References of "Pagès, Marie"
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See detailMolecular phylogeny and systematics of Dipodoidea: a test of morphology-based hypotheses
Lebedev, Vladimir; Bannikova, Anna; Pagès, Marie ULg et al

in Zoologica Scripta (2013), (3),

The superfamily Dipodoidea (Rodentia, Myomorpha) in its current interpretation contains a single family subdivided into six subfamilies. Four of them include morphologically specialized bipedal arid ... [more ▼]

The superfamily Dipodoidea (Rodentia, Myomorpha) in its current interpretation contains a single family subdivided into six subfamilies. Four of them include morphologically specialized bipedal arid-dwelling jerboas (Dipodinae – three-toed jerboas, Allactaginae – fivetoed jerboas, Cardiocraniinae – pygmy jerboas and Euchoreutinae – long-eared jerboas), the other two are represented by more generalized quadrupedal taxa (Zapodinae – jumping mice and Sminthinae – birch mice). Despite considerable effort from morphologists, the taxonomy as well as the phylogeny of the Dipodoidea remains controversial. Strikingly, molecular approach has never been envisaged to investigate these questions. In this study, the phylogenetic relationships among the main dipodoid lineages were reconstructed for the first time using DNA sequence data from four nuclear genes (IRBP, GHR, BRCA1, RAG1). No evidence of conflict among genes was revealed. The same robustly supported tree topology was inferred from the concatenated alignment whatever the phylogenetic methods used (maximum parsimony, maximum-likelihood and Bayesian phylogenetic methods). Sminthinae branches basally within the dipodoids followed by Zapodinae. Monophyletic Cardiocraniinae is sister to all other jerboas. Within the latter, the monophyly of both Dipodinae and Allactaginae is highly supported. The relationships between Dipodinae, Allactaginae and Euchoreutinae should be regarded as unresolved trichotomy. Morphological hypotheses were confronted to findings based on the presented molecular data. As a result, previously proposed sister group relationships between Euchoreutes and Sicista, Paradipus and Cardiocraniinae as well as the monophyly of Cardiocaniinae + Dipodinae were rejected. However, the latter association is consistently supported by most morphological analyses. The basis of the obvious conflict between genes and morphology remains unclear. Suggested modifications to the taxonomy of Dipodoidea imply recognition of three families: Sminthidae, Zapodidae and Dipodidae, the latter including Cardiocraniinae, Euchoreutinae, Allactaginae and Dipodinae as subfamilies. [less ▲]

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See detailToward a Noninvasive Inuit Polar Bear Survey: Genetic Data from Polar Bear Hair Snags
Van Coeverden de Groot, Peter; Wong, Pamela; Harris, Christopher et al

in Wildlife Society Bulletin (2013)

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See detailCytonuclear discordance among Southeast Asian black rats (Rattus rattus complex)
Pagès, Marie ULg

in Molecular Ecology (2013)

Black rats are major invasive vertebrate pests with severe ecological, economic and health impacts. Remarkably, their evolutionary history has received little attention and there is no firm agreement on ... [more ▼]

Black rats are major invasive vertebrate pests with severe ecological, economic and health impacts. Remarkably, their evolutionary history has received little attention and there is no firm agreement on how many species should be recognized within the black rat complex. This species complex is native to India and Southeast Asia. According to current taxonomic classification, there are three taxa living in sympatry in several parts of Thailand, Cambodia and Lao People's Democratic Republic, where this study was conducted: two accepted species (Rattus tanezumi, Rattus sakeratensis) and an additional mitochondrial lineage of unclear taxonomic status referred to here as ‘Rattus R3’. We used extensive sampling, morphological data and diverse genetic markers differing in rates of evolution and parental inheritance (two mitochondrial DNA genes, one nuclear gene and eight microsatellite loci) to assess the reproductive isolation of these three taxa. Two close Asian relatives, Rattus argentiventer and Rattus exulans, were also included in the genetic analyses. Genetic analyses revealed discordance between the mitochondrial and nuclear data. Mitochondrial phylogeny studies identified three reciprocally monophyletic clades in the black rat complex. However, studies of the phylogeny of the nuclear exon IRBP and clustering and assignation analyses with eight microsatellites failed to separate R. tanezumi and R3. Morphometric analyses were consistent with nuclear data. The incongruence between mitochondrial and nuclear (and morphological) data rendered R. tanezumi/R3 paraphyletic for mitochondrial lineages with respect to R. sakeratensis. Various evolutionary processes, such as shared ancestral polymorphism and incomplete lineage sorting or hybridization with massive mitochondrial introgression between species, may account for this unusual genetic pattern in mammals. [less ▲]

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See detailThe optimization of microsatellite genotyping and genetic sexing of non-invasively collected polar bear tissue: Implications for monitoring and census.
Harris, Christopher; Van Coeverden De Groot, Peter; Kamookak, L et al

Conference (2012, April)

The monitoring of Polar Bears in Canada has been completed largely through management unit (MU) wide capture-mark-recapture (CMR) surveys. While this data is very useful at the time of collection, these ... [more ▼]

The monitoring of Polar Bears in Canada has been completed largely through management unit (MU) wide capture-mark-recapture (CMR) surveys. While this data is very useful at the time of collection, these surveys are expensive and take time to plan and execute; cannot be feasibly executed across the polar bear range at intervals that reflect the expected rapid environmental changes in the Arctic; and are disdained by the Inuit as being invasive. As part of recent efforts to explore less expensive and non-invasive methods to monitor polar bears (see Wong et al & Van Coevderden de Groot et al this conference) we are evaluating genetic information obtained from non-invasively collected polar bear tissue. In this work we report on the genetic data obtained from non-invasively collected harisnags recovered from sampling stations erected between May-June 2006-2009 in M’Clintock Channel, Nunavut. Across the 4 years 344 hair snags were collected; following Paetkau (2004) we optimized 6 microsatellite loci to reliably amplify polar bear DNA from this tissue and we modified the procedure of Pages et al (2009) to reliably genetically sex these tissues. Our estimates for two common errors with this type of tissue across all loci – allelic dropout (0.026) and false allele (0.03) - were both less than p =.05. This suggests these errors are not going to significantly affect the accuracy of the consensus genotypes collected from these data. Using consensus genotypes from relevant hairsnags, we posit a minimum of 59 (max 82) unique bears entered our sampling stations. Of these, 24% were female, 64% were male, and 12% could not be sexed. We resampled 2 bears in 2006, 1 in 2007, 0 bears in 2008 and 14 bears in 2009 – the 2009 value reflects significantly increased sampling effort in 2009. Five bears were re-sampled between the non-invasive surveys in 2006-2009. When comparing our data to a subset of cubs and subadults captured during the Taylor et al. (2006) CMR survey of M’Clintock Channel (MU), we found 6 genotype matches. Our sampling stations may have a male bias as the sex ratio from the 1998-2000 CMR study was 42.1% ♂ (Taylor et al 2006) vs. 64% ♂ (this study). We cannot accurately determine the age bias (but see Wong et al this conference). Genetic data from Polar bear faecal samples may provide an unbiased sex and age sample of polar bears in any MU. Any data from these samples will help refine hairsnag derived MKNA estimate of polar bears from any MU. Here we report on our efforts to genotype and genetically sex 95 faecals we have collected from M’Clintock Channel from 2006-2009. Finally, we discuss the implications of these findings, results from other noninvasive work (Wong et al & Van Coevderden de Groot et al this conference) and ongoing/proposed work in the context of i) a non-invasive Inuit-based polar bear activity and health survey, and ii) a more rigorous census method which may allow more precise adjustments of harvest levels than currently possible using infrequently collected CMR data only. [less ▲]

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See detailComplex genetic structures between nascent species in Southeast Asian Black rats (Rattus rattus complex)
Pagès, Marie ULg; Bazin, Eric; Galan, Maxime et al

Scientific conference (2012, January 19)

Black rats are among the major invasive vertebrates with severe ecological, economic and health impacts. Remarkably, their evolutionary history has received little attention and there is no firm agreement ... [more ▼]

Black rats are among the major invasive vertebrates with severe ecological, economic and health impacts. Remarkably, their evolutionary history has received little attention and there is no firm agreement on how many species should be recognized within the Black rat complex. Members of the species complex are native from India and Southeast Asia. Current taxonomy suggests that three taxa live in sympatry in several places of Thailand, Cambodia and Lao People's Democratic Republic where the present study was conducted: two accepted species (Rattus tanezumi, Rattus sakeratensis) and an additional mitochondrial lineage of unclear taxonomic status here referred as ‘Rattus R3’. We used an extensive sampling, morphological data and diverse genetic markers of different evolutionary rates and parental inheritance (two mitochondrial DNA genes, one nuclear gene and eight microsatellite loci) to assess the reproductive isolation between these three taxa. Two close Asian relatives, Rattus argentiventer and Rattus exulans, were included in the genetic analyses for comparison. Genetic analyses revealed discordant patterns between the mitochondrial and the nuclear data. The mitochondrial phylogeny identified three reciprocally monophyletic clades in the Black rat complex. Yet, the phylogeny of the nuclear exon IRBP and the clustering and assignation analyses using the eight microsatellites failed to separate tanezumi and R3. Morphometric analyses reinforced the nuclear data. The incongruence between mitochondrial data and nuclear (and morphological) data, render tanezumi/R3 paraphyletic for mitochondrial lineages with respect to sakeratensis. Different evolutionary processes such as shared ancestral polymorphism and incomplete lineage sorting or hybridization with massive mitochondrial introgression between incipient species may be invoked to account for this unusual genetic pattern in mammals. [less ▲]

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See detailNext-Generation Sequencing for Rodent Barcoding: Species Identification from Fresh, Degraded and Environmental Samples
Galan, Maxime; Pagès, Marie ULg; Cosson, Jean-François

in PLoS ONE (2012), 7(11), 48374

Rodentia are one of the most diverse orders among mammals, with more than 2,000 species currently described. Species assignation based on morphological data alone can present enormous challenges. In this ... [more ▼]

Rodentia are one of the most diverse orders among mammals, with more than 2,000 species currently described. Species assignation based on morphological data alone can present enormous challenges. In this study, we compared the applicability of 100 bp mini-barcodes from cytochrome b and cytochrome c oxidase 1 genes to enable rodent species identification. Based on GenBank sequence datasets of 115 rodent species, a 136 bp fragment of cytochrome b combined with universal rodent primers was selected as the most discriminatory mini-barcode. The efficacy of this new molecular tool was assessed on 946 samples including rodent tissues, feces, museum samples and feces/pellets from predators known to ingest rodents. Utilizing next generation sequencing technologies able to sequence multiple DNAs, 1,140 amplicons were tagged, multiplexed and sequenced together in one single 454 GS-FLX run. Our method was initially validated on a reference sample set including 265 clearly identified rodent tissues, corresponding to 103 different species. Following validation, 85.6% of 555 rodent samples from Europe, Asia and Africa whose species identity was unknown were able to be identified using the BLASTN program and GenBank reference sequences. In addition, our method proved effective even on degraded rodent DNA samples: 91.8% and 75.9% of samples from feces and museum specimens respectively were correctly identified. Finally, we succeeded in determining the diet of 66.7% of the investigated carnivores from their feces and 81.8% of owls from their pellets. Non-rodent species were also identified suggesting that our method is sensitive enough to investigate complete predator diets. This study demonstrates how this molecular identification method combined with high throughput sequencing can open new realms of possibilities in achieving fast, accurate and inexpensive species identification. [less ▲]

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See detailPaleogenetic Analyses Reveal Unsuspected Phylogenetic Affinities between Mice and the Extinct Malpaisomys insularis, an Endemic Rodent of the Canaries
Pagès, Marie ULg; Chevret, Pascale; Gros-Balthazard, Muriel et al

in PLoS ONE (2012), 7(2), 31123

Background: The lava mouse, Malpaisomys insularis, was endemic to the Eastern Canary islands and became extinct at the beginning of the 14th century when the Europeans reached the archipelago. Studies to ... [more ▼]

Background: The lava mouse, Malpaisomys insularis, was endemic to the Eastern Canary islands and became extinct at the beginning of the 14th century when the Europeans reached the archipelago. Studies to determine Malpaisomys’ phylogenetic affinities, based on morphological characters, remained inconclusive because morphological changes experienced by this insular rodent make phylogenetic investigations a real challenge. Over 20 years since its first description, Malpaisomys’ phylogenetic position remains enigmatic. Methodology/Principal Findings: In this study, we resolved this issue using molecular characters. Mitochondrial and nuclear markers were successfully amplified from subfossils of three lava mouse samples. Molecular phylogenetic reconstructions revealed, without any ambiguity, unsuspected relationships between Malpaisomys and extant mice (genus Mus, Murinae). Moreover, through molecular dating we estimated the origin of the Malpaisomys/mouse clade at 6.9 Ma, corresponding to the maximal age at which the archipelago was colonised by the Malpaisomys ancestor via natural rafting. Conclusion/Significance: This study reconsiders the derived morphological characters of Malpaisomys in light of this unexpected molecular finding. To reconcile molecular and morphological data, we propose to consider Malpaisomys insularis as an insular lineage of mouse. [less ▲]

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See detailImmunogenetics as a tool to assess Hantavirus risk in wild rodents
Guivier, Emmanuel; Galan, Maxime; Pagès, Marie ULg et al

Conference (2011, July)

Immunogenetics, the analysis of genetic polymorphisms in specific recognition and immune regulation, is at the core of the study of host-parasite coevolution. We present here a synthesis of our recent ... [more ▼]

Immunogenetics, the analysis of genetic polymorphisms in specific recognition and immune regulation, is at the core of the study of host-parasite coevolution. We present here a synthesis of our recent works based on immune gene polymorphism to illustrate the power of this approach in improving our knowledge of rodent / hantavirus interactions. Two candidate genes (encoding Mx2 protein and β3 integrin) were first investigated at the inter-specific level. Sequence and/or expression polymorphism were compared among twenty murid species, some of them being reservoirs and some others being non reservoirs of hantaviruses. Our results showed that SNPs as well as patterns of selection acting on these genes differed between these rodent species and could mediate their susceptibility to hantaviruses. Four candidate genes (Mx2 gene and three genes from the Major Histocompatibility Complex) were next analyzed among populations of bank voles (Myodes glareolus), the reservoir of Puumala virus (PUUV). We revealed the existence of positive associations between Mhc alleles and PUUV infection in one hand and negative relationships between Tnf-α or Mx2 expression levels and PUUV prevalence in the other hand. These results suggested that tolerance to PUUV could have evolved in endemic areas. Such tolerance could be selected in response to the costs of immune responses that are activated against PUUV. We will conclude on the advantages to combine this immune gene candidate approach with more recent analyses based on genome scan, to deepen our investigation of this intra- and inter-specific variability of rodent tolerance / susceptibility to hantaviruses. [less ▲]

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See detailHow many species in the Black rat complex (Rattus rattus sensu lato) in Southeast Asia?
Pagès, Marie ULg; Galan, Maxime; Chaval, Yannick et al

Conference (2011, July)

Black rats are among the major invasive vertebrates with severe ecological, economic and health impacts. Remarkably, the evolutionary history of black rats has received little attention and there is no ... [more ▼]

Black rats are among the major invasive vertebrates with severe ecological, economic and health impacts. Remarkably, the evolutionary history of black rats has received little attention and there is no firm agreement as how many species should be recognized within the Rattus rattus complex. Members of the species complex are native from India and Southeast Asia. Current taxonomy suggests that four taxa live in sympatry in several places of Thailand and Cambodia where the present study was conducted: three accepted species (R. tanezumi, R. losea, R. argentiventer) and an additional lineage of unclear taxonomic status sometimes referred as Rattus R3. We used an extensive sampling, morphological data and diverse genetic markers of different evolutionary rates and parental inheritance (two mtDNA genes, one nuclear gene and eight microsatellite loci) to assess the genetic structure among the four taxa. Genetic analyses revealed discordant patterns between the mt and the nuclear data. The mt phylogeny identified three reciprocally monophyletic clades corresponding to the four putative taxa while the nuclear phylogeny failed to separate tanezumi and R3. Within geographic localities, microsatellites revealed free gene flow between tanezumi and R3 but no gene flow between those two taxa and losea or argentiventer. Altogether theses analyses do not support the taxon R3 as a valid species and advocate for synonymy with tanezumi. As a consequence, R. tanezumi becomes paraphyletic with respect to losea. Simulation analyses are now ongoing to determine whether a recent speciation event between tanezumi and losea, or an incomplete lineage sorting within tanezumi could explain this uncommon pattern. [less ▲]

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See detailInterpretations of Polar Bear (Ursus maritimus) Tracks by Inuit Hunters: Inter-rater Reliability and Inferences Concerning Accuracy
Wong, Pamela; Van Coeverden de Groot, Peter; Fekken, Cynthia et al

in Canadian Field-Naturalist (2011), 125(2), 140-153

due to their tracking experience in pursuing Polar Bears (Ursus maritimus), Inuit hunters could provide non-invasive estimates of Polar Bear characteristics from tracks, and Polar Bear monitoring programs ... [more ▼]

due to their tracking experience in pursuing Polar Bears (Ursus maritimus), Inuit hunters could provide non-invasive estimates of Polar Bear characteristics from tracks, and Polar Bear monitoring programs could benefit from Inuit input. We determined i) inter-rater reliability of estimates of the sex, age, and size of Polar Bears, and estimates of the age of tracks made by a group of nine Inuit hunters who interpreted 78 tracks; ii) we made preliminary comparisons of sex and size estimates with conventional (scientific) estimates; iii) we catalogued the Polar Bear hunting experience and track interpretation techniques of nine Inuit hunters; and iv) we explored relationships between hunting experience and the ability to interpret tracks. The group of Inuit hunters made reliable and consistent estimates of Polar Bear sex, age, and size, as well as estimates of age of track (after data from one participant was excluded). Although our comparisons are based on small samples, our findings suggest that Inuit hunters may be accurate in estimating the sex of Polar Bears (74.42% agreement with genetic determinations) and the size of Polar Bears from their tracks. our data indicate shared tracking techniques used by hunters may explain high agreement in making specific estimates, while individual hunting experience and particular methods used to interpret tracks may lead to inter-rater reliability and accuracy in interpreting tracks. [less ▲]

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See detailMorphological, chromosomal, and genic differences between sympatric Rattus rattus and Rattus satarae in South India
Pagès, Marie ULg; Corbet, Gordon; Orth, Annie et al

in Journal of Mammalogy (2011), 92(3), 659670

Two morphological forms of black rats (Rattus cf. rattus) were found living in sympatry in high-altitude dense forests of the Nilgiri Mountains, South India. The 1st one, often brown- or gray-bellied ... [more ▼]

Two morphological forms of black rats (Rattus cf. rattus) were found living in sympatry in high-altitude dense forests of the Nilgiri Mountains, South India. The 1st one, often brown- or gray-bellied, also is found commensal in lowland settlements and represents Rattus rattus cf. rufescens (Gray 1837), with a diploid number (2N) of 38 chromosomes. The 2nd form, which has most often a pure white belly, has 2N 5 42 chromosomes and is referable to Rattus r. satarae Hinton, 1918, based on morphological comparison with the holotype. A multidisciplinary study indicates that these 2 forms are characterized by clear-cut differences in biochemistry (electrophoresis of homologous isozymes), molecular sequences (mitochondrial and nuclear DNA), and chromosomes (detailed banding analysis). All these data, coupled to diagnostic morphological characteristics, support the hypothesis that Rattus satarae and Rattus rattus are separate, sympatric species, with no gene flow between them. Their similar external morphology is interpreted as the result of convergence through occupying the same ecological niche. [less ▲]

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See detailPhylogenetic position of the Ohiya rat (Srilankamys ohiensis) based on mitochondrial and nuclear gene sequence analysis
Buzan, Elena; Pagès, Marie ULg; Michaux, Johan ULg et al

in Zoologica Scripta (2011), 40(6), 545-553

We investigated the phylogenetic position the Ohiya rat, endemic to Sri Lanka, Srilankamys (Rodentia, Murinae), within the tribe Rattini based on the combined analysis of three independent genes (a ... [more ▼]

We investigated the phylogenetic position the Ohiya rat, endemic to Sri Lanka, Srilankamys (Rodentia, Murinae), within the tribe Rattini based on the combined analysis of three independent genes (a mitochondrial one and two nuclear exons). Three major lineages (the Maxomys, the Dacnomys and the Rattus divisions) were retrieved as monophyletic groups within the tribe Rattini. Srilankamys was not affiliated to any of the representatives of the Dacnomys division as it was supposed based on morphological characters, but clearly appeared as the first genus to diverge among the Rattus division. The Mindanao Shrew Mouse, Crunomys melanius, emerged as a part of the Maxomys division raising questions about the validity of the Crunomys and the Maxomys divisions as currently defined. Molecular date of divergence between Srilankamys and the other representatives of the Rattus division falls within the interval 6.7 ± 0.74 Mya, coinciding with the time of the isolation of Sri Lanka from the Deccan peninsula and the aridification period owing to the climate change at the end of the Miocene epoch. We suggest that the isolation of Sri Lanka from the continent, reinforced by the action of a seasonal monsoon-dominated climate, would have led to the isolation of some ancestral rodents of the Rattus division, which would have differentiated later into the Ohiya rat by a vicariant process. In a more general point of view, our study supports the previous results obtained on other organisms and evidence that Sri Lanka appears to be characterized by a particular fauna as compared to the Indian mainland. This island would therefore be considered as a specific distinct hotspot of biodiversity. [less ▲]

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See detailInter- and Intraspecific Genetic Biodiversity in South East Asian Rodents: New Insights for Their Conservation
Pagès, Marie ULg; Latinne, Alice ULg; Michaux, Johan ULg

in Zachos, F. E.; Habel, J. C. (Eds.) Biodiversity Hotspots (2011)

South East Asia displays a high level of mammal endemism and the highest number of threatened and data deficient mammal species. However, the South East Asian biodiversity is still highly unexplored ... [more ▼]

South East Asia displays a high level of mammal endemism and the highest number of threatened and data deficient mammal species. However, the South East Asian biodiversity is still highly unexplored. Because of the runaway global changes, a better biological knowledge of this region is urgently required to improve the conservation and the management of its biodiversity. The first aim of this chapter is to present recent published data on a biodiversity inventory of the Rattini murine rodents from this region based on molecular markers (Page`s et al., 2009). In this first study, we applied the method proposed by Pons et al. (2006) that determines with no a priori the locations of ancestral nodes that define putative species in order to investigate the current taxonomy of the Rattini tribe. Our second aim concerns the intraspecific genetic structure of a rare and threatened South East Asian mammal species: the murine rodent Leopoldamys neilli, endemic to karst habitats . In this latter study, our results evidenced a high geographic structure of the genetic diversity of this species. The observed highly divergent genetic lineages would have to be considered as distinct evolutionary units or at least as Management units. These results are essential for the best conservation issues of species endemic to karsts and to South East Asia, in general. In this chapter, we therefore highlight that South East Asia would not be only a hotspot of interspecific but also of intraspecific biodiversity. [less ▲]

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See detailβ3 integrin sequence variation and rodent susceptibility to hantaviruses
Pagès, Marie ULg; Tatard, Caroline; Galan, Maxime et al

Poster (2010, May)

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See detailRevisiting the taxonomy of the Rattini tribe: a phylogeny-based delimitation of species boundaries
Pagès, Marie ULg; Chaval, Yannick; Herbreteau, Vincent et al

Conference (2010, April)

Rodents are recognized as hosts for at least 60 zoonotic diseases and may represent a serious threat for human health. In the context of global environmental changes and increasing mobility of humans and ... [more ▼]

Rodents are recognized as hosts for at least 60 zoonotic diseases and may represent a serious threat for human health. In the context of global environmental changes and increasing mobility of humans and animals, contacts between pathogens and potential animal hosts and vectors are modified, amplifying the risk of disease emergence. An accurate identification of each rodent at a specific level is needed in order to understand their implications in the transmission of diseases. Among the Muridae, the Rattini tribe encompasses 167 species inhabiting South East Asia, a hotspot of both biodiversity and emerging and re-emerging diseases. The region faces growing economical development that affects habitats, biodiversity and health. Rat species have been demonstrated as significant hosts of pathogens but are still difficult to recognize at a specific level using morphological criteria. DNA-barcoding methods appear as accurate tools for rat species identification but their use is hampered by the need of reliable identification of reference specimens. In this study, we explore and highlight the limits of the current taxonomy of the Rattini tribe. We used the DNA sequence information itself as the primary information source to establish group membership and estimate putative species boundaries. We sequenced two mitochondrial and one nuclear genes from 122 rat samples to perform phylogenetic reconstructions. The method of Pons and colleagues (2006) that determines, with no prior expectations, the locations of ancestral nodes defining putative species was then applied to our dataset. To give an appropriate name to each cluster recognized as a putative species, we reviewed information from the literature and obtained sequences from a museum holotype specimen following the ancient DNA criteria. [less ▲]

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See detailGenetic variation within β3 subunit integrin sequences and rodent species susceptibility to pathogenic hantaviruses
Pagès, Marie ULg; Tatard, Caroline; Galan, Maxime et al

Conference (2010, April)

Recent investigations in rodent systematics and epidemiology have led to the discovery of numerous Hantavirus species in Asia. As seroprevalences are very low, the screening of thousands of rodents is ... [more ▼]

Recent investigations in rodent systematics and epidemiology have led to the discovery of numerous Hantavirus species in Asia. As seroprevalences are very low, the screening of thousands of rodents is required to genetically identify these hantaviruses and to determine their human pathogenesis as well as their rodent reservoirs. Pathogenic and non-pathogenic hantaviruses use different integrin receptors to enter cells. In particular, human integrins αIIaβ3 and αvβ3 can mediate cellular entry of hemorragic fever with renal syndrome (HFRS)- and hemorragic pulmonary syndrome (HPS)-causing hantaviruses. In contrast, non-pathogenic or low pathogenic hantaviruses were demonstrated to enter the cell via integrin αvβ1. We tested the hypothesis that amino-acid variation in β3 subunit integrin sequences could provide keys to determine a priori the possibility for a rodent species to carry a human pathogenic hantavirus. We sequenced 330 bp of the β3 chain integrin encompassing the Plexin-Semaphorin-Integrin domain, for 63 individuals corresponding to 14 Asian rodent species. We found 65 variable sites and a high level of divergence between species (up to 12%). Although the genetic variation reflected the neutral phylogeny of these species, we found one site differing between rodent species carrying pathogenic hantaviruses and non reservoir rodent species. We also detected another variable site that could be under positive selection, but only in rodent species that do not carry pathogenic hantaviruses. This site did not exhibit any genetic variation in rodent species that carry hantaviruses. In consequence, it is likely that knowing the amino-acid present at this position for a given rodent species could help us determining a priori whether this species is a reservoir of pathogenic hantaviruses. Further investigations are required to examine whether amino-acid changes at these residues could mediate conformational changes that would prevent the fixation of pathogenic hantaviruses. [less ▲]

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See detailRefining the taxonomy of the Rattini tribe: a phylogeny-based delimitation of species boundaries
Pagès, Marie ULg; Chaval, Yannick; Herbreteau, Vincent et al

in BMC Evolutionary Biology (2010), 10(184), 184

Background: Rodents are recognized as hosts for at least 60 zoonotic diseases and may represent a serious threat for human health. In the context of global environmental changes and increasing mobility of ... [more ▼]

Background: Rodents are recognized as hosts for at least 60 zoonotic diseases and may represent a serious threat for human health. In the context of global environmental changes and increasing mobility of humans and animals, contacts between pathogens and potential animal hosts and vectors are modified, amplifying the risk of disease emergence. An accurate identification of each rodent at a specific level is needed in order to understand their implications in the transmission of diseases. Among the Muridae, the Rattini tribe encompasses 167 species inhabiting South East Asia, a hotspot of both biodiversity and emerging and re-emerging diseases. The region faces growing economical development that affects habitats, biodiversity and health. Rat species have been demonstrated as significant hosts of pathogens but are still difficult to recognize at a specific level using morphological criteria. DNAbarcoding methods appear as accurate tools for rat species identification but their use is hampered by the need of reliable identification of reference specimens. In this study, we explore and highlight the limits of the current taxonomy of the Rattini tribe. <br />Results: We used the DNA sequence information itself as the primary information source to establish group membership and estimate putative species boundaries. We sequenced two mitochondrial and one nuclear genes from 122 rat samples to perform phylogenetic reconstructions. The method of Pons and colleagues (2006) that determines, with no prior expectations, the locations of ancestral nodes defining putative species was then applied to our dataset. To give an appropriate name to each cluster recognized as a putative species, we reviewed information from the literature and obtained sequences from a museum holotype specimen following the ancient DNA criteria. <br />Conclusions: Using a recently developed methodology, this study succeeds in refining the taxonomy of one of the most difficult groups of mammals. Most of the species expected within the area were retrieved but new putative species limits were also indicated, in particular within Berylmys and Rattus genera, where future taxonomic studies should be directed. Our study lays the foundations to better investigate rodent-born diseases in South East Asia and illustrates the relevance of evolutionary studies for health and medical sciences. [less ▲]

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See detailA multi-approach survey as the most reliable tool to accurately assess biodiversity: the example of Thai murine rodents
Chaval, Yannick; Dobigny, Gauthier; Michaux, Johan ULg et al

in Kasetsart Journal. Natural Sciences (2010), 44(4), 590-603

Wildlife surveys rely on an accurate taxonomic framework. Identification tools used to reach this goal are not equivalent and may depend on several objectives and constraints, including sampling ... [more ▼]

Wildlife surveys rely on an accurate taxonomic framework. Identification tools used to reach this goal are not equivalent and may depend on several objectives and constraints, including sampling conservation difficulties, the invasiveness of the sampling techniques, sampling capacity, the relevance of the results, materials needed, the cost and the user time required in the field and laboratory. This article presents and discusses the advantages and limits of each identification tool used in the Ceropath (Community ecology of rodents and their pathogens in South East Asia) program to reach a fast and relevant identification of the rodents sampled. It is concluded that there needs to be a combination of the results from different methods, including the most recent ones, to achieve an improvement in taxonomic identification. [less ▲]

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See detailWhen molecular phylogeny meets medical sciences: Taxonomic problems among rat species in Southeast Asia
Pagès, Marie ULg

Conference (2009, November)

Background: Rodents are recognized as hosts for at least 60 zoonotic diseases and may represent a serious threat for human health. In the context of global environmental changes and increasing mobility of ... [more ▼]

Background: Rodents are recognized as hosts for at least 60 zoonotic diseases and may represent a serious threat for human health. In the context of global environmental changes and increasing mobility of humans and animals, contacts between pathogens and potential animal hosts and vectors are modified, amplifying the risk of disease emergence. An accurate identification of each rodent at a specific level is needed to understand their implications in the transmission of diseases. Among Muridae, the Rattini tribe encompasses 167 species inhabiting South East Asia, a hotspot of both biodiversity and, emerging and re-emerging diseases. The region faces growing economical development that affects habitats, biodiversity and health. Rat species have been demonstrated as main hosts of pathogens but are still difficult to recognize at a specific level using morphological criteria. DNA-barcoding methods appear as the only tool for accurate rat species identifications but their usefulness is hampered by the need of reliable identifications of reference specimens. To provide a rigorous systematic framework for epidemiological surveys, we used DNA data to explore the limits of the current taxonomy of the Rattini tribe. Results: As morphological characters are often misleading, we decided to use the DNA sequence information itself as the primary information source to establish group membership and estimate putative species boundaries. We sequenced two mitochondrial and one nuclear genes from 122 rat samples to perform phylogenetic reconstructions and applied the method developed by Pons and colleagues (2006) that determines with no a prior expectations, the locations of ancestral nodes defining putative species. To give an appropriate name to each cluster recognized as a valid species, we reviewed information from the literature and obtained sequences from a museum holotype specimen following all the ancient DNA criteria. One of the most striking results is that at least 6 putative species including a new cryptic one could exist among the Rattus rattus species group. Conclusions: Using a suitable methodology, this study succeeds in refining the taxonomy of one of the most difficult groups of mammals and lays the foundations to better investigate rodent-born diseases in South East Asia. Recognition of a new cryptic Rattus species in Southeast Asia could have serious implications for human health since each species is expected to have its own ecological traits and to carry its own set of diseases. To finish, first results based on independent nuclear DNA data (microsatellite loci) will be briefly exposed to demonstrate that defining species is not an easy task. [less ▲]

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See detailIntraspecific biodiversity in South East asian rodents: new insights for their conservation
Latinne, Alice ULg; Rivière, Taiana; Pagès, Marie ULg et al

Poster (2009, August)

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