Roland Libois

Beyond the Mediterranean peninsulas: evidence of central European glacial refugia for a temperate forest mammal species, the bank vole (Clethrionomys glareolus)

This study details the phylogeographic pattern of the bank vole, Clethrionomys glareolus, a European rodent species strongly associated with forest habitat. We used sequences of 1011 base pairs of the mitochondrial DNA cytochrome b gene from 207 bank voles collected in 62 localities spread throughout its distribution area. Our results reveal the presence of three Mediterranean (Spanish, Italian and Balkan) and three continental (western, eastern and ‘Ural’) phylogroups. The endemic Mediterranean phylogroups did not contribute to the postglacial recolonization of much of the Palaearctic range of species. Instead, the major part of this region was apparently recolonized by bank voles that survived in glacial refugia in central Europe. Moreover, our phylogeographic analyses also reveal differentiated populations of bank voles in the Ural mountains and elsewhere, which carry the mitochondrial DNA of another related vole species, the ruddy vole (Clethrionomys rutilus). In conclusion, this study demonstrates a complex phylogeographic history for a forest species in Europe which is sufficiently adaptable that, facing climate change, survives in relict southern and northern habitats. The high level of genetic diversity characterizing vole populations from parts of central Europe also highlights the importance of such regions as a source of intraspecific genetic biodiversity.

Mitochondrial phylogeography of the Woodmouse ( Apodemus sylvaticus ) in the Western Palearctic region

We sequenced 965 base pairs of the mitochondrial DNA cytochrome b from 102 woodmice (Apodemus sylvaticus) collected from 40 European localities. The aims of the study were to answer the following questions. (i) Did the Mediterranean peninsulas play a role as refuge for woodmice? (ii) Is genetic variability of A. sylvaticus higher in the Mediterranean region compared with northern Europe? (iii) Are the patterns of the postglacial colonization of Europe by woodmice similar to those presently recognized for other European species? The results provide a clear picture of the impact of the Quaternary glaciations on the genetic and geographical structure of the woodmouse. Our analyses indicate a higher genetic variability of woodmice in the Mediterranean peninsulas compared to northern Europe, suggesting a role of the former as refuge regions for this small mammal. An original pattern of postglacial colonization is proposed where the Iberian and southern France refuge populations colonized almost all European regions. The Sicilian population appears to be very differentiated and highly variable. This emphasizes the importance of this island as a ‘hot spot’ for the intraspecific genetic diversity of the woodmouse. Finally, woodmice in North Africa originated from southwestern Europe, most probably as a result of a recent anthropogenic introduction.

So close and so different: comparative phylogeography of two small mammal species, the Yellow-necked fieldmouse (Apodemus flavicollis) and the Woodmouse (Apodemus sylvaticus) in the Western Palearctic region

In Europe, concordant geographical distribution among genetic lineages within different species is rare, which suggests distinct reactions to Quaternary ice ages. This study aims to determine whether such a discrepancy also affects a pair of sympatric species, which are morphologically and taxonomically closely related but which have slight differences in their ecological habits. The phylogeographic structures of two European rodents, the Yellow-necked fieldmouse (A. flavicollis) and the woodmouse (Apodemus sylvaticus) were, therefore, compared on the basis of mitochondrial DNA cytochrome b (mtDNA cyt b) sequences (965 base pairs) from 196 specimens collected from 59 European localities spread throughout the species distributions. The results indicate that the two species survived in different ways through the Quaternary glaciations. A. sylvaticus survived in the Iberian Peninsula from where it recolonized almost all Europe at the end of the last glaciation. Conversely, the refuge from which A. flavicollis recolonized Europe, including northern Spain, during the Holocene corresponds to the Italo-Balkan area, where A. sylvaticus suffered a serious genetic bottleneck. This study confirms that even closely related species may have highly different phylogeographic histories and shows the importance of ecological plasticity of the species for their survival through climate change. Finally, it suggests that phylogeographic distinctiveness may be a general feature of European species.

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.

Phylogeography of a Nematode (Heligmosomoides polygyrus) in the Western Palearctic region : Persistence of Northern cryptic populations during ice ages?

This study establishes the continental phylogeographical pattern of a European nematode, Heligmosomoides polygyrus (Dujardin, 1845; Heligmosomoidea). We sequenced 687 base pairs of the mitochondrial DNA (mtDNA) cyt b gene for 136 individuals collected in 22 localities. The results revealed that H. polygyrus populations are separated into five major units corresponding to the Italian, northern European (Denmark and Ireland), Iberian, western European, and Balkan populations. Different subclades were also observed within the first two groups. Based on the rate of molecular evolution of H. polygyrus cyt b gene‐estimated to 3.5%–3.7% divergence per million years (Myr) in a previous study – the isolation time of the five clades was estimated between 2.5 ± 0.24 and 1.5 ± 0.23 million years ago. Moreover, H. polygyrus presents a higher genetic variability in the Mediterranean peninsulas as compared to northwestern Europe, highlighting the role of these regions as refuge areas. Like its specific host, the wood mouse Apodemus sylvaticus, H. polygyrus’ pattern of postglacial recolonization of northwestern Europe was initiated from Iberian populations, while Italian and Balkan populations did not expand to the north. The results also suggest the existence of forested and temperate refuges in the southern British Isles during the Quaternary. Finally, the genetic diversity as well as the level of genetic divergence between the lineages of H. polygyrus are compared to those observed in other vertebrate and invertebrate phylogeographical studies: the existence of highly differentiated lineages in H. polygyrus (5%−10% of genetic divergence) highlights that the effects of Pleistocene climate changes on free‐living organisms are also reflected in their obligate parasites.

Plague and the Human Flea, Tanzania

Pulex irritans fleas were more common in villages with high plague incidence.

Geography and host biogeography matter for understanding the phylogeography of a parasite.

The co-evolution between hosts and parasites has long been recognized as a fundamental driver of macro-evolutionary patterns of diversification. The effect of co-differentiation on parasite diversification is, however, often confounded by underlying geographic patterns of host distribution. In order to disentangle the confounding effects of allopatric versus host speciation, the mitochondrial cytochrome b (cyt b) gene was sequenced in seventy individuals of the parasitic nematode genus Heligmosomoides sampled in the six Apodemus mice species common in the western Palearctic region. The nuclear internal transcribed spacers (ITS) 1 and 2 were also sequenced in fifteen parasites to confirm the mitochondrial data. All lineages differentiated according to a geographic pattern and independently from the sampled host species. This suggests that host speciation did not involve concurrent parasite speciation. However, the geographic distribution range of some parasite lineages mirrors that of A. sylvaticus lineages in SW Europe, and that of A. flavicollis lineages in the Balkans and in the Middle East. Thus, regional co-differentiation likely occurred between the parasite and the two sister Apodemus hosts in different parts of their distribution range. We suggest that differences in regional abundances of A. sylvaticus and A. flavicollis are responsible for generating this pattern of regional co-differentiation. This study highlights the importance of integrating both geography and biogeographic information from potential hosts to better understand their parasite phylogeography.

Conservation genetics and population history of the threatened European mink Mustela lutreola , with an emphasis on the west European population

In species of great conservation concern, special attention must be paid to their phylogeography, in particular the origin of animals for captive breeding and reintroduction. The endangered European mink lives now in at least three well‐separated populations in northeast, southeast and west Europe. Our aim is to assess the genetic structure of these populations to identify ‘distinct population segments’ (DPS) and advise captive breeding programmes. First, the mtDNA control region was completely sequenced in 176 minks and 10 polecats. The analysis revealed that the western population is characterized by a single mtDNA haplotype that is closely related to those in eastern regions but nevertheless, not found there to date. The northeast European animals are much more variable (π = 0.012, h = 0.939), with the southeast samples intermediate (π = 0.0012, h = 0.469). Second, 155 European mink were genotyped using six microsatellites. The latter display the same trends of genetic diversity among regions as mtDNA [gene diversity and allelic richness highest in northeast Europe (HE = 0.539, RS = 3.76), lowest in west Europe (HE = 0.379, RS = 2.12)], and provide evidences that the southeast and possibly the west populations have undergone a recent bottleneck. Our results indicate that the western population derives from a few animals which recently colonized this region, possibly after a human introduction. Microsatellite data also reveal that isolation by distance occurs in the western population, causing some inbreeding because related individuals mate. As genetic data indicate that the three populations have not undergone independent evolutionary histories for long (no phylogeographical structure), they should not be considered as distinct DPS. In conclusion, the captive breeding programme should use animals from different parts of the species’ present distribution area.

A relict bank vole lineage highlights the biogeographic history of the Pyrenean region in Europe.

The Pyrenean region exhibits high levels of endemism suggesting a major contribution to the phylogeography of European species. But, to date, the role of the Pyrenees and surrounding areas as a glacial refugium for temperate species remains poorly explored. In the current study, we investigated the biogeographic role of the Pyrenean region through the analyses of genetic polymorphism and morphology of a typical forest‐dwelling small mammal, the bank vole (Myodes glareolus). Analyses of the mitochondrial cytochrome b gene and the third upper molar (M3) show a complex phylogeographic structure in the Pyrenean region with at least three distinct lineages: the Western European, Spanish and Basque lineages. The Basque lineage in the northwestern (NW) Pyrenees was identified as a new clearly differentiated and geographically localized bank vole lineage in Europe. The average M3 shape of Basque bank voles suggests morphological differentiation but also restricted genetic exchanges with other populations. Our genetic and morphological results as well as palaeo‐environmental and fossils records support the hypothesis of a new glacial refugium in Europe situated in the NW Pyrenees. The permissive microclimatic conditions that prevailed for a long time in this region may have allowed the survival of temperate species, including humans. Moreover, local differentiation around the Pyrenees is favoured by the opportunity for populations to track the shift of the vegetation belt in altitude rather than in latitude. The finding of the Basque lineage is in agreement with the high level of endemic taxa reported in the NW Pyrenees.

Biogeography and taxonomy of Apodemus sylvaticus (the woodmouse) in the Tyrrhenian region: Enzymatic variations and mitochondrial DNA restriction pattern analysis

In the western Mediterranean area, the taxonomic status of the various forms of Apodemus sylvaticus is quite unclear. Moreover, though anthropogenic, the origins of the island populations remain unknown in geographical terms. In order to examine the level of genetic relatedness of insular and continental woodmice, 258 animals were caught in 24 localities distributed in Belgium, France, mainland Italy, Sardinia, Corsica and Elba. Electrophoresis of 33 allozymes and mtDNA restriction fragments were performed and a upgma dendrogram built from the indices of genetic divergence. The dendrogram based on restriction patterns shows two main groups: ‘Tyrrhenian’, comprising all the Italian and Corsican animals and ‘North-western’, corresponding to all the other mice trapped from the Pyrenees to Belgium. Since all the Tyrrhenian mice are similar and well isolated from their relatives living on the western edge of the Alpine chain, they must share a common origin. The insular populations are consequently derived from peninsular Italian ones. From a taxonomic point of view and taking the priority rules into account, we have to invalidate A. s. clanceyi Harrison, 1948 and to consider the Tyrrhenian woodmice as belonging to A. s. milleri de Beaux, 1926, whereas the North-western ones must be referred to as the nominal subspecies. As far as the Elban woodmouse is concerned, at the moment we prefer to keep its present subspecific status because we only studied one animal.