Jean-François Cosson

Comparative phylogeography and postglacial colonization routes in Europe

The Quaternary cold periods in Europe are thought to have heavily influenced the amount and distribution of intraspecific genetic variation in both animals and plants. The phylogeographies of 10 taxa, including mammals (Ursus arctos, Sorex spp., Crocidura suaveolens, Arvicola spp.), amphibians (Triturus spp.), arthropods (Chorthippus parallelus), and plants (Abies alba, Picea abies, Fagus sylvatica, Quercus spp.), were analysed to elucidate general trends across Europe. Only a small degree of congruence was found amongst the phylogeographies of the 10 taxa, but the likely postglacial colonization routes exhibit some similarities. A Brooks parsimony analysis produced an unrooted area phylogram, showing that: (i) the northern regions were colonized generally from the Iberic and Balkanic refugia; and (ii) the Italian lineages were often isolated due to the presence of the Alpine barrier. The comparison of colonization routes highlighted four main suture‐zones where lineages from the different refugia meet. Some of the intraspecific genetic distances among lineages indicated a prequaternary divergence that cannot be connected to any particular cold period, but are probably related mainly to the date of arrival of each taxon in the European continent. As a consequence, molecular genetics so far appears to be of limited use in dating Quaternary events.

Landscape connectivity influences gene flow in a roe deer population inhabiting a fragmented landscape: an individual-based approach

Changes in agricultural practices and forest fragmentation can have a dramatic effect on landscape connectivity and the dispersal of animals, potentially reducing gene flow within populations. In this study, we assessed the influence of woodland connectivity on gene flow in a traditionally forest‐dwelling species — the European roe deer — in a fragmented landscape. From a sample of 648 roe deer spatially referenced within a study area of 55 × 40 km, interindividual genetic distances were calculated from genotypes at 12 polymorphic microsatellite loci. We calculated two geographical distances between each pair of individuals: the Euclidean distance (straight line) and the ‘least cost distance’ (the trajectory that maximizes the use of wooded corridors). We tested the correlation between genetic pairwise distances and the two types of geographical pairwise distance using Mantel tests. The correlation was better using the least cost distance, which takes into account the distribution of wooded patches, especially for females (the correlation was stronger but not significant for males). These results suggest that in a fragmented woodland area roe deer dispersal is strongly linked to wooded structures and hence that gene flow within the roe deer population is influenced by the connectivity of the landscape.

Genetic structure is influenced by landscape features: empirical evidence from a roe deer population

The delimitation of population units is of primary importance in population management and conservation biology. Moreover, when coupled with landscape data, the description of population genetic structure can provide valuable knowledge about the permeability of landscape features, which is often difficult to assess by direct methods (e.g. telemetry). In this study, we investigated the genetic structuring of a roe deer population which recently recolonized a fragmented landscape. We sampled 1148 individuals from a 40 × 55‐km area containing several putative barriers to deer movements, and hence to gene flow, namely a highway, rivers and several canals. In order to assess the effect of these landscape features on genetic structure, we implemented a spatial statistical model known as geneland which analyses genetic structure, explicitly taking into account the spatial nature of the problem. Two genetic units were inferred, exhibiting a very low level of differentiation (FST = 0.008). The location of their boundaries suggested that there are no absolute barriers in this study area, but that the combination of several landscape features with low permeability can lead to population differentiation. Our analysis hence suggests that the landscape has a significant influence on the structuring of the population under study. It also illustrates the use of geneland as a powerful method to infer population structure, even in situations of young populations exhibiting low genetic differentiation.

A 454 multiplex sequencing method for rapid and reliable genotyping of highly polymorphic genes in large-scale studies

BackgroundHigh-throughput sequencing technologies offer new perspectives for biomedical, agronomical and evolutionary research. Promising progresses now concern the application of these technologies to large-scale studies of genetic variation. Such studies require the genotyping of high numbers of samples. This is theoretically possible using 454 pyrosequencing, which generates billions of base pairs of sequence data. However several challenges arise: first in the attribution of each read produced to its original sample, and second, in bioinformatic analyses to distinguish true from artifactual sequence variation. This pilot study proposes a new application for the 454 GS FLX platform, allowing the individual genotyping of thousands of samples in one run. A probabilistic model has been developed to demonstrate the reliability of this method.ResultsDNA amplicons from 1,710 rodent samples were individually barcoded using a combination of tags located in forward and reverse primers. Amplicons consisted in 222 bp fragments corresponding to DRB exon 2, a highly polymorphic gene in mammals. A total of 221,789 reads were obtained, of which 153,349 were finally assigned to original samples. Rules based on a probabilistic model and a four-step procedure, were developed to validate sequences and provide a confidence level for each genotype. The method gave promising results, with the genotyping of DRB exon 2 sequences for 1,407 samples from 24 different rodent species and the sequencing of 392 variants in one half of a 454 run. Using replicates, we estimated that the reproducibility of genotyping reached 95%.ConclusionsThis new approach is a promising alternative to classical methods involving electrophoresis-based techniques for variant separation and cloning-sequencing for sequence determination. The 454 system is less costly and time consuming and may enhance the reliability of genotypes obtained when high numbers of samples are studied. It opens up new perspectives for the study of evolutionary and functional genetics of highly polymorphic genes like major histocompatibility complex genes in vertebrates or loci regulating self-compatibility in plants. Important applications in biomedical research will include the detection of individual variation in disease susceptibility. Similarly, agronomy will benefit from this approach, through the study of genes implicated in productivity or disease susceptibility traits.

Effects of forest fragmentation on frugivorous and nectarivorous bats in French Guiana

The effects of tropical forest fragmentation on frugivorous and nec- tarivorous bats were studied on recent islands created by the flooding of a dam in French Guiana. Study sites include forest islands isolated by water, and control plots in nearby continuous forest. Studies began 1 y before the onset of forest fragmentation and encompassed the first 3 y after flooding. Forest fragmentation greatly modified the diversity and abundance of bats. Changes occurred more rapidly in the smallest fragments than in the largest one, and trends were remark- ably similar among all the studied islands. Bat captures in islands were charac- terised by the scarcity of understorey frugivores. Differences in home range size and foraging strategies may explain why understorey fruit bat species are more sensitive to fragmentation than canopy ones. Changes in the frugivorous bat com- munity may have indirect consequences on both the demographic and the genetic structures of plant populations inside forest fragments.

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

BackgroundRodents 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.ResultsWe 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.ConclusionsUsing 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.

Phylogeographical footprints of the Strait of Gibraltar and Quaternary climatic fluctuations in the western Mediterranean: a case study with the greater white-toothed shrew, Crocidura russula (Mammalia: Soricidae).

We used mitochondrial cyt b sequences to investigate the phylogenetic relationships of Crocidura russula (sensu lato) populations across the Strait of Gibraltar, western Europe, Maghreb, and the Mediterranean and Atlantic islands. This revealed very low genetic divergence between European and Moroccan populations. The application of a molecular clock previously calibrated for shrews suggested that the separation of European from Moroccan lineages occurred less than 60 000 bp, which is at least 5 million years (Myr) after the reopening of the Strait of Gibraltar. This means that an overwater dispersal event was responsible for the observed phylogeographical structure. In contrast, genetic analyses revealed that Moroccan populations were highly distinct from Tunisian ones. According to the molecular clock, these populations separated about 2.2 million years ago (Ma), a time marked by sharp alternations of dry and humid climates in the Maghreb. The populations of the Mediterranean islands Ibiza, Pantelleria, and Sardinia were founded from Tunisian populations by overwater dispersal. In conclusion, overwater dispersal across the Strait of Gibraltar, probably assisted by humans, is possible for small terrestrial vertebrates. Moreover, as in Europe, Quaternary climatic fluctuations had a major effect on the phylogeographical structure of the Maghreb biota.

Spatial genetic structure of a small rodent in a heterogeneous landscape

Gene flow in natural populations may be strongly influenced by landscape features. The integration of landscape characteristics in population genetic studies may thus improve our understanding of population functioning. In this study, we investigated the population genetic structure and gene flow pattern for the common vole, Microtus arvalis, in a heterogeneous landscape characterised by strong spatial and temporal variation. The studied area is an intensive agricultural zone of approximately 500 km2 crossed by a motorway. We used individual‐based Bayesian methods to define the number of population units and their spatial borders without prior delimitation of such units. Unexpectedly, we determined a single genetic unit that covered the entire area studied. In particular, the motorway considered as a likely barrier to dispersal was not associated with any spatial genetic discontinuity. Using computer simulations, we demonstrated that recent anthropogenic barriers to effective dispersal are difficult to detect through analysis of genetic variation for species with large effective population sizes. We observed a slight, but significant, pattern of isolation by distance over the whole study site. Spatial autocorrelation analyses detected genetic structuring on a local scale, most probably due to the social organisation of the study species. Overall, our analysis suggests intense small‐scale dispersal associated with a large effective population size. High dispersal rates may be imposed by the strong spatio‐temporal heterogeneity of habitat quality, which characterises intensive agroecosystems.

Migration and recovery of the genetic diversity during the increasing density phase in cyclic vole populations

In cyclic populations, high genetic diversity is currently reported despite the periodic low numbers experienced by the populations during the low phases. Here, we report spatio‐temporal monitoring at a very fine scale of cyclic populations of the fossorial water vole (Arvicola terrestris) during the increasing density phase. This phase marks the transition from a patchy structure (demes) during low density to a continuous population in high density. We found that the genetic diversity was effectively high but also that it displayed a local increase within demes over the increasing phase. The genetic diversity remained relatively constant when considering all demes together. The increase in vole abundance was also correlated with a decrease of genetic differentiation among demes. Such results suggest that at the end of the low phase, demes are affected by genetic drift as the result of being small and geographically isolated. This leads to a loss of local genetic diversity and a spatial differentiation among demes. This situation is counterbalanced during the increasing phase by the spatial expansion of demes and the increase of the effective migration among differentiated demes. We provide evidences that in cyclic populations of the fossorial water voles, the relative influence of drift operating during low density populations and migration occurring principally while population size increases interacts closely to maintain high genetic diversity.

Ecological changes in recent land-bridge islands in French Guiana, with emphasis on vertebrate communities

In 1993 a multidisciplinary project investigating the effects of tropical rainforest fragmentation on land-bridge islands created by a hydroelectric reservoir was initiated in French Guiana (the Saint Eugene Fragmentation Project, SEFP). The main focus of the study is documenting changes in vertebrate groups, including lizards, birds, non-flying small mammals, bats and primates, that have marked differences in dispersal capacities. Here we summarize results of the first 4 years of research on SEFP (1 year pre-fragmentation, 3 years post-fragmentation), comparing islands with nearby control plots in continuous forest. Our results suggest that forest fragmentation has rapidly modified vertebrate diversity, regardless of the ability of species to disperse over water. Species present on islands do not represent a random sample of those present before isolation. Rather, a common suite of species has rapidly become dominant on each island, and these species share the following ecological traits: (1) they exhibit some of the largest body sizes in their guild, (2) they are generalists in habitat and food requirements, (3) they are naturally abundant in undisturbed forests, and (4) they have a wide geographic range yet are restricted to tropical rainforest. These results are interpreted in light of other studies of rainforest fragmentation.