Genetic pattern of the recent recovery of European otters in southern France

in Ecography (2008), 31(2), 176-186

We investigated how landscape affects the population genetic structure and the dispersal of the elusive European otter Lutra lutra in a contemporary colonization context, over several generations and at ... [more ▼]

We investigated how landscape affects the population genetic structure and the dispersal of the elusive European otter Lutra lutra in a contemporary colonization context, over several generations and at the level of hydrographic basins. Our study area included 10 basins located in the Cevennes National Park (CNP), at the southern front of the natural otter recovery in France. Each basin comprised 50 to 300 km of permanent rivers that were surveyed for otter presence from 1991 to 2005. Faecal samples collected in 2004 and 2005 in this area were genotyped at 9 microsatellite loci, resulting in the identification of 70 genetically distinct individuals. Bayesian clustering methods were used to infer genetic structure of the populations and to compare recent gene flow to the observed colonization. At the regional level, we identified 2 distinct genetic clusters (NE and SW; FST=0.102) partially separated by ridges, suggesting that the CNP was recolonized by 2 genetically distinct otter populations. At the basin level, the genetic distance between groups of individuals in different basins was positively correlated to the mean slope separating these basins. The probable origins and directions of individual movements (i.e. migration between clusters and basin colonization inside clusters) were inferred from assignment tests. This approach shows that steep and dry lands can stop, impede or divert the dispersal of a mobile carnivore such as the otter. [less ▲]

VIABILITY OF THE NORTHEAST ATLANTIC HARBOUR PORPOISE AND SEAL POPULATION (GENETIC AND ECOLOGICAL STUDY)

Report (2007)

Harbour porpoises (Phocoena phocoena) and harbour seals (Phoca vitulina) are far more abundant along our coast compared to the beginning of the nineties. Human impact on these species is however hard to ... [more ▼]

Harbour porpoises (Phocoena phocoena) and harbour seals (Phoca vitulina) are far more abundant along our coast compared to the beginning of the nineties. Human impact on these species is however hard to establish, mainly due to lack of information on marine mammal population ecology, density, distribution and diversity. This project aims to gain further knowledge on the viability of the harbour porpoise and harbour seal populations in the North Sea (focusing mainly on its southern Bight) through - The characterisation of their genetic structure and diversity (through mtDNA and microsatellites in harbour porpoises) - A better understanding of their feeding ecology (through δ13C and δ15N measurements in muscles) - The assessment of their susceptibility of being trapped accidentally in fishing nets (post-mortem investigations) Harbour porpoise and harbour seal occupied the top trophic levels but displayed different feeding habits as inferred from their δ13C and δ15N mean values. Harbour porpoises displayed lower mean δ15N values suggesting a lower trophic position likely oriented towards small planktivorous fish such as herring and lesser sandeel. However, both their recent high abundance and their dietary preferences might lead to a higher susceptibility to by-catch as revealed by the significant emergence of net entrapment and net marks revealed by post-mortem investigations. The question rises about the sustainability of these incidental captures. Furthermore, genetic investigations revealed a higher fragmentation of the porpoises collected along the coast of France, Belgium and Netherlands. This apparent fragmentation is of particular importance from a conservation point of view and enhances the fact to protect in priority these last populations. Our study showed importance of multidisciplinary approaches (post-mortem investigations, stable isotope measurements (δ13C and δ15N measurements) and genetic investigations using mtDNA and microsatellites) to apprehend the question of marine mammal survival in our waters. [less ▲]

Mandibles and molars of the wood mouse, Apodemus sylvaticus (L.): integrated latitudinal pattern and mosaic insular evolution

in Journal of Biogeography (2007), 34(2), 339-355

Aim The distinct nature of island populations has traditionally been attributed either to adaptation to particular insular conditions or to random genetic effects. In order to assess the relative ... [more ▼]

Aim The distinct nature of island populations has traditionally been attributed either to adaptation to particular insular conditions or to random genetic effects. In order to assess the relative importance of these two disparate processes, insular effects were addressed in the European wood mouse, Apodemus sylvaticus (Linnaeus, 1758). Location Wood mice from 33 localities on both mainland and various Atlantic and western Mediterranean islands were considered. This sampling covers only part of the latitudinal range of A. sylvaticus but included the two main genetic clades identified by previous studies. Islands encompass a range of geographical conditions (e.g. small islands fringing the continent through large and isolated ones). Methods The insular syndrome primarily invokes variations in body size, but ecological factors such as release from competition, niche widening and food availability should also influence other characters related to diet. In the present study, the morphology of the wood mice was quantified based on two characters involved in feeding: the size and shape of the mandibles and first upper molars. The size of the mandible is also a proxy for the body size of the animal. Patterns of morphological differentiation of both features were estimated using twodimensional outline analysis based on Fourier methods. Results Significant differences between mainland and island populations were observed in most cases for both the mandibles and molars. However, molars and mandibles displayed divergent patterns. Mandible shape diverged mostly on islands of intermediate remoteness and competition levels, whereas molars exhibited the greatest shape differentiation on small islands, such as Port-Cros and Porquerolles. A mosaic pattern was also displayed for size. Body and mandible size increased on Ibiza, but molar size remained similar to mainland populations. Mosaic patterns were, however, not apparent in the mainland populations. Congruent latitudinal variations were evident for the size and shape of both mandibles and molars. Main conclusions Mosaic evolution appears to characterize insular divergence. The molar seems to be more prone to change with reduced population size on small islands, whereas the mandible could be more sensitive to peculiar environmental conditions on large and remote islands. [less ▲]

Parasites and the island syndrome: the colonization of the western Mediterranean islands by Heligmosomoides polygyrus (Dujardin, 1845)

in Journal of Biogeography (2006), 33(7), 1212-1222

Aim Populations of free-living vertebrates on islands frequently differ from their mainland counterparts by a series of changes in morphometric, life-history, behavioural, physiological and genetic traits ... [more ▼]

Aim Populations of free-living vertebrates on islands frequently differ from their mainland counterparts by a series of changes in morphometric, life-history, behavioural, physiological and genetic traits, collectively referred to as the 'island syndrome'. It is not known, however, whether the 'island syndrome' also affects parasitic organisms. The present study establishes the colonization pattern of the Mediterranean islands by the nematode Heligmosomoides polygyrus, a direct and specific parasite of rodent hosts of the Apodemus genus, and evaluates the effects of island colonization by this species on two components of the island syndrome: the loss of genetic diversity and the enlargement of the ecological niche. Location Heligmosomoides polygyrus was sampled on seven western Mediterranean islands - Corsica, Crete, Elba, Majorca, Minorca, Sardinia and Sicily - as well as in 20 continental locations covering the Mediterranean basin. Methods The mitochondrial cytochrome b gene (690 base pairs) was sequenced in 166 adult H. polygyrus individuals sampled in the 27 continental and island locations. Phylogenetic reconstructions in distance, parsimony, maximum likelihood and Bayesian posterior probabilities were carried out on the whole cytochrome b gene data set. The levels of nucleotide, haplotype and genetic divergence (Kimura two-parameter distance estimator) diversities were estimated in each island population and in the various continental lineages. Results Phylogenetic reconstructions show that the mainland origins of H. polygyrus were continental Spain for the Balearic Islands (Majorca, Minorca), northern Italy for the Tyrrhenian Islands (Corsica, Sardinia, Elba), southern Italy for Sicily, and the Balkan region for Crete. A comparison of island H. polygyrus populations with their mainland source populations revealed two characteristic components of the island syndrome in this parasite. First, island H. polygyrus populations display a significant loss of genetic diversity, which is related (r(2) = 0.73) to the distance separating the island from the mainland source region. Second, H. polygyrus exhibits a niche enlargement following insularization. Indeed, H. polygyrus in Corsica is present in both A. sylvaticus and Mus musculus domesticus, while mainland H. polygyrus populations are present exclusively in Apodemus hosts. Main conclusions Our results show that H. polygyrus has undergone a loss of genetic diversity and a niche (host) enlargement following colonization of the western Mediterranean islands. To our knowledge, this study provides the first evidence for components of the 'island syndrome' in a parasitic nematode species. [less ▲]

Taxonomy, evolutionary history and biogeography of the broad-toothed field mouse (Apodemus mystacinus) in the eastern Mediterranean area based on mitochondrial and nuclear genes

in Biological Journal of the Linnean Society (2005), 85(1), 53-63

The broad-toothed field mouse (Apodemus mystacinus) is distributed throughout the Balkan Peninsula, Asia Minor and the Middle East. It is generally split into two different specific entities: Apodemus ... [more ▼]

The broad-toothed field mouse (Apodemus mystacinus) is distributed throughout the Balkan Peninsula, Asia Minor and the Middle East. It is generally split into two different specific entities: Apodemus epimelas occurs on the Balkan Peninsula and A. mystacinus inhabits Asia Minor and the Middle East. This analysis, based on two mitochondrial regions (cytochrome b and the D-loop) and the interstitial retinol binding protein (IRBP) nuclear gene, confirms an important level of genetic divergence between the animals from these regions and their separation from each other at least 4.2-5.1 Mya, which is in favour of a distinct specific status. Finally, the broad-toothed field mice from southwestern Turkey appear to be closely related to the animals from Crete but highly distinct from the populations of the other Oriental regions. This supports a distinct subspecific level (A. m. rhodius) for the insular animals and also for those from south-western Turkey. From a biogeographical point of view, it can be assumed that either late Pliocene or early Pleistocene cooling led to the isolation of two main groups of A. mystacinus, one in the Balkan region and the other one in Turkey and the Near East (Syria and Israel). In this region, it is suggested that a more recent event appeared during the Quaternary period, isolating broad-toothed field mice in Crete and leading to the appearance of two well-differentiated genetic groups: one in Crete and south-western Turkey, and the other widespread in northern and eastern Turkey as well as in the Near East. © 2005 The Linnean Society of London. [less ▲]

Phylogeography of Harbour Porpoise (Phocoena phocoena) in the Eastern North Atlantic and in the Black Sea Explored by the Analyses of Nuclear and Mitochondrial DNA

Poster (2005)

Study of the genetic population structure and the demographic history of the harbour porpoise (Phocoena phocoena) has been nearly comprehensive throughout its distribution in North Atlantic, most studies ... [more ▼]

Study of the genetic population structure and the demographic history of the harbour porpoise (Phocoena phocoena) has been nearly comprehensive throughout its distribution in North Atlantic, most studies using the mitochondrial control region as a genetic marker. Although these studies have shown population structure in some parts of the North Atlantic, mitochondrial DNA is a single, maternally inherited locus and therefore insufficient to fully characterize population structure and history. Polymorphism at 11 microsatellite loci was analyzed in harbour porpoises collected throughout the range of the species in the Central and Eastern North Atlantic from the Iberian peninsula northward to Arctic waters (Portugal, Spain, bay of Biscay, Irish waters, English Channel, the southern bay of the North Sea, Norway, Faroe Islands, and Iceland) and also along the coasts of the Black Sea (Turkey, Ukraine, Bulgaria and Georgia). Multilocus tests for allele frequency differences and population structure estimates indicate complete genetic isolation between Atlantic and Black Sea porpoises. No fine population structure was observed within the Black Sea, and this population displayed a low genetic diversity compared to those of Atlantic. These results can be interpreted in the light of the demographic history of this relict population and the strong founder effect and bottleneck it may have undergone in its past evolution. In Eastern North Atlantic waters, microsatellite data revealed fine scale partitioning of the genetic variation. These results will be compared to the pattern previously reported based on the analysis of the mtDNA control region, and seem to correlate with variation in oceanographic features. [less ▲]

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 Heredity (2005), 94(1), 52-63

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 ... [more ▼]

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. [less ▲]

Genetic spatial structure of European common hamsters (Cricetus cricetus)--a result of repeated range expansion and demographic bottlenecks.

in Molecular Ecology (2005), 14(5), 1473-83

The spatial genetic structure of common hamsters (Cricetus cricetus) was investigated using three partial mitochondrial (mt) genes and 11 nuclear microsatellite loci. All marker systems revealed ... [more ▼]

The spatial genetic structure of common hamsters (Cricetus cricetus) was investigated using three partial mitochondrial (mt) genes and 11 nuclear microsatellite loci. All marker systems revealed significant population differentiation across Europe. Hamsters in central and western Europe belong largely to two allopatric mitochondrial lineages south and northwest of the Carpathian and Sudetes. The southern group, 'Pannonia', comprises populations inside the Carpathian basin (Czech Republic, Hungary) while the second group, 'North', includes hamsters from Belgium, the Netherlands, France, and Germany. Isolation of the lineages is maintained by a combination of geographical and ecological barriers. Both main phylogeographical groups show signs of further subdivision. North is separated into highly polymorphic central German and less polymorphic western populations, which most likely split during late glacial expansion (15,000-10,000 bp). Clock estimates based on haplotype distributions predict a divergence of the two major lineages 85,000-147,000 bp. Expansion times fall during the last glaciation (115,000-10,000 bp) corroborating fossil data, which identify Cricetus cricetus as characteristic of colder climatic phases. Despite the allopatry of mt haplotypes, there is an overlap of nuclear microsatellite alleles between phylogeographical units. Although there are strong evidence that Pannonian hamsters have persisted inside the Carpathian basin over the last 50,000 years, genetic differentiation among European hamsters has mainly been caused by immigration from different eastern refugia. Possible source populations are likely to be found in the Ukrainian and the southern Russian plains--core areas of hamster distribution. From there, hamsters have repeatedly expanded during the Quaternary. [less ▲]

Phylogeographic history of the yellow-necked fieldmouse (Apodemus flavicollis) in Europe and in the Near and Middle East.

in Molecular Phylogenetics & Evolution (2004), 32(3), 788-98

The exact location of glacial refugia and the patterns of postglacial range expansion of European mammals are not yet completely elucidated. Therefore, further detailed studies covering a large part of ... [more ▼]

The exact location of glacial refugia and the patterns of postglacial range expansion of European mammals are not yet completely elucidated. Therefore, further detailed studies covering a large part of the Western Palearctic region are still needed. In this order, we sequenced 972 bp of the mitochondrial DNA cytochrome b (mtDNA cyt b) from 124 yellow-necked fieldmice (Apodemus flavicollis) collected from 53 European localities. The aims of the study were to answer the following questions: Did the Mediterranean peninsulas act as the main refuge for yellow-necked fieldmouse or did the species also survive in more easterly refugia (the Caucasus or the southern Ural) and in Central Europe? What is the role of Turkey and Near East regions as Quaternary glacial refuges for this species and as a source for postglacial recolonisers of the Western Palearctic region? The results provide a clear picture of the impact of the quaternary glaciations on the genetic and geographic structure of the fieldmouse. This species survived the ice ages in two main refuges, the first one in the Italo-Balkan region; the second one in Turkey and the Near East regions. It is from the Balkan refuge that it recolonised all European regions at the end of the last glaciation. The Turkish and Near East populations are distinct from the European ones and they did not recolonise the Palearctic region probably because: (i) they were blocked by the Black Sea and the Caucasus, (ii) the long term presence of fieldmice populations in the Balkans prevented their expansion. These are genetically differentiated from the European and Russian ones and could be described as a particular subspecies. This result emphasises the importance of Turkey and the Near and Middle East regions as a refuge for Palearctic mammals. [less ▲]

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

in Molecular Ecology (2003), 12(3), 685-97

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 ... [more ▼]

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. [less ▲]