killing and prey base depletion. Additionally, habitat loss by land degradation and conversion has led to the isolation of some subpopulations, potentially decreasing gene flow and i...
Data
Results of the Bayesian clustering analysis with Structure v2.3.4 software performed on the SNP database, reporting the ΔK values calculated according to Evanno et al. [55] with the CLUMPAK web server. (A) refers to the analysis conducted at the continental scale, including all samples (K = 2), while (B) reports the results for the analysis conduct...
Data
FCA performed on the whole microsatellite dataset at the continental scale with Genetix v4.05. Yellow: Burkina Faso, CAR, Benin and Congo samples (West-Central lineage), blue: Tanzanian and South African samples (East-Southern lineage). (TIF)
Data
Estimation of the number of populations based on microsatellite data, analysed by STRUCTURE. (A) Probability of successive partitions of the data into an increasing number of clusters obtained at the continental scale. (B) Probability of successive partitions of the data into an increasing number of clusters obtained at the Tanzanian scale. (C) Pop...
Data
Phylogenetic tree reconstruction including all 17 haplotypes identified within the P. leo species. The tree was constructed with the maximum likelihood (ML) method using PhyML v3.0. Bootstrap support (above 800) are indicated on the branches. Orange: West-Central lineage, blue: East-Southern lineage. (TIF)
Data
Neighbor-joining tree reconstructed with Tassel v5.2.15 based on the SNPs database. Sample colors were attributed according to the STRUCTURE assignment posterior probabilities (Fig 5). BUR: Burkina Faso, CAR: Central African Republic, Green dot: root position. (TIF)
Data
Details of the four microsatellite mixes designed within the present study. The primers were initially described by Menotti-Raymond et al. [39] for the Felis catus species. The two last columns report the expected allele sizes and heterozygosities. (DOCX)
Data
List of P. leo haplotypes identified in the present study, including details about the geographic locations, corresponding lineage, number of samples included and new GenBank accession numbers. Numbers marked in bold represent the newly sequenced cytb gene. (?) indicates an uncertain sample origin, e.g. samples collected in zoos. CAR stands for Cen...
Data
List of the collected samples included in the present study. The table summarizes the sample origin (country and sampling locality), the number of samples collected at each locality, and gives a reference ID to Fig 1. (DOCX)
Data
Statistical analyses details and results of the cytb tree and network reconstruction, as well as the cytb genetic diversities estimations. (DOCX)
Data
Correlogram of the average autocorrelation coefficient (r) for 18 distance classes of 50 km each. Dashed lines represent the 95% upper (U) and lower (L) bounds of the null distribution assuming no spatial structure. Error bars represent the 95% confidence intervals around r. (TIF)
Data
Geographic distribution of the three Cytochrome b haplotypes found in Tanzania (N = 38 samples). It is worth noting that at the Tanzanian country scale, some structures could also be highlighted based on the cytb haplotype distribution, as displayed on the present figure. Three distinct mitochondrial haplotypes (hap2, 13 and 17; S3 Table) were iden...
Article
Full-text available
Both exogenous and endogenous retroviruses have long been studied in mice, and some of the earliest mouse studies focused on the heritability of genetic factors influencing permissivity and resistance to infection. The prototypic retroviral restriction factor, Fv1, is now understood to exhibit a degree of control across multiple retroviral genera a...
Article
The riparian European mink (Mustela lutreola), currently surviving in only three unconnected sites in Europe, is now listed as a critically endangered species in the IUCN Red List of Threatened Species. Habitat loss and degradation, anthropogenic mortality, interaction with the feral American mink (Neovison vison), and infectious diseases are among...
Article
Full-text available
Phylogeographic lineages are interpreted as the product of repeated isolation in glacial refugia, leading to vicariant differentiation. Being restricted to a given geographic area could also promote adaptive divergence in response to local conditions. The role of phylogeny and climate in the evolution of the bank vole (Myodes glareolus) was investi...
Article
Full-text available
Genetic diversity may decrease from the centre to the margin of a species distribution range due to neutral stochastic processes. Selection may also alter genetic diversity in non-neutral markers, such as genes associated with the immune system. Both neutral processes and selection on the immune system are thus expected to affect the spatial distri...
Article
Full-text available
Detailed information on the distribution and abundance of animals is often difficult to establish for rare and elusive species. Here we report on genetic analyses confirming the presence of the Kam dwarf hamster 500 km north of its known distribution in China where it was earlier thought to be endemic. Our finding was made during a study on disease...
Article
In this study, the interactions between two semi-aquatic mammals, the endangered Pyrenean desman Galemys pyrenaicus and the Eurasian water shrew Neomys fodiens, were investigated through the analysis of their summer diet using next-generation sequencing methods, combined with analyses of prey selectivity and trophic overlap. The diet of these preda...
Article
Full-text available
The Pyrenean desman, a threatened, semiaquatic mammal, is considered a specialist predator feeding on aquatic benthic invertebrates. This categorization comes from visual identification of prey in scat or gut contents, often based on a limited number of samples and locations. We combined diet analyses using next-generation sequencing methods with a...
Article
Full-text available
We examined the natural population structure of the Turkish hamster (Mesocricetus brandti) by analysing partial mitochondrial sequences of the control region and the cytochrome b gene. Evolutionary lineages were defined on haplotype clusters in genetic trees and a median-joining network. Most significant divergence events in M. brandti nested in th...
Article
Microbiome studies generally focus on the gut microbiome, which is composed of a large proportion of commensal bacteria. Here we propose a first analysis of the liver microbiome using next generation sequencing as a tool to detect potentially pathogenic strains. We used Peromyscus leucopus, the main reservoir host species of Lyme disease in eastern...
Article
Full-text available
Upon re-examination of the samples included in this study, the authors have established that Cal6 is Apodemus flavicollis and not Apodemus sylvaticus as originally reported [1]. The identification of the Apodemus mice samples was completed following the protocol described in Michaux et al. [2] based on the sequencing of a mitochondrial cytochrome b...
Article
Full-text available
The wood mouse Apodemus sylvaticus is an opportunistic rodent that is found throughout most of the European mainland. It is present on many islands around the margins of the continent and in northern Africa. The species has been the subject of previous phylogeographical studies, although these have focussed on the more southerly part of its range....
Article
Full-text available
Robust identification of species and significant evolutionary units (ESUs) is essential to implement appropriate conservation strategies for endangered species. However, definitions of species or ESUs are numerous and sometimes controversial, which might lead to biased conclusions, with serious consequences for the management of endangered species....
Article
Full-text available
This study aimed to develop a set of SNP markers with high resolution and accuracy within the African buffalo. Such a set can be used, among others, to depict subtle population genetic structure for a better understanding of buffalo population dynamics. In total, 18.5 million DNA sequences of 76 bp were generated by next generation sequencing on an...
Article
Full-text available
Paedomorphosis and metamorphosis are two major developmental processes that characterize the evolution of complex life cycles in many lineages. Whereas these processes were fixed in some taxa, they remained facultative in others, with alternative phenotypes expressed in the same populations. From a genetic perspective, it is still unknown whether s...
Article
Full-text available
Importance: 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. Therefore, GALV and KoRV may have arisen via a cross-species transfer from an intermediate host that ov...
Technical Report
Full-text available
The EU NON-NATIVE SPECIES RISK ANALYSIS – RISK ASSESSMENT TEMPLATE for Neovison vison was made as an argument to introduce this species on the EU Invasive Alien Species list. The first Union list of 37 plant and animal species was introduced in August 2016 and another 12 were added in August 2017. However, this accounts for just 3% of all IAS belie...
Poster
Full-text available
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. Its ecological relationships with other semi aquatic mammals like the aquatic shrew (Neomys fodiens) or the European otter (Lutra lut...
Article
Full-text available
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 translo-cation of few adult nase i...
Article
The Pyrenean desman (Galemys pyrenaicus) is a small semi-aquatic mammal endemic to the Pyrenean Mountains and the northern half of the Iberian Peninsula. This species is currently considered as vulnerable in the IUCN Red List and has been suffering from habitat loss and fragmentation for decades but little is known about the impact of water flow mo...
Article
The Pyrenean desman (Galemys pyrenaicus) is a small, semiaquatic mammal endemic to the Pyrenean Mountains and the northern half of the Iberian Peninsula where it lives in cold and well-oxygenated flowing mountain streams. This species is currently classified as vulnerable on the IUCN Red List and has been undergoing habitat loss and fragmentation f...
Article
Full-text available
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 Frenc...