A multi-approach survey as the most reliable tool to accurately assess biodiversity: the example of Thai murine rodents

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

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

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

Genetic and historic evidence for climate-driven population fragmentation in a top cetacean predator: the harbour porpoises in European water.

in Proceedings of the Royal Society B : Biological Sciences (2010), 277(1695), 2829-37

Recent climate change has triggered profound reorganization in northeast Atlantic ecosystems, with substantial impact on the distribution of marine assemblages from plankton to fishes. However, assessing ... [more ▼]

Recent climate change has triggered profound reorganization in northeast Atlantic ecosystems, with substantial impact on the distribution of marine assemblages from plankton to fishes. However, assessing the repercussions on apex marine predators remains a challenging issue, especially for pelagic species. In this study, we use Bayesian coalescent modelling of microsatellite variation to track the population demographic history of one of the smallest temperate cetaceans, the harbour porpoise (Phocoena phocoena) in European waters. Combining genetic inferences with palaeo-oceanographic and historical records provides strong evidence that populations of harbour porpoises have responded markedly to the recent climate-driven reorganization in the eastern North Atlantic food web. This response includes the isolation of porpoises in Iberian waters from those further north only approximately 300 years ago with a predominant northward migration, contemporaneous with the warming trend underway since the 'Little Ice Age' period and with the ongoing retreat of cold-water fishes from the Bay of Biscay. The extinction or exodus of harbour porpoises from the Mediterranean Sea (leaving an isolated relict population in the Black Sea) has lacked a coherent explanation. The present results suggest that the fragmentation of harbour distribution range in the Mediterranean Sea was triggered during the warm 'Mid-Holocene Optimum' period (approx. 5000 years ago), by the end of the post-glacial nutrient-rich 'Sapropel' conditions that prevailed before that time. [less ▲]

Revisiting the taxonomy of the Rattini tribe: a phylogeny-based delimitation of species boundaries.

in BMC Evolutionary Biology (2010), 10

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

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

Mitochondrial phylogeography of the edible dormouse (Glis glis) in the western Palearctic region

in Journal of Mammalogy (2010), 91(1), 233-242

This study describes in detail the phylogeoraphic pattern Of the edible dormouse (Glis glis) a European rodent With pronounced hibernating behavior We Used sequences of 831 base pairs of the mitochondrial ... [more ▼]

This study describes in detail the phylogeoraphic pattern Of the edible dormouse (Glis glis) a European rodent With pronounced hibernating behavior We Used sequences of 831 base pairs of the mitochondrial DNA cytochrome-b gene from 130 edible dormice collected at 43 localities (throughout Its distribution. Our results reveal presence of 3 main haplogroups: Sicilian, South Italian (restricted to the Calabrian region) (a widespread lineage corresponding to all remaining western, central. and eastern European populations). Examination of paleontological data confirms refugial regions for G,Its in the 3 Mediterranean peninsulas, although overall low genetic diversity is found. The low diversity of the European lineage Is probably the result refugium. Other factors, such as the of a recent expansion (dated around 2.000( years ago) from a single ecological constraints oil the species, way have caused genetic bottlenecks that reinforced the low genetic variability of G glis. This work could have important implications for strategies to conserve the edible dormouse by defining important areas for their conservation DOI: 10.1644/08-MAMM-A-392R1.1 [less ▲]

Molecular phylogeography of the common dormouse, Muscardinus avellanarius, in Europe

Conference (2009, September)

The common dormouse, Muscardinus avellanarius is naturally rare in Europe. Recently, natural scarcity has been exacerbated by anthropogenic environmental damages. This specie is now regarded as rare or ... [more ▼]

The common dormouse, Muscardinus avellanarius is naturally rare in Europe. Recently, natural scarcity has been exacerbated by anthropogenic environmental damages. This specie is now regarded as rare or endangered, attracting conservation related research and active habitat management to assist its survival. Furthermore, obligatory thermophilous species are probably more affected by cold phases than cold-tolerant organisms. The evolutionary history of the common dormouse would therefore show significant differences compared to other species. To better understand the genetic variation and structure of this species, we developed a phylogeographic study based on sequences of 700 base pairs of the mitochondrial DNA cytochrome b gene from 102 specimens collected throughout its palearctic distribution. The obtained dataset was analysed using different phylogenetic reconstruction as well as other methods adapted to phylogeography. The analysis of the mtDNA reveals a number of surprises. The results show two major genetic lineages: the first corresponding to the Western and Italian populations; the second comprising the Balkan and the Northern populations. Furthermore, the analyses tend to propose a scenario of multiple refugia in the Italian peninsula. This pattern of ‘refugia within-refugia’ has important implications in interpreting the distribution patterns of genetic diversity within the southern peninsulas. The Calabria region and Sicily could be “hot spots” of intraspecific biodiversity of Muscardinus avellanarius. These regions would thus deserve attention when deciding Evolutionary Significant Units (“ESU) for conservation of this species. [less ▲]

Refining the taxonomy of the Rattini tribe: a phylogeny-based delimitation of species boundaries

Poster (2009, August)

Among mammals, rodents are recognized as the major hosts and vectors of zoonoses and represent a serious threat for human health. Because of global change, interactions between hosts and pathogens are ... [more ▼]

Among mammals, rodents are recognized as the major hosts and vectors of zoonoses and represent a serious threat for human health. Because of global change, interactions between hosts and pathogens are dramatically modified leading to new unexpected disease risks. To predict some of these, accurate identification of each rodent at specific level is needed. Among Muridae, the Rattini tribe encompasses 167 species inhabiting South East Asia, a hotspot of biodiversity facing with a growing economical development, affecting habitats, biodiversity and health but also a hot place of emerging and re-emerging diseases. Rat species were demonstrated as main hosts of pathogens but are difficult to recognize at a specific level using morphological criteria. DNA-barcoding methods appear as promising tools for accurate rat species identifications but their achievement is hampered by the need of reliable identifications as a departure. To provide a rigorous systematic framework for epidemiological surveys, we carried out a taxonomic revision of the Rattini tribe. As morphological characters are misleading, we decided to use the DNA sequence information itself as the primary information source to establish group membership and define species boundaries. We sequenced two mitochondrial and one nuclear genes from 122 rat samples to perform phylogenetic reconstructions and applied the method developed by Pons and colleagues (2006) that determines with no a priori the locations of ancestral nodes defining putative species. To name each cluster recognized as a valid species, we obtained sequence from museum holotype specimen, illustrating how huge opportunities ancient DNA analysis may offer to taxonomists. [less ▲]

Rodent biodiversity in South East Asia: the case of the Rattini group and the endemic karst rodent, Laonastes aenigmamous

Scientific conference (2009, March 20)

Among mammals, rodents are recognized as the major hosts and vectors of zoonoses and represent a serious threat for human health. Because of global change, interactions between hosts and pathogens are ... [more ▼]

Among mammals, rodents are recognized as the major hosts and vectors of zoonoses and represent a serious threat for human health. Because of global change, interactions between hosts and pathogens are dramatically modified leading to new unexpected disease risks. To predict some of these, accurate identification of each rodent at specific level is needed. Among Muridae, the Rattini tribe encompasses 167 species inhabiting South East Asia, a hotspot of biodiversity facing with a growing economical development, affecting habitats, biodiversity and health but also a hot place of emerging and re-emerging diseases. Rat species were demonstrated as main hosts of pathogens but are difficult to recognize at a specific level using morphological criteria. DNA-barcoding methods appear as promising tools for accurate rat species identifications but their achievement is hampered by the need of reliable identifications as a departure. To provide a rigorous systematic framework for epidemiological surveys, we carried out a taxonomic revision of the Rattini tribe. As morphological characters are misleading, we decided to use the DNA sequence information itself as the primary information source to establish group membership and define species boundaries. We sequenced two mitochondrial and one nuclear genes from 122 rat samples to perform phylogenetic reconstructions and applied the method developed by Pons and colleagues (2006) that determines with no a priori the locations of ancestral nodes defining putative species. To name each cluster recognized as a valid species, we obtained sequence from museum holotype specimen, illustrating how huge opportunities ancient DNA analysis may offer to taxonomists. Moreover, we will present some examples of intra-specific genetic biodiversity on rodents from SEA using phylogeographic approaches. [less ▲]

Species identification, molecular sexing and genotyping using non-invasive approaches in two wild bovids species: Bos gaurus and Bos javanicus.

in Zoo Biology (2009), 28(2), 127-36

Since the second Indochina war, habitat destruction and overhunting has resulted in fragmentation of the remaining populations of Bos javanicus and B. gaurus. Nowadays, both species are in serious danger ... [more ▼]

Since the second Indochina war, habitat destruction and overhunting has resulted in fragmentation of the remaining populations of Bos javanicus and B. gaurus. Nowadays, both species are in serious danger, especially the gaur. In Vietnam, where these species have become almost impossible to capture in the wild, non-invasive investigations are the only feasible approach to obtain data on populations. However, non-invasive derived DNA, especially in tropical areas, is usually characterized by low concentrations, poor quality and/or contamination from alien DNA. To assist in tropical conservation management, baseline information is provided here on assessing the reliability of species identification, molecular sexing and microsatellite genotyping using fecal DNA from B. gaurus and B. javanicus. For species identification using bovine fecal samples, cytochrome b fragment between positions 867 and 1140 was found to contain species diagnostic sites, which distinguishes the four species encountered in the region: B. gaurus, B. indicus, B. javanicus and B. taurus. For sex determination, primers were initially tested on DNA obtained from blood. Then, these primers were successfully used on DNA derived from fecal material. Finally, we also evaluate the feasibility of non-invasive microsatellite genotyping on fecal samples collected in Vietnamese nature reserves. The results presented here improve on current molecular methods based on fecal material obtained from tropical areas. [less ▲]

Isolation, characterization and PCR multiplexing of polymorphic microsatellite markers in the edible dormouse, Glis glis

in Molecular Ecology Resources (2009), 9(3), 885-887

We isolated and characterized 10 dinucleotide microsatellite loci in the edible dormouse, Glis glis (Linnaeus). Four multiplex panels were developed. Loci were amplified in samples from two geographically ... [more ▼]

We isolated and characterized 10 dinucleotide microsatellite loci in the edible dormouse, Glis glis (Linnaeus). Four multiplex panels were developed. Loci were amplified in samples from two geographically distant populations (Torgny in Belgium and Montseny in Spain). All loci were polymorphic in Spain but four were monomorphic in Belgium. Individuals from Belgium and Spain exhibited an average allelic diversity of 1.9 and 3.3 and an observed heterozygosity ranging from 0.08 to 0.47 and from 0.04 to 0.72, respectively. [less ▲]

Recent discoveries of new hantaviruses widen their range and question their origins.

in Annals of the New York Academy of Sciences (2008), 1149

Hantaviruses belong to the Bunyaviridae family. While usually hosted by wild mammals, they are potentially pathogenic for humans, and several serologically distinct groups associated with different ... [more ▼]

Hantaviruses belong to the Bunyaviridae family. While usually hosted by wild mammals, they are potentially pathogenic for humans, and several serologically distinct groups associated with different syndromes have been identified. Yet, investigations have mostly been conducted where human infections by hantaviruses constitute a real and well-identified public health problem, i.e., the holarctic and neotropical areas. Some hantaviruses have also been described from a Suncus murinus in India and a Bandicota indica in Thailand. In addition, recent investigations in Cambodia revealed new Hantavirus types. More recently, two new Hantavirus species were described: Sangassou from a Hylomyscus simus, and Tanganya from a Crocidura theresae, both from Africa (Guinea), thus strongly questioning the current views about geographic range, evolution, and epidemiology of hantaviruses. In such a framework, we have conducted a survey of Hantavirus diversity in Southeast Asia which allows us to isolate the Thailand virus and address questions about the taxonomy of their rodent hosts. Here we present a molecular analysis of representatives of all currently known Hantavirus species, thus allowing the comparison between the newly described ones with a large range sample of rodent hantaviruses. Our results clearly point to the presence of a particular lineage of hantaviruses in Southeast Asia. It also strongly suggests that new viruses, additional mammalian hosts and different related syndromes in humans are likely to be discovered in the near future, particularly in Southeast Asia and in Africa, where Muridae rodents are highly diversified. Furthermore, additional work is also urgently needed to investigate the hantaviruses associated with Crociduridae and Soricidae. [less ▲]