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See detailGlobal parasite and Rattus rodent invasions: The consequences for rodent-borne diseases
Morand, Serge; Bordes, Frédéric; Chen, Hsuan-Wien et al

in Integrative Zoology (2015)

We summarize the current knowledge on parasitism-related invasion processes of the globally invasive Rattus lineages, originating from Asia, and how these invasions have impacted the local epidemiology of ... [more ▼]

We summarize the current knowledge on parasitism-related invasion processes of the globally invasive Rattus lineages, originating from Asia, and how these invasions have impacted the local epidemiology of rodent-borne diseases. Parasites play an important role in the invasion processes and successes of their hosts through multiple biological mechanisms such as "parasite release", "immunocompetence advantage", “biotic resistance” and "novel weapon". Parasites may also greatly increase the impact of invasions by spillover of parasites and other pathogens, introduced with invasive hosts, into new hosts potentially leading to novel emerging diseases. Another potential impact is the ability of the invader to amplify local parasites by spill-back. In both cases, local fauna and humans may be exposed to new health risks, which may decrease biodiversity and may potentially cause increases in human morbidity and mortality. Here we review the current knowledge on these processes and propose some research priorities. [less ▲]

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See detailInfluence of past and future climate changes on the distribution of three Southeast Asian murine rodents
Latinne, Alice ULg; Meynard, Christine; Herbreteau, Vincent et al

in Journal of Biogeography (2015)

Aim: We tested the influence of Pleistocene climatic fluctuations and the potential effect of future climate change on Southeast Asian small mammal distributions using two forest-dwelling (Leopoldamys ... [more ▼]

Aim: We tested the influence of Pleistocene climatic fluctuations and the potential effect of future climate change on Southeast Asian small mammal distributions using two forest-dwelling (Leopoldamys herberti and Leopoldamys sabanus) and one karst (Leopoldamys neilli) endemic rodent species as models. Location: Southeast Asia. Methods: We used presence–absence data of genetically identified individuals, bioclimatic variables and species distribution modelling techniques to predict potential distributions of the three studied species under current, past [Last Interglacial (LIG) and Last Glacial Maximum (LGM)] and future conditions. We applied a variety of modelling techniques and then used consensus techniques to draw up robust maps of potential distribution ranges at all stages. Results: According to our models, these three Leopoldamys species did not experience significant range contraction during the LGM. Our models revealed substantial range contraction during the LIG for L. herberti in northern Indochina, while its distribution expanded in southern Indochina. Evidence of a southward range expansion during that period was also obtained for L. neilli, whereas L. sabanus remained widely distributed in insular Southeast Asia but experienced a range contraction on the Thai-Malay Peninsula. The two future climate change scenarios used predicted that large climatically suitable areas would still be available in the future for the three species. Main conclusions: Our model predictions contradict the well-established hypothesis that Southeast Asian forest-dwelling species were confined to small refugia during the LGM. Moreover, our results suggest that some Southeast Asian taxa may have been distributed in their refugial state during the LIG rather than the LGM. This could be because of vegetation changes that may have occurred at that time as a result of the increased seasonality observed during the LIG. These Pleistocene refugia may have been localized in northern Indochina but our study also revealed that southern Indochina could provide major potential refugia. [less ▲]

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See detailProgress on research on rodents and rodent-borne zoonoses in Southeast Asia
Blasdell, Kim; Bordes, Frédéric; Chaisiri, Kittipong et al

in Wildlife Research (2015), 42(2), 98-107

This review aims to synthesize the knowledge on the taxonomy of Southeast Asian murine rodents and the challenges associated with the identification of habitat preferences and associated rodent-borne ... [more ▼]

This review aims to synthesize the knowledge on the taxonomy of Southeast Asian murine rodents and the challenges associated with the identification of habitat preferences and associated rodent-borne diseases. Recent studies concerning the Rattini tribe have identified unclear species boundaries that would benefit from further investigation. The development of barcoding may allow more accurate identification of rodents, specifically for complex species. However, knowledge on the distribution and habitat specializations of many common murine rodents is still scarce, particularly regarding the specific habitat preferences of most synanthropic rodent species (Rattus tanezumi or Rattus exulans). Several studies have analyzed the prevalence of major rodent-borne diseases in Southeast Asia and it appears that the greatest risk of rodent zoonoses are in the lowland rainfed and irrigated landscapes, generally in and around rice fields. [less ▲]

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See detailGenetic structure of fragmented southern populations of African Cape Buffalo (Syncerus caffer caffer) based on microsatellite analysis
Smitz, Nathalie ULg; Cornélis, Daniel; Chardonnet, Philippe et al

Poster (2014, December 12)

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See detailCo-evolution of the parasitic fungi Pneumocystis and their Muridae rodent hosts in Southeast Asia
Latinne, Alice ULg; Bezé, François; Morand, Serge et al

Conference (2014, December 12)

Pneumocystis species are opportunistic and airborne-transmitted fungi that infect the lungs of numerous mammalian species. These highly diversified fungi are characterized by strong host specificity ... [more ▼]

Pneumocystis species are opportunistic and airborne-transmitted fungi that infect the lungs of numerous mammalian species. These highly diversified fungi are characterized by strong host specificity, probably associated with co-speciation. In this study, we investigate the Pneumocystis genetic diversity and infection rate in Muridae rodents of Southeast Asia in relation to environmental habitats. A total of 445 wild rodents belonging to 18 Southeast Asian Muridae species were tested for the presence of Pneumocystis in their lungs through PCR amplification of two Pneumocystis mitochondrial genes (mtLSU rRNA and mtSSU rRNA). Pneumocystis DNA was detected in 215 (48.3%) out of these 445 rodents. Eight highly divergent Pneumocystis lineages were retrieved in our phylogenetic tree. Three of these lineages correspond to the described species Pneumocystis murina (infecting Mus species), P. carinii (infecting Rattus species) and P. wakefieldiae (also infecting Rattus species). Three individuals belonging to Rattus norvegicus were found co-infected by both P. carinii and P. wakefieldiae. The five remaining lineages may correspond to several new undescribed Pneumocystis species and infect the lungs of Cannomys (lineage 1), Bandicota (lineage 2), Berylmys (lineage 3), Rattus (lineage 4) and Maxomys, Niviventer and Leopoldamys (lineage 5) Muridae genera. The congruence between phylogenies of Pneumocystis and their rodent hosts has been tested using co-phylogenetic analyses and the number of inferred co-speciation events is significantly greater than expected by chance. Rodent species, age and sex have no influence on the Pneumocystis infection rate among Muridae rodents but individuals trapped close to human settlements in patchy habitat were more likely infected by Pneumocystis parasites. [less ▲]

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See detailGenetic structure of fragmented southern populations of African Cape buffalo (Syncerus caffer caffer)
Smitz, Nathalie ULg; Cornelis, Daniel; Chardonnet, Philippe et al

in BMC Evolutionary Biology (2014), 14

Background African wildlife experienced a reduction in population size and geographical distribution over the last millennium, particularly since the 19th century as a result of human demographic ... [more ▼]

Background African wildlife experienced a reduction in population size and geographical distribution over the last millennium, particularly since the 19th century as a result of human demographic expansion, wildlife overexploitation, habitat degradation and cattle-borne diseases. In many areas, ungulate populations are now largely confined within a network of loosely connected protected areas. These metapopulations face gene flow restriction and run the risk of genetic diversity erosion. In this context, we assessed the “genetic health” of free ranging southern African Cape buffalo populations (S.c. caffer) and investigated the origins of their current genetic structure. The analyses were based on 264 samples from 6 southern African countries that were genotyped for 14 autosomal and 3 Y-chromosomal microsatellites. Results The analyses differentiated three significant genetic clusters, hereafter referred to as Northern (N), Central (C) and Southern (S) clusters. The results suggest that splitting of the N and C clusters occurred around 6000 to 8400 years ago. Both N and C clusters displayed high genetic diversity (mean allelic richness (Ar) of 7.217, average genetic diversity over loci of 0.594, mean private alleles (Pa) of 11), low differentiation, and an absence of an inbreeding depression signal (mean FIS = 0.037). The third (S) cluster, a tiny population enclosed within a small isolated protected area, likely originated from a more recent isolation and experienced genetic drift (FIS = 0.062, mean Ar = 6.160, Pa = 2). This study also highlighted the impact of translocations between clusters on the genetic structure of several African buffalo populations. Lower differentiation estimates were observed between C and N sampling localities that experienced translocation over the last century. Conclusions We showed that the current genetic structure of southern African Cape buffalo populations results from both ancient and recent processes. The splitting time of N and C clusters suggests that the current pattern results from human-induced factors and/or from the aridification process that occurred during the Holocene period. The more recent S cluster genetic drift probably results of processes that occurred over the last centuries (habitat fragmentation, diseases). Management practices of African buffalo populations should consider the micro-evolutionary changes highlighted in the present study. [less ▲]

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See detailDiet analysis of Leopoldamys neilli, a cave-dwelling rodent in Southeast Asia, using Next-Generation Sequencing from feces
Latinne, Alice ULg; Galan, Maxime; Waengsothorn, Surachit et al

in Journal of Cave and Karst Studies (2014), 76(2), 139-145

Leopoldamys neilli is a Murinae rodent endemic to limestone karst of Thailand and the Lao PDR, but its ecology and the reasons of its endemism to karst are still totally unknown. The aim of this pilot ... [more ▼]

Leopoldamys neilli is a Murinae rodent endemic to limestone karst of Thailand and the Lao PDR, but its ecology and the reasons of its endemism to karst are still totally unknown. The aim of this pilot study was to examine the plant composition of the diet of L. neilli at the level of order and family using DNA for molecular identification and to compare it with two other forest-dwelling Leopoldamys species, L. herberti and L. sabanus. A 202bp fragment of the rbcL gene was amplified and sequenced for twenty-three fecal samples of the three species using 454 pyrosequencing. We successfully identified a total of seventeen orders and twenty-one plant families, corresponding to thirty-three putative species, in the feces of these three Leopoldamys species. Solanaceae were the most common plants in the diet of L.neilli regardless of the region and sampling season, and they were also present in feces of both L. herberti and L. sabanus. The Araceae, Fabaceae, and Apocynaceae families were also identified in feces of L. neilli collected in various regions of Thailand and at different seasons. Plants of the Oleaceae family are consumed by both L. herberti and L. sabanus but were not found in the diet of L. neilli. Further improvements of the study, such as the use of additional genes, the creation of a reference collection, the microhistological examination of plant fragments to determine which parts of the plant are consumed, and the analysis of the animal diet of Leopoldamys are suggested to enhance the quality and accuracy of the results obtained. [less ▲]

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See detailIs Leopoldamys neilli (Rodentia, Muridae) a synonym of Leopoldamys herberti? A reply to Balakirev et al. (2013)
Latinne, Alice ULg; Chaval, Yannick; Waengsothorn, Surachit et al

in Zootaxa (2013), 3731(4), 589-598

Recently, Balakirev et al. (2013) presented a taxonomic revision of the genus Leopoldamys based on phylogenetic analyses. They identified five main Leopoldamys genetic lineages and suggested to rename ... [more ▼]

Recently, Balakirev et al. (2013) presented a taxonomic revision of the genus Leopoldamys based on phylogenetic analyses. They identified five main Leopoldamys genetic lineages and suggested to rename several of them. According to these authors, the genetic lineage previously thought to belong to L. edwardsi (lineage L1) should be assigned to L. revertens while L. neilli (lineage L2) should be considered as a junior synonym of L. herberti. Using molecular and morphological data from a large sampling of Leopoldamys specimens, the aim of the present study was to investigate the taxonomic status of L. herberti and L. neilli. This study reveals that, contrary to Balakirev et al.’s statement, both genetic lineages L1 and L2 occur in Nakhon Ratchasima Province, close to the type locality of L. herberti. We also show that the external measurements and color pattern of L. herberti are highly similar to those of L1 specimens but are not consistent with the morphology of L2 specimens. Therefore these results strongly suggest that L. herberti should be assigned to the genetic lineage L1. Consequently L. neilli should not be considered as a junior synonym of L. herberti and this study confirms that the appropriate name of the genetic lineage L2 is L. neilli. Moreover, as our results show that L. herberti should be assigned to the lineage L1, this name has nomenclatural priority over L. revertens, the species name suggested by Balakirev et al. (2013) for this lineage. [less ▲]

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See detailDiversity and endemism of Murinae rodents in Thai limestone karsts
Latinne, Alice ULg; Waengsothorn, Surachit; Rojanadilok, Prateep et al

in Systematics and Biodiversity (2013), 11(3), 323-344

This study aims to investigate the species diversity of rodents living in karst ecosystems of Thailand. A survey has been conducted throughout Thailand, 122 karsts sampled and 477 Murinae rodents live ... [more ▼]

This study aims to investigate the species diversity of rodents living in karst ecosystems of Thailand. A survey has been conducted throughout Thailand, 122 karsts sampled and 477 Murinae rodents live-trapped. Phylogenetic reconstructions were carried out using two mitochondrial markers (cytb, COI). A sequence-based species delimitation method completed by the analysis of the level of genetic divergence was then applied to define species boundaries within our dataset. The phylogenetic position of Niviventer hinpoon was also investigated and sequences obtained from the holotype specimen of this species were used to reliably identify samples of N. hinpoon. A total of 12 described Murinae species, corresponding to 17 deeply divergent genetic lineages, were encountered in limestone karsts of Thailand. Our study revealed an important genetic diversity within the traditionally recognized species Maxomys surifer (four highly divergent genetic lineages), Leopoldamys neilli (two highly divergent genetic lineages) and Berylmys bowersi (two highly divergent genetic lineages). These species could be considered as species complex and require further taxonomic work. This study also provides valuable information on the distribution of the two rodent species endemic to limestone karsts of Thailand, L. neilli and N. hinpoon. Leopoldamys neilli was the most abundant species encountered in Thai karsts during our survey. However, L. neilli specimens from western Thailand are genetically highly divergent from the remaining populations of L. neilli and could represent a separate species. Niviventer hinpoon, phylogenetically closely related to N. fulvescens, is much rarer and its distribution limited to central Thailand. Most of the other captured species are typically associated with forest ecosystems. This study suggests that limestone karsts play a key role in the preservation of the rodent species endemic to such habitat, but they would also provide refuges for the forest-dwelling Murinae rodents in deforested regions. [less ▲]

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See detailEvolutionary history of Leopoldamys neilli, a karst endemic rodent in Southeast Asia, and implications for its conservation
Latinne, Alice ULg; Waengsothorn, Surachit; Michaux, Johan ULg

Conference (2013, August 15)

In this study, we have investigated the phylogeography of Leopoldamys neilli, a Murinae rodent species endemic to limestone karsts in Southeast Asia, on the basis of mitochondrial and nuclear markers ... [more ▼]

In this study, we have investigated the phylogeography of Leopoldamys neilli, a Murinae rodent species endemic to limestone karsts in Southeast Asia, on the basis of mitochondrial and nuclear markers. Both mitochondrial and nuclear markers support a large-scale population structure of four main groups within L. neilli 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 during Plio-Pleistocene. This study revealed an unexpected high level of intraspecific diversity within L. neilli. Consequently, the four main L. neilli population groups should be considered as four distinct Evolutionarily Significant Units (ESUs) and require appropriate management and conservation plans. [less ▲]

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See detailCyrtodactylus sanook (Squamata: Gekkonidae), a new cave-dwelling gecko from Chumphon Province, southern Thailand
Pauwels, Olivier S.G.; Sumontha, Montri; Latinne, Alice ULg et al

in Zootaxa (2013), 3635(3), 275-285

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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 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 detailLe côté obscur des milieux souterrains du sud-est asiatique
Latinne, Alice ULg

in L'Echo des Rhinos (2012), 76

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See detailDiversity and endemism of Murinae rodents in Thai limestone karsts: a genetic approach
Latinne, Alice ULg

Doctoral thesis (2012)

Limestone karsts are characterized by an important species richness and high levels of endemic species of plants, vertebrates and invertebrates adapted to this extreme environment. However, in Southeast ... [more ▼]

Limestone karsts are characterized by an important species richness and high levels of endemic species of plants, vertebrates and invertebrates adapted to this extreme environment. However, in Southeast Asia, karst ecosystems suffer from a considerable lack of scientific data and remain widely unknown despite their high biological importance. Combining field investigations with phylogeographic and phylogenetic analyses based on several kinds of molecular markers, this thesis aims at exploring the diversity and endemism of Murinae rodents in limestone karsts of Thailand. Thai limestone karsts host two endemic Murinae rodent species, Leopoldamys neilli and Niviventer hinpoon. This thesis reveals that L. neilli is more largely distributed in Thailand than indicated by previous records available in the literature. The species has been recorded in numerous limestone karsts of Thailand with the exception of its peninsular area. L. neilli has also been discovered in central Laos. Moreover our niche modeling study indicates that large tracts of suitable habitat for this species may also occur in several regions of Indochina. L. neilli populations are highly fragmented and a deep genealogical divergence among its lineages is observed. 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. These results indicate that L. neilli populations are isolated on karsts such as on islands and that migrations among them are reduced. Our findings also 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. Moreover, the western populations of L. neilli are genetically and morphologically highly divergent from the other populations and could represent a separate species. This strong phylogeographic pattern is not observed for other Murinae species with lower levels of ecological specialization such as Leopoldamys edwardsi and Rattus tanezumi. Finally, this thesis provides preliminary information about the diet of L. neilli and indicates that plants of the Solanaceae family constitute an important part of its diet. The phylogeographic structure of N. hinpoon is not similar to the one of L. neilli. In contrast to L. neilli, N. hinpoon is confined to central Thailand and mitochondrial markers used in this study indicated that this species is genetically homogenous and characterized by a single mitochondrial lineage. Valuable data to refine the conservation status of L. neilli and N. hinpoon, two species currently listed as Data Deficient on the IUCN Red List have been gathered during this study. Three main threats to the long-term subsistence of L. neilli have been identified: (1) the high fragmentation of its population, (2) the large-scale destruction of limestone karsts in Southeast Asia, and (3) the intense trapping of this species for human consumption in northeastern Thailand. Therefore we propose to consider L. neilli as “Near threatened” on the IUCN Red List. However, if the western lineage of L. neilli represents a separate species, it should be listed as “Vulnerable”. Due to its small distribution range and the high threats that its habitat is facing in central Thailand, N. hinpoon would also be qualified as “Vulnerable” on the IUCN Red List. In addition to karst endemic species, this thesis reveals that Thai limestone karsts host high levels of Murinae rodent diversity. A sequence-based species delimitation method completed by the analysis of the level of genetic divergence was used to define species boundaries within our rodent samples collected in limestone karsts. A total of 12 described Murinae species, corresponding to 17 putative species based on our genetic criteria, were encountered in limestone karsts of Thailand. Most of these species are associated to forest ecosystems. Therefore this study suggests that limestone karsts could play a key role in the preservation of the rodent biodiversity by providing refuges for the forest-dwelling Murinae rodents in deforested regions. An important cryptic diversity has been detected within the traditionally recognized species Maxomys surifer and Berylmys bowersi. They could be considered as species complex and require further taxonomic work. The potential distribution of Leopoldamys edwardsi and Leopoldamys sabanus, two species also distributed in Thailand, has been investigated using niche modeling techniques. The predicted distribution ranges of these two species suggest a clear geographical separation between them, with the potential distribution of L. edwardsi being limited to the northern part of Indochina while L. sabanus is mainly distributed in the Sundaic region. Our findings also suggest that these two species could have survived in large areas of Southeast Asia during Quaternary ice ages without large scale extinction and that no drastic modification of the distribution of these species will occur in the future due to climate changes. In conclusion, using various genetic approaches, this work gains important insights into the Murinae rodent diversity of Thai limestone karsts and represents the first detailed study of karst endemic rodent species in Southeast Asia. [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 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 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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