Novel insights into the diet of the Pyrenean desman (Galemys pyrenaicus) using next-generation sequencing molecular analyses

[Departement_IRSTEA]EauxInternational audienceThe Pyrenean desman, a threatened, semiaquatic mammal, is considered a specialist predator feeding on aquatic benthic invertebrates. This categorization comes from visual identification of prey in scat or gut contents, often based on a limited number of samples and locations. We combined diet analyses using next-generation sequencing methods with an extensive survey to explore the summer diet of Pyrenean desmans across the French Pyrenees. This study thus provides an unprecedented level of detail on the trophic ecology of Pyrenean desmans. Our results revealed a diverse diet containing a high proportion of rare prey and substantial consumption of terrestrial prey, which suggests a more generalist diet than previously understood. Three diet groups were identified, with significant differences in prey composition. These differences were not related to geographic location, but rather to local environmental variables. The spatial variation in diet was likely induced by local abiotic parameters that affect prey availability or use of foraging habitats

Molecular phylogeny of the whole Apodemus genus based on the complete mitochondrial genome and two nuclear genes.

The Apodemus genus is composed of 20 different species distributed throughout the Palearctic region. It is subdivised into two subgenera: - the Sylvaemus subgenus corresponding to the majority of the species living in the Western Part of the Palearctic region; - the Apodemus subgenus, associating most of the Asian species. Although these rodent species are very common and are spread in many European and Asian habitats, their evolutionary history and their phylogenetic relationships are still largely unknown. Previous studies developed on a restricted number of genetic markers and a subset of the Apodemus species gave partial information concerning these aspects. However, many gaps still remain even if such information would be particularly important not only in fundamental taxonomy but also in the field of epidemiology. Indeed many Apodemus species are reservoirs of different pathogens, like the Hantaviruses. A better knowledge of their evolutionary relationships would help to better understand virus spill-overs, which seem to exist among several Apodemus species. The aim of our study was to analyse for the first time in a single research, the totality of the 20 Apodemus species, using as genetic markers, the whole mitochondrial genome as well as two nuclear genes. The phylogenetic analyses based on 20 000 nuclear and mitochondrial DNA base pairs, give a clear pictures of the phylogenetic relationships existing among these species. These results will be compared with the different Hantavirus strains already identified on this rodent group

A new method to identify the endangered Pyrenean desman (<em>Galemys pyrenaicus</em>) and to study its diet, using next generation sequencing from faeces

International audienceThe Pyrenean desman (Galemys pyrenaicus) is a small endangered semi-aquatic mammal endemic to the Pyrenean Mountains and to the northern half of the Iberian Peninsula whose ecology and biology are still poorly known. The aim of this study was to identify Pyrenean desman faeces and to analyze its diet from this material using next-generation sequencing methods. We amplified and sequenced a small DNA minibarcode (133 bp) of the COI gene in twenty-four putative faeces samples of Pyrenean desman and successfully identified the species in 16 samples. Other identified species were mammals, birds and amphibians, evidencing the potential application of our methods to a larger panel of taxa. In the Pyrenean desman faeces, we were able to identify nineteen prey species with a positive match (more than 98% of identity with a reference sequence) and eleven putative prey species with lower identity scores (90-96%). The nineteen species belonged to four orders and eleven families among which Trichoptera and Hydropsychidae were the most frequent, respectively. Future improvements could be obtained by extending the reference DNA sequence collection to reach precise identifications over the Desman's range and by increasing the sampling to gain a better knowledge of the local diet of this endangered species. Such information is of great importance to propose the best management measures for its conservation

A new method to identify the endangered Pyrenean desman (Galemys pyrenaicus) and to study its diet, using next generation sequencing from faeces

the Pyrenean Mountains and to the northern half of the Iberian Peninsula whose ecology and biology are still poorly known. The aim of this study was to identify Pyrenean desman faeces and to analyze its diet from this material using next-generation sequencing methods. We amplified and sequenced a small DNA minibarcode (133 bp) of the COI gene in twenty-four putative faeces samples of Pyrenean desman and successfully identified the species in 16 samples. Other identified species were mammals, birds and amphibians, evidencing the potential application of our methods to a larger panel of taxa. In the Pyrenean desman faeces, we were able to identify nineteen prey species with a positive match (more than 98% of identity with a reference sequence) and eleven putative prey species with lower identity scores (90–96%). The nineteen species belonged to four orders and eleven families among which Trichoptera and Hydropsychidae were the most frequent, respectively. Future improvements could be obtained by extending the reference DNA sequence collection to reach precise identifications over the Desman’s range and by increasing the sampling to gain a better knowledge of the local diet of this endangered species. Such information is of great importance to propose the best management measures for its conservation

Novel insights into the diet of the Pyrenean desman Galemys pyrenaicus using next-generation sequencing molecular analyses.

[Departement_IRSTEA]EauxInternational audienceThe Pyrenean desman, a threatened, semiaquatic mammal, is considered a specialist predator feeding on aquatic benthic invertebrates. This categorization comes from visual identification of prey in scat or gut contents, often based on a limited number of samples and locations. We combined diet analyses using next-generation sequencing methods with an extensive survey to explore the summer diet of Pyrenean desmans across the French Pyrenees. This study thus provides an unprecedented level of detail on the trophic ecology of Pyrenean desmans. Our results revealed a diverse diet containing a high proportion of rare prey and substantial consumption of terrestrial prey, which suggests a more generalist diet than previously understood. Three diet groups were identified, with significant differences in prey composition. These differences were not related to geographic location, but rather to local environmental variables. The spatial variation in diet was likely induced by local abiotic parameters that affect prey availability or use of foraging habitats

Phylogeography of the striped field mouse, Apodemus agrarius (Rodentia: Muridae), throughout its distribution range in the Palaearctic region

International audienceTo better understand the evolutionary history of oriental wildlife newcomers in Europe, we studied the phylogeography and demographic history of the striped field mouse, Apodemus agrarius, throughout its Palaearctic distribution area. Genetic datasets including cytochrome b gene sequences and microsatellite markers were analysed using a large range of population genetics methodologies, including coalescent models and approximate Bayesian computations. Our results showed high mitochondrial genetic homogeneity among A. agrarius populations throughout the Palaearctic region, but microsatellite markers detected a finer population structure with the genetic differentiation of populations from the Eastern and Western distribution ranges. The Western colonisation likely originated from Far East Russian populations during one of the last interglacials. After their colonisation of the Central Asia and Western regions, the Central Palaearctic populations became isolated from their Eastern relatives. Our coalescent-based approaches suggested a separation between these two distribution ranges around 38 kya or more recently (around 11 kya). Limited gene flow still happened between populations in the two main distribution ranges, mainly from the Eastern to Western populations. Our study, for the first time, provides an overview of the evolutionary and demographic history of the striped field mouse throughout the Palaearctic region. A. agrarius appears to be an Asiatic immigrant and a relatively new member of the European fauna community. This study further confirms the important role of Far East Asian regions as a source of European biodiversity