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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 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 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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See detailWhen morphometrics meet genetics: the case of the common dormouse, Muscardinus avellanarius
Mouton, Alice ULg; Renaud, Sabrina; Michaux, Johan ULg

Poster (2011, July)

The aim of the study is to apply geometric morphometrics to the study of evolutionary processes that might have driven intra-specific differentiation of the common dormouse Muscardinus avellanarius in ... [more ▼]

The aim of the study is to apply geometric morphometrics to the study of evolutionary processes that might have driven intra-specific differentiation of the common dormouse Muscardinus avellanarius in Europe. The analysis of phenotypic features appears as a valuable complement to genetic analyses, providing a insight into evolutionary processes such as differentiation by vicariance or adaptation to different environments. Previous genetic studies based on mtDNA genes revealed a complex phylogeographic pattern for the common dormouse with the presence of two highly divergent lineages subdivided into geographic sublineages. We thus investigated whether this genetic differentiation leads to morphometric differences. We examined 150 museum specimens of dormouse from 34 localities in 12 countries. For each specimen, the size and shape of the first upper molar was quantified using an outline analysis based on Fourier methods. A geographic structure emerges from the morphometric pattern of differentiation, partially corresponding to the expectations based on the genetic results. The main differentiation, however, was unexpected and revealed a divergent Austrian cluster. This region was not documented so far for genetic analyses and morphometric data therefore challenge a more extensive sampling of this species that might reveal the existence of a further lineage. [less ▲]

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See detailConservation genetics : new tools and hope for threatened species.
Michaux, Johan ULg

in abstract book of the 6th European congress of mammalogy (2011)

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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 <br />highest number of threatened and data deficient mammal species. However, the <br />South East Asian biodiversity is still highly ... [more ▼]

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

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See detailGlobal population structure of the stable fly (Stomoxys calcitrans) inferred by mitochondrial and nuclear sequence data
Dsouli-Aymes, N.; Michaux, Johan ULg; De Stordeur, E. et al

in Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics of Infectious Diseases (2011), 11(2), 334-342

Stomoxys calcitrans (Diptera: Muscidae: Stomoxyini), a synanthropic fly with a worldwide distribution, is recognized to have an important medical and veterinary impact. We conducted a phylogeographic ... [more ▼]

Stomoxys calcitrans (Diptera: Muscidae: Stomoxyini), a synanthropic fly with a worldwide distribution, is recognized to have an important medical and veterinary impact. We conducted a phylogeographic analysis based on several populations from five major zoogeographic regions of the world in order to analyse population genetic structure of S. calcitrans and to trace its global dispersion. Results from mitochondrial (COI, Cyt-b and ND1-16S) and nuclear (ITS2) DNA show a substantial differentiation of Oriental populations (first lineage) from the Afrotropical, Palearctic, Nearctic, Neotropical and Oceanian populations (second lineage). The divergence time analyses suggest the separation between the two lineages approximately in mid-Pleistocene. Oriental populations are isolated and would not have participated in the colonization of other regions, unlike the Afrotropical one which seems to be the source of S. calcitrans dispersion towards other regions. Demographic analyses indicate that Oriental, Afrotropical and Palearctic regions have undergone a population expansion during late Pleistocene-early Holocene. The expansion time of this cosmopolitan species could have been influenced by continental human expansions and by animal domestication. © 2010 Elsevier B.V. [less ▲]

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See detailPhylogenetic analyses of mitochondrial and nuclear data in haematophagous flies support the paraphyly of the genus Stomoxys (Diptera: Muscidae)
Dsouli, N.; Delsuc, F.; Michaux, Johan ULg et al

in Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics of Infectious Diseases (2011), 11(3), 663-670

The genus Stomoxys Geoffroy (Diptera; Muscidae) contains species of parasitic flies that are of medical and economic importance. We conducted a phylogenetic analysis including 10 representative species of ... [more ▼]

The genus Stomoxys Geoffroy (Diptera; Muscidae) contains species of parasitic flies that are of medical and economic importance. We conducted a phylogenetic analysis including 10 representative species of the genus including multiple exemplars, together with the closely related genera Prostomoxys Zumpt, Haematobosca Bezzi, and Haematobia Lepeletier & Serville. Phylogenetic relationships were inferred using maximum likelihood and Bayesian methods from DNA fragments from the cytochrome c oxidase subunit I (COI, 753. bp) and cytochrome b (CytB, 587. bp) mitochondrial genes, and the nuclear ribosomal internal transcribed spacer 2 (ITS2, 426. bp). The combination of mitochondrial and nuclear data strongly supports the paraphyly of the genus Stomoxys because of the inclusion of Prostomoxys saegerae Zumpt. This unexpected result suggests that Prostomoxys should be renamed into Stomoxys. Also, the deep molecular divergence observed between the subspecies Stomoxys niger niger Macquart and S. niger bilineatus Grünbreg led us to propose that they should rather be considered as distinct species, in agreement with ecological data. Bayesian phylogenetic analyses support three distinct lineages within the genus Stomoxys with a strong biogeographical component. The first lineage consists solely of the divergent Asian species S. indicus Picard which appears as the sister-group to all remaining Stomoxys species. The second clade groups the strictly African species Stomoxys inornatus Grünbreg, Stomoxys transvittatus Villeneuve, Stomoxys omega Newstead, and Stomoxys pallidus Roubaud. Finally, the third clade includes both African occurring and more widespread species such as the livestock pest Stomoxys calcitrans Linnaeus. Divergence time estimates indicate that the genus Stomoxys originated in the late Oligocene around 30 million years ago, with the major lineages diversifying in the Early Miocene between 20 and 15 million years ago at a time when temperate forests developed in the Northern Hemisphere. © 2011 Elsevier B.V. [less ▲]

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See detailBayesian analysis of hybridization and introgression between the endangered european mink (Mustela lutreola) and the polecat (Mustela putorius)
Cabria, M. T.; Michaux, Johan ULg; Gómez-Moliner, B. J. et al

in Molecular Ecology (2011), 20(6), 1176-1190

Human-mediated global change will probably increase the rates of natural hybridization and genetic introgression between closely related species, and this will have major implications for conservation of ... [more ▼]

Human-mediated global change will probably increase the rates of natural hybridization and genetic introgression between closely related species, and this will have major implications for conservation of the taxa involved. In this study, we analyse both mitochondrial and nuclear data to characterize ongoing hybridization and genetic introgression between two sympatric sister species of mustelids, the endangered European mink (Mustela lutreola) and the more abundant polecat (M. putorius). A total of 317 European mink, 114 polecats and 15 putative hybrid individuals were collected from different localities in Europe and genotyped with 13 microsatellite nuclear markers. Recently developed Bayesian methods for assigning individuals to populations and identifying admixture proportions were applied to the genetic data. To identify the direction of hybridization, we additionally sequenced mtDNA and Y chromosomes from 78 individuals and 29 males respectively. We found that both hybridization and genetic introgression occurred at low levels (3% and 0.9% respectively) and indicated that hybridization is asymmetric, as only pure polecat males mate with pure European mink females. Furthermore, backcrossing and genetic introgression was detected only from female first-generation (F1) hybrids of European mink to polecats. This latter result implies that Haldane's rule may apply. Our results suggest that hybridization and genetic introgression between the two species should be considered a rather uncommon event. However, the current low densities of European mink might be changing this trend. © 2011 Blackwell Publishing Ltd. [less ▲]

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See detailPreliminary assessment of the genetic population structure of the enigmatic species Laonastes aenigmamus (Rodentia: Diatomyidae)
Rivière-Dobigny, T.; Herbreteau, V.; Khamsavath, K. et al

in Journal of Mammalogy (2011), 92(3), 620-628

Described in 2005, Laonastes aenigmamus is the only species of Diatomyidae. The known distribution of this rodent encompasses only the rugged mountains of the Khammouan karst in central Lao People's ... [more ▼]

Described in 2005, Laonastes aenigmamus is the only species of Diatomyidae. The known distribution of this rodent encompasses only the rugged mountains of the Khammouan karst in central Lao People's Democratic Republic. We used a sample of 52 specimens to survey population structure by sequencing 887 base pairs of the cytochrome-b gene. The overall haplotype diversity was low (0.789 ± 0.039 SD), with 14 haplotypes identified, whereas the nucleotide diversity was high (0.015 ± 0.008 SD). Phylogenetic and haplotypic network reconstructions revealed 3 well-supported and rather divergent lineages with mutational steps ranging from 28 to 32. Identified haplotype groups correspond to localities, suggesting that populations of L. aenigmamus are geographically structured. Mismatch distributions suggest population stability. An exact test for population differentiation confirms a significant level of differentiation. Taking into account human pressure increasingly threatening this ecosystem, we provide preliminary insights on the genetically discrete population structure of this enigmatic mammal species. © American 2011 Society of Mammalogists. [less ▲]

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See detailOrigin and putative colonization routes for invasive rodent taxa in the democratic Republic of Congo
Kaleme, P. K.; Bates, J. M.; Belesi, H. K. et al

in African Zoology (2011), 46(1), 133-145

The threat posed by biological invasions is well established. An important consideration in preventing the spread of invasives and also subsequent introductions lies in understanding introduction pathways ... [more ▼]

The threat posed by biological invasions is well established. An important consideration in preventing the spread of invasives and also subsequent introductions lies in understanding introduction pathways. The Democratic Republic of the Congo (DRC) houses a large percentage of the world's biodiversity, yet no national strategy exists to deal with the growing number of invasive alien species. Amongst these are the house mouse and ship and Norwegian rats. By comparing our result to published data, we show that species were possibly introduced into the DRC via two routes. The first is via the western seaport at Kinshasa where specimens of M. m. domesticus and R. rattus on the western and northwestern side of the DRC show ties with European haplotypes. The second is via the east where specimens of R. rattus appear linked to Arab and southeast Asian haplotypes. Future work should consider more comprehensive sampling throughout the DRC to more accurately investigate the occurrence of invasive species throughout the country as well as extend sampling to other African countries. [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 detailIsolation, characterization and PCR multiplexing of polymorphic microsatellite markers in the threatened murine rodent, Leopoldamys neilli
Latinne, Alice ULg; Waengsothorn, Surachit; Risterucci, Ange Marie et al

in Conservation Genetics Resources (2011), 3

Leopoldamys neilli is a threatened murine rodent species endemic to limestone karsts of Thailand. Twelve microsatellite loci were identified using the method of microsatellite-enriched libraries ... [more ▼]

Leopoldamys neilli is a threatened murine rodent species endemic to limestone karsts of Thailand. Twelve microsatellite loci were identified using the method of microsatellite-enriched libraries. Polymorphism was assessed in samples (N=62) from four geographically distinct populations in Thailand. Number of alleles per locus ranged from 9 to 15 (average 11.6). Observed and expected heterozygosities varied from 0.28 to 1.0 and from 0.44 to 0.91, respectively. There was no evidence for linkage disequilibrium, however, four loci showed evidence of departure from Hardy–Weinberg equilibrium in one population. Presence of null alleles was not detected in all the 12 loci. These first microsatellites primers developed for L. neilli will provide information on the fine-scale genetic structure of this threatened species and will help in the development of future conservation policies. [less ▲]

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See detailEvidence of complex phylogeographic structure for the threatened rodent Leopoldamys neilli, in Southeast Asia
Latinne, Alice ULg; Waengsothorn, Surachit; Herbreteau, Vincent et al

in Conservation Genetics (2011), 12

Leopoldamys neilli is a threatened murine rodent species endemic to limestone karsts of Thailand. We have studied the phylogeography of L. neilli using two mitochondrial markers (cytb, COI) and one ... [more ▼]

Leopoldamys neilli is a threatened murine rodent species endemic to limestone karsts of Thailand. We have studied the phylogeography of L. neilli using two mitochondrial markers (cytb, COI) and one nuclear fragment (bfibr), in order to assess the influence of its endemicity to karst habitat. One hundred fifteen individuals of L. neilli were collected in 20 localities throughout the geographic range of this species in Thailand. Our study revealed strong geographic structure of the mtDNA genetic diversity: six highly differentiated, allopatric genetic lineages were observed in our dataset. They exhibit a very high degree of genetic divergence, low gene flow among lineages and low levels of haplotype and nucleotide diversities within lineages. Our results suggest that L. neilli’s populations are highly fragmented due to the scattered distribution of its karst habitat. The most divergent lineage includes the populations from western Thailand, which have been separated from the other genetic lineages since at least the Early Pleistocene. The other lineages are more closely related and have diverged since the Middle Pleistocene. This study revealed an unexpected high level of genetic differentiation within L. neilli and highlighted the high endemicity of this species to limestone karsts. Our results enhance the importance of protecting limestone habitats to preserve not only the species but also intraspecific diversity. [less ▲]

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See detailThai limestone karsts: an impending biodiversity crisis
Latinne, Alice ULg; Waengsothorn, Surachit; Herbreteau, Vincent et al

in The 1st EnvironmentAsia International Conference (2011)

Due to the high level of endemic species that they support and the high threats they are facing, such as unsustainable limestone quarrying, hunting and urbanization, limestone karsts are recognized as ... [more ▼]

Due to the high level of endemic species that they support and the high threats they are facing, such as unsustainable limestone quarrying, hunting and urbanization, limestone karsts are recognized as biodiversity hotspots needing urgent protection. The first aim of our study was to investigate the mammal rodent diversity of Thai limestone karsts. Our second aim was to examine the diversity at a finer scale than the species level (intraspecific biodiversity) using phylogeographic approaches. Therefore, we studied the phylogeographic structure of a threatened rodent, endemic to limestone karsts of Thailand, the Murinae Leopoldamys neilli. We sampled 76 limestone karsts in whole Thailand and live-trapped 444 rodents including 115 Leopoldamys neilli. Our study revealed an important rodent diversity in Thai limestone karsts. Besides endemic rodent species, karsts also host typical forest species to which they provide forest refugia in deforested regions. At the intraspecific level, our study revealed an unexpected high level of genetic differentiation within the rodent species L. neilli. As each limestone area of Thailand is characterized by a particular genetic lineage of L. neilli, the destruction of these karsts would lead to the disappearance of unique intraspecific strains not found elsewhere. Our results highlight the importance of protecting limestone habitats to preserve not only their interspecific but also intraspecific rodent diversity that is highly threatened as more than 20% of limestone karsts in Thailand have already been quarried. Management plans of limestone, a non-renewable resource, should urgently take into account this high biological importance of karsts. [less ▲]

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