Gene flow across secondary contact zones of the Emys orbicularis complex in the Western Mediterranean and evidence for extinction and re‐introduction of pond turtles on Corsica and Sardinia (Testudines: Emydidae)

European pond turtles represent a phylogeographically deeply structured complex of distinct taxa. Here, we use mitochondrial DNA sequences (cytochrome b gene) and eight polymorphic microsatellite loci to investigate genetic differentiation and gene flow of Sicilian, Corsican and Sardinian pond turtles and of subspecies involved in two secondary contact zones in the Pyrenean region and Southern Italy. Mitochondrial and microsatellite differentiation is largely concordant in populations from the core regions of the distribution ranges of the studied taxa. Both marker systems provide no evidence for gene flow between Sicilian pond turtles (Emys trinacris) and Southern Italian subspecies of E. orbicularis. By contrast, in the contact zones limited gene flow occurs between distinct subspecies of E. orbicularis. Although the Southern Italian contact zone is significantly older than the Pyrenean contact zone of Holocene age, patterns of asymmetric introgression are similar. Introgressive hybridization leads to the exchange of mitochondria, but microsatellite data indicate only a few individuals with mixed ancestry. This suggests that incipient isolating mechanisms maintain largely discrete nuclear genomic gene pools. Furthermore, this implies that Southern Italy acted as a hotspot rather than as a melting pot of genetic diversity during the last glacial. Pond turtles from Corsica and Sardinia are not differentiated from continental populations of the subspecies E. o. galloitalica, neither in the mitochondrial nor in the quickly evolving microsatellite markers. As the fossil record argues for a continuous presence of pond turtles on both islands since the Middle Pleistocene, this suggests that the native island populations became extinct and the extant turtles were later introduced by prehistoric settlers. The lack of genetic differentiation of pond turtles from Corsica and Sardinia supports the view that the subspecies described from these islands are not valid.     

Historical introgression and the role of selective vs. neutral processes in structuring nuclear genetic variation (AFLP) in a circumpolar marine fish, the capelin (Mallotus villosus)

The capelin (Mallotus villosus) is a widespread marine fish species for which previous work has identified geographically distinct mtDNA clades, the frontiers of which are well within adult and larval dispersal capabilities. Here, we use AFLPs to test for the presence of nuclear gene flow among clades. In addition, we evaluate genetic structuring within one clade, the Northwest Atlantic (NWA). We found that each of the mtDNA clades corresponds with a unique nuclear DNA genetic cluster. Within the NWA clade, we detected individuals with small but significant amounts of genetic ancestry from other clades, likely due to historical introgression. Further support for historical introgression comes from analyses of variance in locus-specific differentiation, which support introgression between some clades and divergence without gene flow between others. Within the NWA, we identified two genetic clusters that correspond to sites in geographically adjacent areas. However, these clusters differ primarily at 'outlier' loci, and a genetic subdivision (K=2) was not supported by genetic clustering programs using neutral loci. Significant neutral F(ST) differentiation was found only between sites that otherwise differed at outlier loci. Thus, these populations may be in the initial stages of 'isolation by adaptation'. These results suggest strong between-clade reproductive isolation despite opportunities for gene flow and support the hypothesis that selection can contribute to divergence in otherwise 'open' systems.     

Phylogeographic analysis reveals a deep lineage split within North Atlantic Littorina saxatilis

Phylogeographic studies provide critical insight into the evolutionary histories of model organisms; yet, to date, range-wide data are lacking for the rough periwinkle Littorina saxatilis, a classic example of marine sympatric speciation. Here, we use mitochondrial DNA (mtDNA) sequence data to demonstrate that L. saxatilis is not monophyletic for this marker, but is composed of two distinct mtDNA lineages (I and II) that are shared with sister species Littorina arcana and Littorina compressa. Bayesian coalescent dating and phylogeographic patterns indicate that both L. saxatilis lineages originated in the eastern North Atlantic, around the British Isles, at approximately 0.64 Ma. Both lineages are now distributed broadly across the eastern, central and western North Atlantic, and show strong phylogeographic structure among regions. The Iberian Peninsula is genetically distinct, suggesting prolonged isolation from northeastern North Atlantic populations. Western North Atlantic populations of L. saxatilis lineages I and II predate the last glacial maximum and have been isolated from eastern North Atlantic populations since that time. This identification of two distinct, broadly distributed mtDNA lineages further complicates observed patterns of repeated incipient ecological speciation in L. saxatilis, because the sympatric origins of distinct ecotype pairs on eastern North Atlantic shores may be confounded by admixture of divergent lineages.     

Viola rupestris: molecular analyses to elucidate postglacial migration in Western Europe

Aim Our aim was to elucidate the postglacial migration of Viola rupestris F.W. Schmidt, with its two subspecies, rupestris and relicta Jalas, in Europe, using molecular methods. Location Norway, Sweden, Finland, England, the Netherlands, France and Switzerland. Methods Isoenzymes were analysed from 49 populations of Viola rupestris s.lat. Based on former experience of variation in the taxon, the following were included: aspartate aminotransferase, leucine/aminopeptidase, and phosphoglucomutase, yielding a total of nine interpretable and six variable (putative) loci. Results Six multilocus phenotypes were revealed (A–F). Phenotype A (only one individual) is restricted to northern Norway, B is shared by all populations in northern Norway and an isolated population on the west coast of southern Norway (Møre). Phenotype B comes close to C, co‐occurring with D in England, the latter also occurring in southern France. Phenotypes E and F occur in the rest of Europe. Main conclusions Viola rupestris ssp. relicta Jalas, previously known only from northern Scandinavia (northern unicentric), was discovered on the west coast of southern Norway (Møre), making the taxon ‘bicentric’. Populations are connected through a putative migration route from the Grands Causses in southern France (Massif Central) via England and western Norway to northern Scandinavia. The Grands Causses might represent a glacial refugium.     

Molecular evidence for glacial refugia of mountain plants in the European Alps

Many mountain ranges have been strongly glaciated during the Quaternary ice ages, and the locations of glacial refugia of mountain plants have been debated for a long time. A series of detailed molecular studies, investigating intraspecific genetic variation of mountain plants in the European Alps, now allows for a first synopsis. A comparison of the phylogeographic patterns with geological and palaeoenvironmental data demonstrates that glacial refugia were located along the southwestern, southern, eastern and northern border of the Alps. Additional glacial refugia were present in central Alpine areas, where high-elevation plants survived the last glaciation on ice-free mountain tops. The observed intraspecific phylogeographies suggest general patterns of glacial survival, which conform to well-known centres of Alpine species diversity and endemism. This implies that evolutionary or biogeographic processes induced by climatic fluctuations act on gene and species diversity in a similar way.     

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 post-glacial 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.     

Phylogeography of the Russian flying squirrel (Pteromys volans): implication of refugia theory in arboreal small mammal of Eurasia

A phylogeographical study of the Russian (Siberian) flying squirrel (Pteromys volans) was carried out using the complete mitochondrial (mt) cytochrome b gene sequences with special reference to the refugia theory for the arboreal traits of this species. We examined 31 specimens from 24 localities, resulting in 28 haplotypes. One breeding specimen with a unique haplotype from Hokkaido, Japan was included in the phylogenetic analysis. There were three mtDNA lineages: Hokkaido, Far Eastern, and northern Eurasia. Divergence data among lineages demonstrated that the Hokkaido group separated from the other groups during the Holsteinian interglacial. The phylogeographical pattern of P. volans is different from that previously reported for terrestrial rodents associated with treeless habitats. Unlike grasslands, forests decreased during glaciation and moved southward because of the cold and arid environmental conditions. The glacial refugia of P. volans would have been associated with forest dynamics in the Pleistocene.     

Phylogeographic analysis of the red seaweed Palmaria palmata reveals a Pleistocene marine glacial refugium in the English Channel

Phylogeography has provided a new approach to the analysis of the postglacial history of a wide range of taxa but, to date, little is known about the effect of glacial periods on the marine biota of Europe. We have utilized a combination of nuclear, plastid and mitochondrial genetic markers to study the biogeographic history of the red seaweed Palmaria palmata in the North Atlantic. Analysis of the nuclear rDNA operon (ITS1-5.8S-ITS2), the plastid 16S-trnI-trnA-23S-5S, rbcL-rbcS and rpl12-rps31-rpl9 regions and the mitochondrial cox2-3 spacer has revealed the existence of a previously unidentified marine refugium in the English Channel, along with possible secondary refugia off the southwest coast of Ireland and in northeast North America and/or Iceland. Coalescent and mismatch analyses date the expansion of European populations from approximately 128,000 BP and suggest a continued period of exponential growth since then. Consequently, we postulate that the penultimate (Saale) glacial maximum was the main event in shaping the biogeographic history of European P. palmata populations which persisted throughout the last (Weichselian) glacial maximum (c. 20,000 BP) in the Hurd Deep, an enigmatic trench in the English Channel.     

Microdistribution of chironomids (Diptera: Chironomidae) in Alpine streams: an autoecological perspective

Chironomid communities from three glacial and three non-glacial high mountain streams in three Alpine river basins were analyzed (Conca, Niscli, Cornisello, NE Italy, 46°N, 10°E). Eighteen sampling reaches belonging to five stream types (kryal, subkryal, glacio-rhithral, kreno-rhithral, outlet) were investigated. At each reach, geomorphological, physical, chemical and biological data were collected. Field surveys were carried out during three periods per year from 1996 to 1998: immediately after spring snowmelt, in mid-summer and in early autumn. In all, 439 zoobenthos samples were collected from 5 to 10 microhabitats of 0.1m² in each reach and date using a standard pond net (mesh size of 250m). About 50% of individuals collected were chironomids (26673 specimens, 53 taxa), with densities ranging from 4 to 2652indm^–2. With few exceptions, they dominated as number of taxa and individuals in all reaches. Chironomid subfamilies Diamesinae and Orthocladiinae were most abundant, especially in glacial reaches, where Diamesa spp. constituted up to 100% of the total fauna. Chironomid distribution was analyzed in relation to 37 abiotic variables, referring to stream origin, hydrology, geomorphology, physics and chemistry. Diamesa steinboecki, D. latitarsis gr. A and Pseudokiefferiella parva were the taxa best associated with glacial conditions (i.e. high channel instability or presence of bedrock, high suspended solids and total phosphorous content, low conductivity and silica content, highly variable diel discharge and low mean temperature), while Pseudodiamesa branickii, Corynoneura spp., Eukiefferiella spp., Parorthocladius nudipennis, Tvetenia calvescens/bavarica, Thienemaniella spp. and Micropsectra atrofasciata were mostly associated with non-glacial conditions. Substratum particle size, water depth, current velocity, the presence of riffles/pools and of mosses/algae (Hydrurus foetidus) were the major factors affecting microdistribution of chironomids in the investigated streams.