Can tooth differentiation help to understand species coexistence? The case of wood mice in China

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

Origin and putative colonization routes for invasive rodent taxa in the democratic Republic of Congo

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

Post-glacial colonisation of Europe by the wood mouse, Apodemus sylvaticus : evidence of a northern refugium and dispersal with humans

The wood mouse Apodemus sylvaticus is an opportunistic rodent that is found throughout most of the European mainland. It is present on many islands around the margins of the continent and in northern Africa. The species has been the subject of previous phylogeographic studies but these have focussed on the more southerly part of its range. A substantial number of new samples, many of them from the periphery of the species’ range, contribute to an exceptional dataset comprising 981 mitochondrial cytochrome b sequences. These new data provide sufficient resolution to transform our understanding of the species’ survival through the last glaciation and its subsequent re-colonisation of the continent. The deepest genetic split we found is in agreement with previous studies and runs from the Alps to central Ukraine, but we further distinguish two separate lineages in wood mice to the north and west of this line. It is likely that this part of Europe was colonised from two refugia, putatively located in the Iberian peninsula and the Dordogne or Carpathian region. The wood mouse therefore joins the growing number of species with extant populations that appear to have survived the Last Glacial Maximum in northern refugia, rather than solely in traditionally recognised refugial locations in the southern European peninsulas. Furthermore, the existence of a northern refugium for the species was predicted in a study of mitochondrial variation in a specific parasite of the wood mouse, demonstrating the potential value of data from parasites to phylogeographic studies. Lastly, the presence of related haplotypes in widely disparate locations, often on islands or separated by substantial bodies of water, demonstrates the propensity of the wood mouse for accidental human-mediated transport

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

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

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

Integrating hydrological features and genetically validated occurrence data in occupancy modeling of an endemic and endangered semi-aquatic mammal species, Galemys pyrenaicus, in a Pyrenean catchment

As freshwater habitats are among the most endangered, there is an urgent need to identify critical areas for conservation, especially those that are home to endangered species. The Pyrenean desman (Galemys pyrenaicus) is a semi-aquatic mammal whose basic ecological requirements are largely unknown, hindering adequate conservation planning even though it is considered as a threatened species. Species distribution modelling is challenging for freshwater species. Indeed, the complexity of aquatic ecosystems (e.g., linear and hierarchical ordering) must be taken into account as well as imperfect sampling. High-quality and relevant hydrological descriptors should also be used. To understand the influence of environmental covariates on the occupancy and detection of the Pyrenean desman, we combine both a robust sign-survey data set (i.e. with genetic validation ensuring true presence information) and a hydrological model to simulate the flow regime across a whole catchment. Markovian site-occupancy analysis, taking into account sign detection and based on spatially adjacent replicates, indicated a positive influence of heterogeneity of substrate and shelters, and a negative influence of flow variability on Pyrenean desman detection. This valuable information should help to improve monitoring programs for this endangered species. Our results also highlighted a spatially clustered distribution and a positive influence of stream flow and number of tributaries on occupancy. Hence, modifications of flow regime (e.g. hydropower production, irrigation, climate change) and habitat fragmentation appear to be major threats for this species, altering the connectivity between tributaries and the mainstream river as well as between adjacent sub-catchments

Rise of oceanographic barriers in continuous populations of a cetacean: the genetic structure of harbour porpoises in Old World waters

<p>Abstract</p> <p>Background</p> <p>Understanding the role of seascape in shaping genetic and demographic population structure is highly challenging for marine pelagic species such as cetaceans for which there is generally little evidence of what could effectively restrict their dispersal. In the present work, we applied a combination of recent individual-based landscape genetic approaches to investigate the population genetic structure of a highly mobile extensive range cetacean, the harbour porpoise in the eastern North Atlantic, with regards to oceanographic characteristics that could constrain its dispersal.</p> <p>Results</p> <p>Analyses of 10 microsatellite loci for 752 individuals revealed that most of the sampled range in the eastern North Atlantic behaves as a 'continuous' population that widely extends over thousands of kilometres with significant isolation by distance (IBD). However, strong barriers to gene flow were detected in the south-eastern part of the range. These barriers coincided with profound changes in environmental characteristics and isolated, on a relatively small scale, porpoises from Iberian waters and on a larger scale porpoises from the Black Sea.</p> <p>Conclusion</p> <p>The presence of these barriers to gene flow that coincide with profound changes in oceanographic features, together with the spatial variation in IBD strength, provide for the first time strong evidence that physical processes have a major impact on the demographic and genetic structure of a cetacean. This genetic pattern further suggests habitat-related fragmentation of the porpoise range that is likely to intensify with predicted surface ocean warming.</p

Pan-African Genetic Structure in the African Buffalo (Syncerus caffer): Investigating Intraspecific Divergence

The African buffalo (Syncerus caffer) exhibits extreme morphological variability, which has led to controversies about the validity and taxonomic status of the various recognized subspecies. The present study aims to clarify these by inferring the pan-African spatial distribution of genetic diversity, using a comprehensive set of mitochondrial D-loop sequences from across the entire range of the species. All analyses converged on the existence of two distinct lineages, corresponding to a group encompassing West and Central African populations and a group encompassing East and Southern African populations. The former is currently assigned to two to three subspecies (S. c. nanus, S. c. brachyceros, S. c. aequinoctialis) and the latter to a separate subspecies (S. c. caffer). Forty-two per cent of the total amount of genetic diversity is explained by the between-lineage component, with one to seventeen female migrants per generation inferred as consistent with the isolation-with-migration model. The two lineages diverged between 145 000 to 449 000 years ago, with strong indications for a population expansion in both lineages, as revealed by coalescent-based analyses, summary statistics and a star-like topology of the haplotype network for the S. c. caffer lineage. A Bayesian analysis identified the most probable historical migration routes, with the Cape buffalo undertaking successive colonization events from Eastern toward Southern Africa. Furthermore, our analyses indicate that, in the West-Central African lineage, the forest ecophenotype may be a derived form of the savanna ecophenotype and not vice versa, as has previously been proposed. The African buffalo most likely expanded and diverged in the late to middle Pleistocene from an ancestral population located around the current-day Central African Republic, adapting morphologically to colonize new habitats, hence developing the variety of ecophenotypes observed today