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See detailCryptic diversity in brevipalpus mites (tenuipalpidae)
Navia, D.; Mendonça, R. S.; Ferragut, F. et al

in Zoologica Scripta (2013), 42(4), 406-426

Defining the taxonomic identity of organisms is a prerequisite for their study, and in the case of economically important species, misidentification may lead to the application of inappropriate prevention ... [more ▼]

Defining the taxonomic identity of organisms is a prerequisite for their study, and in the case of economically important species, misidentification may lead to the application of inappropriate prevention and control strategies. Flat mites of the Brevipalpus genus include several crop pests and the systematics of these mites represents a challenge for acarologists. Many of the most economically important Brevipalpus species have repeatedly been inaccurately identified. Such problematic classification has been attributed to the likely occurrence of cryptic species in the genus. In this study, we used an integrative approach that combined molecular analyses, including sequence-based species delimitation, with detailed morphological identification using traits that have recently showed to be taxonomically informative. Sequences of mitochondrial cytochrome c oxidase subunit I (COI) were obtained from individuals collected from host plants belonging to 14 genera and 13 families across 29 locations in the Americas (Brazil, Chile, USA). The phylogenetic analyses included previously published Brevipalpus sequences from GenBank, and the final data set was classified into 44 haplotypes. Six putative species were recognised by COI-based species delimitation analysis, and morphological evidence supported each of these species. The integrative approach revealed the occurrence of cryptic species in the Brevipalpus genus and contributed to the clarification of previously noted incongruences. The results presented here allow for the evaluation of taxonomic characteristics in a phylogenetic context and indicate new characters for the differentiation of Brevipalpus species. In addition, Brevipalpus incognitus n. sp. Ferragut & Navia, a cryptic species detected in this study, is described based on morphological and molecular traits. Implications of the advances in Brevipalpus systematics presented herein with respect to pest management are briefly discussed. © 2013 The Norwegian Academy of Science and Letters. [less ▲]

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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 detailCombined Mitochondrial and Nuclear Markers Revealed a Deep Vicariant History for Leopoldamys neilli, a Cave-Dwelling Rodent of Thailand
Latinne, Alice ULg; Waengsothorn, Surachit; Rojanadilok, Prateep et al

in PLoS ONE (2012), 7(10), 47670

Background: Historical biogeography and evolutionary processes of cave taxa have been widely studied in temperate regions. However, Southeast Asian cave ecosystems remain largely unexplored despite their ... [more ▼]

Background: Historical biogeography and evolutionary processes of cave taxa have been widely studied in temperate regions. However, Southeast Asian cave ecosystems remain largely unexplored despite their high scientific interest. Here we studied the phylogeography of Leopoldamys neilli, a cave-dwelling murine rodent living in limestone karsts of Thailand, and compared the molecular signature of mitochondrial and nuclear markers. Methodology/Principal Findings: We used a large sampling (n = 225) from 28 localities in Thailand and a combination of mitochondrial and nuclear markers with various evolutionary rates (two intronic regions and 12 microsatellites). The evolutionary history of L. neilli and the relative role of vicariance and dispersal were investigated using ancestral range reconstruction analysis and Approximate Bayesian computation (ABC). Both mitochondrial and nuclear markers support a large-scale population structure of four main groups (west, centre, north and northeast) and a strong finer structure within each of these groups. A deep genealogical divergence among geographically close lineages is observed and denotes a high population fragmentation. Our findings suggest that the current phylogeographic pattern of this species results from the fragmentation of a widespread ancestral population and that vicariance has played a significant role in the evolutionary history of L. neilli. These deep vicariant events that occurred during Plio-Pleistocene are related to the formation of the Central Plain of Thailand. Consequently, the western, central, northern and northeastern groups of populations were historically isolated and should be considered as four distinct Evolutionarily Significant Units (ESUs). Conclusions/Significance: Our study confirms the benefit of using several independent genetic markers to obtain a comprehensive and reliable picture of L. neilli evolutionary history at different levels of resolution. The complex genetic structure of Leopoldamys neilli is supported by congruent mitochondrial and nuclear markers and has been influenced by the geological history of Thailand during Plio-Pleistocene. [less ▲]

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See detailDevelopment of noninvasive genetic identification methods and polymorphic microsatellites for the Pyrenean desman (Galemys pyrenaicus)
Gillet, François ULg; Cabria Garrido, Maria Teresa; Némoz, Mélanie et al

Poster (2012, August)

The Pyrenean desman (Galemys pyrenaicus) is probably one of the most threatened European mammal species. This small insectivorous and semi-aquatic species is endemic to the Pyrenean Mountains and of the ... [more ▼]

The Pyrenean desman (Galemys pyrenaicus) is probably one of the most threatened European mammal species. This small insectivorous and semi-aquatic species is endemic to the Pyrenean Mountains and of the north of the Iberic Peninsula. Many biologic aspects of this species are currently suffering from a major lack of information, particularly those concerning its genetics. Therefore the implementation of conservative efforts for the Pyrenean Desman remains extremely difficult. In order to improve the knowledge of this vulnerable species and notably, to better understand its distribution area, the first aim of our research was to develop non invasive genetic identification methods based on faeces. The second aim was the development of several polymorphic microsatellites markers in order to have a first look at the genetic structure of the Pyrenean Desman in its French distribution area. The identification methods were developed on the basis of the sequencing of a small mitochondrial DNA (cyt b) fragment as well as a RFLP method. These approaches led to the identification of the Pyrenean desman and to the differentiation of the latter from two other species living in the same type of habitat, the white-throated dipper (Cinclus cinclus) and the water shrew (Neomys fodiens). More than fifteen polymorphic microsatellites markers could be found for the Pyrenean Desman and their genotyping revealed a low number of alleles per locus (two to five). The results of this preliminary work tend to show a low genetic diversity for the Pyrenean Desman but this result needs to be confirmed in the future with a more extended and complete study. [less ▲]

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See detailMolecular phylogeny and evolutionary history of Dipodoidea (Rodentia, Mammalia)
Pisano, Julie ULg; Pagès, Marie; Condamine, Fabien et al

Conference (2012, July)

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See detailNuclear genetic structure of Myodes glareolus in Fennoscandia with a particular emphasis on the contact zones - Preliminary results
Pisano, Julie ULg; Henttonen, Heikki; Galan, Maxime et al

Poster (2012, July)

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See detailPhylogeography and evolutionary history of Leopoldamys neilli, a Murinae rodent endemic to limestone karsts, in Thailand
Latinne, Alice ULg; Waengsothorn, Surachit; Herbreteau, Vincent et al

Conference (2012, May 15)

Limestone karsts are highly threatened biodiversity hotspots supporting high levels of endemic species. Karsts are patchy distributed within Southeast Asia and their isolation from one another give them ... [more ▼]

Limestone karsts are highly threatened biodiversity hotspots supporting high levels of endemic species. Karsts are patchy distributed within Southeast Asia and their isolation from one another give them the features of “islands on the continent” and has important consequences for the genetic structure of endemic taxa. In present study, we have studied the phylogeography of Neill’s Rat Leopoldamys neilli, a threatened Murinae rodent species endemic to limestone karsts of Thailand, on the basis of two mitochondrial markers, two nuclear fragments, as well as twelve microsatellite loci. Our study gave evidence of a complex and strong geographic structure of the genetic diversity for L. neilli. Several highly differentiated genetic lineages were observed throughout Thailand. These results suggest a severe fragmentation of L. neilli’s populations, correlated to the fragmented distribution of its habitat and highlight its high endemicity to limestone karsts. The evolutionary history of L. neilli was investigated using Approximate Bayesian computation (ABC) and our results suggest that the current phylogeographic pattern of this species result from several deep vicariant events during Plio-Pleistocene. To conclude, this study revealed an unexpected high level of intraspecific diversity within L. neilli. These results consolidate the importance to strengthen the protection of limestone habitats and to preserve not only their high interspecific but also intraspecific diversity. [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 detailEvidence of a complex phylogeographic structure in the common dormouse, Muscardinus avellanarius (Rodentia: Gliridae)
Mouton, Alice ULg; Grill, Andrea; Sara, Maurizio et al

in Biological Journal of the Linnean Society (2012), 105(3), 648-664

This is the first mitochondrial phylogeography of the common dormouse, Muscardinus avellanarius (Linnaeus, 1758), a hibernating rodent strictly protected in Europe (Habitat Directive, annex IV; Bern ... [more ▼]

This is the first mitochondrial phylogeography of the common dormouse, Muscardinus avellanarius (Linnaeus, 1758), a hibernating rodent strictly protected in Europe (Habitat Directive, annex IV; Bern Convention, annex III). The 84 individuals of M. avellanarius, sampled throughout the distributional range of the species, have been sequenced at the mitochondrial DNA gene (cytochrome b, 704 base pairs). The results revealed two highly divergent lineages, with an ancient separation around 7.7 Mya and a genetic divergence of 7.7%. Lineage 1 occurs in Western Europe (France, Belgium, and Switzerland) and Italy, and lineage 2 occurs in Central–Northern Europe (Poland, Germany, Latvia, and Lithuania), on the Balkan Peninsula, and in Turkey. Furthermore, these two lineages are subdivided into five sublineages genetically isolated with a strong geographical association. Therefore, lineage 1 branches into two further sublineages (Western European and Italian), whereas lineage 2 contained three sublineages (Central–Northern European, Turkish, and Balkan). We observed low genetic diversity within the sublineages, in contrast to the significant level of genetic differentiation between them. The understanding of genetic population structure is essential for identifying units to be conserved. Therefore, these results may have important implications for M. avellanarius conservation. [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 detailA unifying model for the analysis of phenotypic, genetic, and geographic data
Guillot, G.; Renaud, S.; Ledevin, R. et al

in Systematic Biology (2012), 61(6), 897-911

Recognition of evolutionary units (species, populations) requires integrating several kinds of data, such as genetic or phenotypic markers or spatial information in order to get a comprehensive view ... [more ▼]

Recognition of evolutionary units (species, populations) requires integrating several kinds of data, such as genetic or phenotypic markers or spatial information in order to get a comprehensive view concerning the differentiation of the units. We propose a statistical model with a double original advantage: (i) it incorporates information about the spatial distribution of the samples, with the aim to increase inference power and to relate more explicitly observed patterns to geography and (ii) it allows one to analyze genetic and phenotypic data within a unified model and inference framework, thus opening the way to robust comparisons between markers and possibly combined analyses. We show from simulated data as well as real data that our method estimates parameters accurately and is an improvement over alternative approaches in many situations. The power of this method is exemplified using an intricate case of inter- and intraspecies differentiation based on an original data set of georeferenced genetic and morphometric markers obtained on Myodes voles from Sweden. A computer program is made available as an extension of the R package Geneland. © 2012 The Author(s). [less ▲]

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See detailRépartition spatiale du Desman des Pyrénées (Galemys pyrenaicus) en France et premier aperçu de sa structure génétique
Gillet, François ULg; D'Amico, Frank; Blanc, Frédéric et al

Conference (2012)

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See detailCan tooth differentiation help to understand species coexistence? The case of wood mice in China
Ledevin, R.; Quéré, J.-P.; Michaux, Johan ULg et al

in Journal of Zoological Systematics and Evolutionary Research (2012), 50(4), 315-327

Five wood mice Apodemus species occur across China, in allopatry but also in sympatry up to cases of syntopy. They all share a similar external appearance, similar habitats of grasslands and forests and a ... [more ▼]

Five wood mice Apodemus species occur across China, in allopatry but also in sympatry up to cases of syntopy. They all share a similar external appearance, similar habitats of grasslands and forests and a generalist feeding behaviour. This overall similarity raises questions about the mechanisms insuring competition avoidance and allowing the coexistence of the species. In this context, a morphometric analysis of two characters related to feeding (mandible and molar) addressed the following issues: (1) Were the species actually different in size and/or shape of these characters, supporting their role in resource partitioning? (2) Did this pattern of phenotypic divergence match the neutral genetic differentiation, suggesting that differentiation might have occurred in a former phase of allopatry as a result of stochastic processes? (3) Did the species provide evidence of character displacement when occurring in sympatry, supporting an ongoing role of competition in the interspecific divergence? Results evidenced first that different traits, here mandibles and molars, provided discrepant pictures of the evolution of the Apodemus group in China. Mandible shape appeared as prone to vary in response to local conditions, blurring any phylogenetic or ecological pattern, whereas molar shape evolution appeared to be primarily driven by the degree of genetic differentiation. Molar size and shape segregated the different species in the morphospace, suggesting that these features may be involved in a resource partitioning between Apodemus species. The morphological segregation of the species, likely achieved by processes of differentiation in isolation promoted by the complex landscape of China, could contribute to competition avoidance and hence explain why no evidence was found of character displacement. © 2012 Blackwell Verlag GmbH. [less ▲]

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See detailDiscongruence of Mhc and cytochrome b phylogeographical patterns in Myodes glareolus (Rodentia: Cricetidae)
Malé, P.-J. G.; Martin, J.-F.; Galan, M. et al

in Biological Journal of the Linnean Society (2012), 105(4), 881-899

In the present study, a phylogeographical approach was developed to analyse the influence of selection and history on a major histocompatibility complex (Mhc) class II gene polymorphism in European bank ... [more ▼]

In the present study, a phylogeographical approach was developed to analyse the influence of selection and history on a major histocompatibility complex (Mhc) class II gene polymorphism in European bank vole (Myodes glareolus) populations. We focused on exon 2 of the Dqa gene because it is highly variable in a large array of species and appears to evolve under pathogen-mediated selection in several rodent species. Using single-strand conformation polymorphism analysis and sequencing techniques, 17 Dqa-exon2 alleles, belonging to at least two different copies of Dqa gene, were detected over the distribution range of M.glareolus. Evidence of selection was found using molecular and population analyses. At the molecular level, we detected 13 codons evolving under positive selection pressures, most of them corresponding to regions coding for putative antigen binding sites of the protein. At the European level, we compared patterns of population structure for the Dqa-exon2 and cytochrome b (cyt b) gene. We did not detect any spatial genetic structure among M.glareolus populations for the Dqa-exon2. These results strongly differed from those obtained using the cyt b gene, which indicated a recent phylogeographical history closely linked to the last glacial events. Seven mitochondrial lineages have yet been described, which correspond to major glacial refugia. Altogether, our results revealed clear evidence of balancing selection acting on Dqa-exon2 and maintaining polymorphism over large geographical areas despite M.glareolus history. It is thus likely that Mhc phylogeographical variability could have been shaped by local adaptation to pathogens. © 2012 The Linnean Society of London. [less ▲]

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See detailMorphometric and genetic structure of the edible dormouse (Glis glis): A consequence of forest fragmentation in Turkey
Helvaci, Z.; Renaud, S.; Ledevin, R. et al

in Biological Journal of the Linnean Society (2012), 107(3), 611-623

Past climatic fluctuations influenced forest habitats and impacted heavily the distribution of forest species, such as the edible dormouse, by changing the distribution and composition of forests ... [more ▼]

Past climatic fluctuations influenced forest habitats and impacted heavily the distribution of forest species, such as the edible dormouse, by changing the distribution and composition of forests themselves. Such effects may be valid for ongoing climate change as well. To improve our understanding of the edible dormouse's history and how it responded to changes in its environment, we investigated its variation across the understudied zone of Northern Turkey using two complementary markers of differentiation: the mitochondrial cytochrome b gene for genetics, and size and shape of the first upper molar for phenotypic differences. Genetic and morphometric results were strongly discrepant. Genetic analyses evidenced an amazing homogeneity throughout the Eurasian range of the edible dormouse, whereas morphometrics pointed to a complex, step-wise differentiation along the Black Sea coast, the main signal being an opposition between Easternmost and Westernmost Turkish dormice. The genetic homogeneity suggests that this phenotypic differentiation is not the inheritance of glacial refuges, but the consequence of a more recent post-glacial isolation. The transition between the European and Asian groups is located eastwards from the Marmara straits, undermining its claimed role as an efficient barrier but stressing the importance of climatic and vegetational factors. A secondary differentiation between populations from the Central Black Sea coast and Easternmost regions was evidenced, attributed to a complex interplay of climatic, topographic, anthropogenic, and ecological factors. Turkey, at the crossroad of European and Asian species, heavily impacted by the current global change including climatic and anthropogenic factors, appears of importance for understanding the historical dynamics of differentiation and exchanges between populations that shaped the current distribution of Eurasian species and their future survival. © 2012 The Linnean Society of London. [less ▲]

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See detailUsing phylogeography to promote dormouse conservation: the case of Muscardinus avellanarius (Rodentia, Gliridae)
Mouton, Alice ULg; Grill, Andrea; Sara, Maurizio et al

in Peckiana (2012), 8

This study describes the phylogeographic history of the common dormouse, Muscardinus avellanarius, a rodent strictly protected in Europe (Habitat Directive, annex IV ; Bern Convention, annex III ). We ... [more ▼]

This study describes the phylogeographic history of the common dormouse, Muscardinus avellanarius, a rodent strictly protected in Europe (Habitat Directive, annex IV ; Bern Convention, annex III ). We analyzed the genetics of 120 common dormice across the species’ range, using sequence data from the mitochondrial cytochrome b gene (704 pb). The dataset obtained was analyzed using different phylogenetic reconstructions as well as other methods adapted to phylogeography. A complex phylogeographic pattern has been retrieved from the mitochondrial DN A gene, with the presence of two highly divergent lineages. These two lineages are themselves subdivided into five sublineages, which should be regarded as independent conservation units. Low genetic diversity was observed within each of the lineages, in contrast to an important level of genetic differentiation between them. These results have important implications for the conservation of this dormouse and will help to propose the best management measures for this species. [less ▲]

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See detailEvidence of complex phylogeographic structure for the threatened rodent Leopoldamys neilli endemic to limestone karsts of Thailand
Latinne, Alice ULg; Waengsothorn, Surachit; Herbreteau, Vincent et al

Conference (2011, July 21)

Limestone karsts are highly threatened biodiversity hotspots supporting huge levels of endemic species. Karsts are patchy distributed within Southeast Asia and their isolation from one another give them ... [more ▼]

Limestone karsts are highly threatened biodiversity hotspots supporting huge levels of endemic species. Karsts are patchy distributed within Southeast Asia and their isolation from one another give them the features of “islands on the continent”. We have studied the phylogeography of Neill’s Rat Leopoldamys neilli, a threatened murine rodent species endemic to limestone karsts of Thailand, in order to assess the influence of its endemicity to karst habitat on its phylogeographic pattern. Two hundred twenty-two individuals of L. neilli were collected in 26 limestone karsts throughout the geographical range of this species and were used in this study. Phylogeographic structure and population genetics of L. neilli were investigated on the basis of two mitochondrial markers, the cytochrome b gene and the cytochrome c oxydase subunit I gene, two nuclear fragments, the β-fibrinogen intron 7 and the intron 1 of the X-linked gene G6pd, and 12 microsatellite loci. Our study gave evidence of a complex and strong geographic structure of the genetic diversity for L. neilli. Several highly differentiated genetic lineages were observed throughout Thailand. These results suggest a severe fragmentation of L. neilli’s populations, correlated to the fragmented distribution of its habitat and highlight its high endemicity to limestone karsts. In conclusion, this study revealed an unexpected high level of intraspecific diversity within L. neilli. These results consolidate the importance to strengthen the protection of limestone habitats and to preserve not only their huge interspecific but also intraspecific diversity. [less ▲]

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See detailDevelopment of non invasive genetic identification methods for the Pyrenean desman (Galemys pyrenaicus) and first study of its genetic structure in France
Gillet, François ULg; Cabria Garrido, Maria Teresa; Némoz, Mélanie et al

Poster (2011, July)

The Pyrenean desman (Galemys pyrenaicus) is probably one of the most threatened European mammal species. This small insectivorous and semi-aquatic species is endemic to the Pyrenean Mountains and of the ... [more ▼]

The Pyrenean desman (Galemys pyrenaicus) is probably one of the most threatened European mammal species. This small insectivorous and semi-aquatic species is endemic to the Pyrenean Mountains and of the north of the Iberic Peninsula. Many biologic aspects of this species are currently suffering from a major lack of information, particularly those concerning its genetics. Therefore the implementation of conservative efforts for the Pyrenean desman remains extremely difficult. In order to improve the knowledge of this vulnerable species and notably, to better understand its distribution area, the first aim of our research was to develop non invasive genetic identification methods based on faeces. The second aim was to have a first look at the phylogeographic structure of the Pyrenean desman. The identification methods were developed on the basis of the sequencing of a small mitochondrial DNA (cyt b) fragment as well as a RFLP method. These approaches led to the identification of the Pyrenean desman and to the differentiation of the latter from two other species living in the same type of habitat, the white-throated dipper (Cinclus cinclus) and the water shrew (Neomys fodiens). Two haplotypes were found in the studied Pyrenean populations but no phylogeographic structure could be established. A dozen of microsatellites markers were also developed during this work and 5 of these were found to be polymorphic. The results of this preliminary work tend to show a low genetic diversity for the Pyrenean desman but this result needs to be confirmed in the future with a more extended and complete study. [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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