Molecular phylogeography of the viperine snake Natrix maura (Serpentes: Colubridae): Evidence for strong intraspecific differentiation

The molecular phylogeography of the viperine snake, Natrix maura (Linnaeus, 1758), was investigated using complete sequences of the mitochondrial cytochrome b gene and genomic ISSR-PCR fingerprinting. In a total of 120 samples, 44 unique cytochrome b haplotypes were found which defined three major genetic lineages associated with samples from Morocco, Tunisia and Europe, respectively. The same lineages were supported by nuclear data. A possible fourth lineage exists in southern Spain. Genetic distances of cytochrome b sequences between the three main lineages were in the range of 3.9–5.6%, suggesting independent evolution since the early Pliocene. Distinction of the three major lineages at the subspecies or species level is discussed to account taxonomically for the high intraspecific variation in the viperine snake. A more detailed analysis of the European samples based on genetic diversity indices and a network reconstruction suggests a complex Pleistocene history for the viperine snake in Europe. Clear differentiation was found between populations south and north of the central Iberian mountain ranges, suggesting Pleistocene glacial refugia both in the southern and northern Iberian peninsula. In the south, genetic diversity was associated with the main river valleys, whereas northern haplotypes were more broadly distributed, indicating gene flow or postglacial range expansions. Unexpectedly high levels of genetic variation in southeastern France and northwestern Italy would be compatible with the hypothesis of a glacial refugium north of the Pyrenees or in Italy. However, due to the dependence of N. maura on warm climates, the assumption of a northern refugium seems unwarranted. We believe that further sampling in northern Spain is likely to reveal genetically diverse populations which could have served as sources for postglacial recolonization of France and Italy.     

Genetic divergence and phylogeographic relationships among european perch (Perca fluviatilis) populations reflect glacial refugia and postglacial colonization

We used the widely distributed freshwater fish, perch (Perca fluviatilis), to investigate the postglacial colonization routes of freshwater fishes in Europe. Genetic variability within and among drainages was assessed using mitochondrial DNA (mtDNA) D-loop sequencing and RAPD markers from 55 populations all over Europe as well as one Siberian population. High level of structuring for both markers was observed among drainages and regions, while little differentiation was seen within drainages and regions. Phylogeographic relationships among European perch were determined from the distribution of 35 mtDNA haplotypes detected in the samples. In addition to a distinct southern European group, which includes a Greek and a southern Danubian population, three major groups of perch are observed: the western European drainages, the eastern European drainages including the Siberian population, and Norwegian populations from northern Norway, and western side of Oslofjord. Our data suggest that present perch populations in western and northern Europe were colonized from three main refugia, located in southeastern, northeastern and western Europe. In support of this, nested cladistic analysis of mtDNA clade and nested clade distances suggested historical range expansion as the main factor determining geographical distribution of haplotypes. The Baltic Sea has been colonized from all three refugia, and northeastern Europe harbours descendants from both eastern European refugia. In the upper part of the Danube lineages from the western European and the southern European refugia meet. The southern European refugium probably did not contribute to the recolonization of other western and northern European drainages after the last glaciation. However, phylogenetic analyses suggest that the southern European mtDNA lineage is the most ancient, and therefore likely to be the founder of all present perch lineages. The colonization routes used by perch probably also apply to other freshwater species with similar distribution patterns.     

Population genetic structure among populations of three predaceous nabid species: Nabis alternatus Parshley, Nabis roseipennis Reuter and Nabis americoferous Carayon (Hemiptera: Nabidae)

An electrophoretic survey of 28 presumptive loci distributed among 15 enzyme systems was conducted to determine the genetic structure among local populations of three predaceous nabid species: Nabis alternatus, N. roseipennis and N.americoferous in human-disturbed habitat. For all three species, F_IS values indicated a deficiency of heterozygotes at most loci in most populations. The amount of genetic differentiation based on the standardized variance, F_ST when combined across all poulations was 0.100 for N. alternatus, 0.189 for N. roseipennis, and 0.335 for N. americoferous. When local populations were grouped according to a set of defined geographical limits, based on the naturally occurring spatial arrangement of the sampled localities, some unexpected patterns of genetic variation were revealed. The degree of genetic differentiation detected among local populations of nabids is discussed in light of the frequent disruptions and ecological changes in their ephemeral habitats.     

The influence of Pleistocene glacial refugia on tawny owl genetic diversity and phylogeography in western Europe

The glacial refugia hypothesis indicates that during the height of the Pleistocene glaciations the temperate species that are today widespread in western Europe must have survived in small and climatically favourable areas located in the southern peninsulas of Iberia, Italy and Balkans. One such species is the tawny owl, a relatively sedentary, nonmigratory bird presently distributed throughout Europe. It is a tree-nesting species closely associated with deciduous and mixed coniferous woodlands. In this study I used control region mtDNA sequences from 187 individuals distributed among 14 populations to determine whether current genetic patterns in tawny owl populations were consistent with postglacial expansion from peninsular refugia. European, North African and Asian tawny owls were found to represent three distinct lineages, where North Africa is the sister clade to all European owls. Within Europe, I found three well-supported clades that correspond to each of the three allopatric refugia. Expansion patterns indicate that owls from the Balkan refugium repopulated most of northern Europe, while expansion out of Iberia and Italy had only regional effects leading to admixture in France. Estimates of population divergence times between refugia populations are roughly similar, but one order of magnitude smaller between Greece and northern Europe. Based on a wide range of mutation rates and generation times, divergence between refugia appears to date to the Pleistocene.     

Biogeographical connections between the Maghreb and the Mediterranean peninsulas of southern Europe

The glacial–interglacial cycles have caused severe range modifications of species' distributions. In Europe, thermophilic species had to retreat into geographically distinct southern refugia during glaciations. This process produced strong genetic imprints, which are still detectable by the present pattern of genetic differentiation and the distribution of regional diversity. To reveal the biogeographical imprints in the western Mediterranean, we analysed 26 populations of the butterfly Maniola jurtina spread over large areas of its European and North African distribution range. The samples were analysed using allozyme electrophoresis. We detected three genetic groups, divided into Western Europe, Central/Eastern Europe, and Italy with the Maghreb. The North African samples randomly cluster within the Italian samples. Even the population sampled in Morocco is genetically closely related to these samples and not to the geographically neighbouring Iberian ones. Parameters of genetic diversity showed similar values over the whole study area. The observed genetic pattern reflects possible glacial refugia in Europe located in the Iberian Peninsula and the Balkans. For North Africa and Italy, our data reveal a colonization of Africa originating from Italy.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 98 , 693–703.     

Mitochondrial differentiation and biogeography of Hyla meridionalis (Anura: Hylidae): an unusual phylogeographical pattern

Aim To study the patterns of genetic variation and the historical events and processes that influenced the distribution and intraspecific diversity in Hyla meridionalis Boettger, 1874. Location Hyla meridionalis is restricted to the western part of the Mediterranean region. In northern Africa it is present in Tunisia, Algeria and Morocco. In south‐western Europe it is found in the south of France, north‐western Italy and north‐eastern and south‐western Iberian Peninsula. There are also insular populations, as in the Canaries and Menorca. Methods Sampling included 112 individuals from 36 populations covering the range of the species. We used sequences of mitochondrial DNA Cytochrome Oxidase I (COI) for the phylogeographical analysis (841 bp) and COI plus a fragment including part of tRNA lysine, ATP synthase subunits 6 and 8 and part of Cytochrome Oxidase III for phylogenetic analyses (2441 bp). Phylogenetic analyses were performed with paup *4.0b10 (maximum likelihood, maximum parsimony) and Mr Bayes 3.0 (Bayesian analysis). Nested clade analysis was performed using tcs 1.18 and Geo Dis 2.2. A dispersal‐vicariant analysis was performed with diva 1.0 to generate hypotheses about the geographical distribution of ancestors. Results We found little genetic diversity within samples from Morocco, south‐western Europe and the Canary Islands, with three well‐differentiated clades. One is distributed in south‐western Iberia and the High Atlas, Anti‐Atlas and Massa River in Morocco. The second is restricted to the Medium Atlas Mountains. The third one is present in northern Morocco, north‐eastern Iberia, southern France and the Canaries. These three groups are also represented in the nested clade analysis. Sequences from Tunisian specimens are highly divergent from sequences of all other populations, suggesting that the split between the two lineages is ancient. diva analysis suggests that the ancestral distribution of the different lineages was restricted to Africa, and that an explanation of current distribution of the species requires three different dispersal events. Main conclusions Our results support the idea of a very recent colonization of south‐western Europe and the Canary Islands from Morocco. South‐western Europe has been colonized at least twice: once from northern Morocco probably to the Mediterranean coast of France and once from the western coast of Morocco to southern Iberia. Human transport is a likely explanation for at least one of these events. Within Morocco, the pattern of diversity is consistent with a model of mountain refugia during hyperarid periods within the Pleistocene. Evaluation of the phylogenetic relationships of Tunisian haplotypes will require an approach involving the other related hylid taxa in the area.     

Strait of Gibraltar: an effective gene-flow barrier for wind-pollinated Carex helodes (Cyperaceae) as revealed by DNA sequences, AFLP, and cytogenetic variation

The Strait of Gibraltar is the most important barrier disconnecting the landmasses of Europe and Africa on the western Mediterranean extreme. Carex helodes is a wind-pollinated species endemic to the western Mediterranean. Because molecular and cytogenetic data allow the inference of its evolutionary history, we analyzed variations in chromosome number, including meiotic chromosome behavior, amplified fragment length polymorphism (AFLP) fingerprints, and nucleotide substitutions in plastid and nuclear DNA sequences. Cytogeographic results showed that the African populations have stabilized at a single chromosome number of 2n = 74, whereas the most frequent cytotype in Iberia is 2n = 72. Phylogenetic reconstructions of 17 sequences from nine closely related species revealed that C. helodes is monophyletic and that the Moroccan populations are embedded in the Iberian lineages. The haplotype network is also consistent with a European origin of the northern African haplotype. AFLP analysis also revealed hierarchical levels of genetic variation compatible with a founder effect process responsible for the African populations. All sources of evidence support the hypothesis that the Strait of Gibraltar has been an effective gene-flow barrier, generating two isolated evolutionary lineages after their dispersal. Recent connections between the two lineages appear unlikely, whereas active gene flow occurs among populations within the two lineages.     

Intraspecific allozymatic differentiation reveals the glacial refugia and the postglacial expansions of European Erebia medusa (Lepidoptera: Nymphalidae)

Allozyme analysis of Erebia medusa over large regions of Europe revealed a significant population differentiation (F_ST: 0.149 ± 0.016). A UPGMA-analysis showed a division into four major lineages with mean inter-group genetic distances ranging from 0.051 (±0.010) to 0.117 (±0.024). An AMOVA revealed that rather more than two-thirds of the variance between samples was being between these lineages and less than one-third within lineages. An eastern group included the samples from the Czech Republic, Slovakia and north-eastern Hungary. This genetic lineage expressed significantly higher genetic diversity than the other three. A second lineage was formed by the samples from France and Germany. The two samples from western Hungary represent a third delimited lineage and the sample from northern Italy a fourth. We suppose that this genetic differentiation took place during the last ice-age in four disjunct refugia. The genetically more diverse eastern genetic lineage might have evolved in a relatively large refugium in south-eastern Europe. We assume that the other three lineages developed in relatively small relict areas around the Alps. It is likely for the western lineage that its ice-age distribution showed at least one disjunction in late Würm with the consequence of further genetic differentiation. Most probably, the eastern lineage colonized postglacial Central Europe using two alternative routes: one north and one south of the Carpathians. Up to now, neither similar glacial refugia, nor comparable secondary disjunctions in late Würm, are reported for any other animal or plant species.     

Genetic variation of Ardisia crenata in south China revealed by nuclear microsatellite

Ardisia crenata Sims, one of the most widely distributed Ardisia in the world, is an important ornamental and medicinal plant species. Using 7 polymorphic nuclear microsatellite loci, we studied the genetic variation of 20 natural populations of A. crenata across its distribution centre, the south China. Significant deviation from Hardy-Weinberg equilibrium in all populations and at all loci were detected, and the fixation index was high (F_IS = 0.725), indicating that inbreeding may be dominant in the mixed mating system of this self-compatible species. The average genetic diversity within populations was relatively low (H_S = 0.321). There was significant genetic differentiation among populations (F_ST = 0.583), which may be resulted from high level of inbreeding and low level of gene flow. A. crenata in south China can be roughly divided into eastern group and western group, consistent with the floristic division of Sino-Himalayan forest subkingdom and Sino-Japanese forest subkingdom. It was suggested that there may be separated glacial refugia in each region.     

Dispersal, landscape occupancy and population structure in the butterfly Melanargia galathea

Dispersal is a key ecological process linking metapopulation dynamics in the landscape to distribution patterns at larger spatial scales. In this study, we investigated the landscape occupancy and genetic population structure of a butterfly species, Melanargia galathea. Several landscapes differing in composition and structure were sampled as well as populations at different spatial scales. We found that M. galathea occupied 91.3% of all habitat patches available within a particular landscape, probably due to a dominance of landscape scale processes such as rescue effect and recolonisation. A high level of genetic polymorphism within the sampled populations and a very low amount of genetic differentiation between populations was observed (G_st=0.034), characteristic of species with high dispersal capacity and/or high density. High dispersal rates ensured considerable gene mixing at the landscape scale while the influence of distance on dispersal success was detected at the regional and continental scales by a significant amount of isolation by distance. We also found that, at the landscape scale, the dispersal of this butterfly species was influenced by the spatial distribution of its habitat patches.

Zusammenfassung

Die Ausbreitung ist ein ökologischer Schlüsselprozess, der die Metapopulationsdynamik in einer Landschaft mit den Verbreitungsmustern auf einer größeren räumlichen Skala verbindet. In dieser Studie untersuchten wir die Verbreitungsmuster und die genetische Populationsstruktur einer Schmetterlingsart, Melanargia galathea. Es wurden sowohl einige Landschaften beprobt, die sich in der Zusammensetzung und der Struktur unterschieden, als auch Populationen auf verschiedenen räumlichen Skalen. Wir fanden, dass M. galathea 91.3% aller verfügbaren Habitatflecken in einer bestimmten Landschaft besetzte, möglicherweise aufgrund der Dominanz von Landschaftsskalenprozessen wie “Rescue-Effekt” und Rekolonisation. Es wurde ein hoher genetischer Polymorphismuslevel und ein sehr geringer Umfang genetischer Differenzierung innerhalb der beprobten Populationen beobachtet (G_st=0.034), was charakteristisch für Arten mit einer großen Ausbreitungsfähigkeit und/oder hoher Dichte ist. Hohe Ausbreitungsraten sicherten eine beträchtliche Genvermischung auf der Landschaftsskala, während der Einfluss der Entfernung auf den Verbreitungserfolg auf der regionalen und kontinentalen Skala durch einen signifikanten Anteil der Isolation aufgrund von Entfernung festgestellt wurde. Wir fanden auch, dass auf der Landschaftsskala die Ausbreitung dieses Schmetterlings durch die räumliche Verteilung der Habitatflecken beeinflusst wurde.     

Phylogeography, genetic structure and diversity in the endangered bearded vulture (Gypaetus barbatus, L) as revealed by mitochondrial DNA

Bearded vulture populations in the Western Palearctic have experienced a severe decline during the last two centuries that has led to the near extinction of the species in Europe. In this study we analyse the sequence variation at the mitochondrial control region throughout the species range to infer its recent evolutionary history and to evaluate the current genetic status of the species. This study became possible through the extensive use of museum specimens to study populations now extinct. Phylogenetic analysis revealed the existence of two divergent mitochondrial lineages, lineage A occurring mainly in Western European populations and lineage B in African, Eastern European and Central Asian populations. The relative frequencies of haplotypes belonging to each lineage in the different populations show a steep East-West clinal distribution with maximal mixture of the two lineages in the Alps and Greece populations. A genealogical signature for population growth was found for lineage B, but not for lineage A; futhermore the Clade B haplotypes in western populations and clade A haplo-types in eastern populations are recently derived, as revealed by their peripheral location in median-joining haplotype networks. This phylogeographical pattern suggests allopatric differentiation of the two lineages in separate Mediterranean and African or Asian glacial refugia, followed by range expansion from the latter leading to two secondary contact suture zones in Central Europe and North Africa. High levels of among-population differentiation were observed, although these were not correlated with geographical distance. Due to the marked genetic structure, extinction of Central European populations in the last century re-sulted in the loss of a major portion of the genetic diversity of the species. We also found direct evidence for the effect of drift altering the genetic composition of the remnant Pyrenean population after the demographic bottleneck of the last century. Our results argue for the management of the species as a single population, given the apparent ecological exchangeability of extant stocks, and support the ongoing reintroduction of mixed ancestry birds in the Alps and planned reintroductions in Southern Spain.     

Phylogeography and genetic structuring of European nine-spined sticklebacks (Pungitius pungitius)-mitochondrial DNA evidence

As a consequence of colonisation from different glacial refugia, many northern European taxa are split into distinct western and eastern lineages. However, as for the nine-spined stickleback (Pungitius pungitius), the exact location of the contact zone between lineages often remains poorly known. We assessed the genetic differentiation and diversity in the nine-spined stickleback within Europe using 1037 base pairs of cytochrome b sequence for 320 individuals from 57 locations, including pond, lake, river, and coastal habitats. Our main aims were (i) to locate the contact zone between the previously recognized western and eastern lineages, (ii) investigate latitudinal patterns in genetic diversity, (iii) compare genetic diversity among different habitat types, and (iv) date the known split between eastern and western lineages. The data revealed the split between eastern and western to be located across the Danish Straits and roughly following the Norway/Sweden border to the North. Reference sites from Canada form their own clades, and one of the Canadian sites was found to have a haplotype common to the Eastern European lineage, possibly representing an ancestral polymorphism. The split between the two European clades was dated to approximately 1.48 million years ago (Mya), and between Canada and Europe to approximately 1.62 Mya. After controlling for habitat effects, nucleotide (but not haplotype) diversity across populations decreased with increasing latitude. Coastal populations showed significantly higher haplotype diversity (but not nucleotide diversity) than pond populations, but there were no detectable differences in haplotype diversity among different freshwater habitat types (viz. river, lake and pond populations), or between coastal and lake/river populations. Sequences were found to cluster according to their geographic proximity, rather than by habitat type, and all habitat types were found within each major clade, implying that colonisation and adaptation between the coastal and freshwater environments in different regions must have occurred in parallel.     

Phylogeography of western Palaearctic reptiles – Spatial and temporal speciation patterns

A phylogeographic analysis of eight species complexes of European reptiles was performed using different molecular methods. While mitochondrial genes (mainly cytochrome b sequences) enabled conclusions about phylogeography and differentiation, additional application of bisexually inherited markers provided information about speciation stages. As species with similar distribution patterns in southern and Central Europe were selected, matching phylogeographic patterns are useful for drawing general conclusions:

(1) The species complexes are in different stages of speciation. In some cases, cryptic species were detected.

(2) Highest genetic diversity occurs in southern Europe, the Near East and the Caucasus, regions corresponding with glacial refuges in the Iberian, Apennine and Balkan Peninsulas as well as in Turkey and the Caucasus. Often, several microrefugia must have existed in close neighbourhood. Additional microrefugia were located in southern France and in the Carpathian Basin.

(3) North Africa and the Middle East did not serve as glacial refuges for Central or northern European lineages and are typically inhabited by independent clades.

(4) Evidence for multiple range retractions and expansions, which were postulated for the times of Pleistocene climatic oscillations, could be found in the Balkans, but in Central Europe their traces have been wiped out by the last glacial. Only the Holocene invasion has left imprints in the genomes from this area.

(5) Central and northern Europe were recolonized from Balkan and Pontic refugia in the Holocene.

(6) Groups from the Iberian and Apennine Peninsulas rarely conquered other regions. This limitation can be attributed to the barrier function of the Pyrenees and the Alps.

Ancient forest fragmentation or recent radiation? Testing refugial speciation models in chameleons within an African biodiversity hotspot

Aim East Africa is one of the most biologically diverse regions, especially in terms of endemism and species richness. Hypotheses put forward to explain this high diversity invoke a role for forest refugia through: (1) accumulation of new species due to radiation within refugial habitats, or (2) retention of older palaeoendemic species in stable refugia. We tested these alternative hypotheses using data for a diverse genus of East African forest chameleons, Kinyongia. Location East Africa. Methods We constructed a dated phylogeny for Kinyongia using one nuclear and two mitochondrial markers. We identified areas of high phylogenetic diversity (PD) and evolutionary diversity (ED), and mapped ancestral areas to ascertain whether lineage diversification could best be explained by vicariance or dispersal. Results Vicariance best explains the present biogeographic patterns, with divergence between three major Kinyongia clades (Albertine Rift, southern Eastern Arc, northern Eastern Arc) in the early Miocene/Oligocene (> 20 Ma). Lineage diversification within these clades pre‐dates the Pliocene (> 6 Ma). These dates are much older than the Plio‐Pleistocene climatic shifts associated with cladogenesis in other East African taxa (e.g. birds), and instead point to a scenario whereby palaeoendemics are retained in refugia, rather than more recent radiations within refugia. Estimates of PD show that diversity was highest in the Uluguru, Nguru and East Usambara Mountains and several lineages (from Mount Kenya, South Pare and the Uluguru Mountains) stand out as being evolutionarily distinct as a result of isolation in forest refugia. PD was lower than expected by chance, suggesting that the phylogenetic signal is influenced by an unusually low number of extant lineages with long branch lengths, which is probably due to the retention of palaeoendemic lineages. Main conclusions The biogeographic patterns associated with Kinyongia are the result of long evolutionary histories in isolation. The phylogeny is dominated by ancient lineages whose origins date back to the early Miocene/Oligocene as a result of continental wide forest fragmentation and contraction due to long term climatic changes in Africa. The maintenance of palaeoendemic lineages in refugia has contributed substantially to the remarkably high biodiversity of East Africa.     

Is the last glaciation the only relevant event for the present genetic population structure of the meadow brown butterfly Maniola jurtina (Lepidoptera: Nymphalidae)?

Phylogeographical studies are available for a considerable number of European species, but few analyses exist for temperate species with very large and fairly continuous populations that are also absent from Northern Europe. Therefore, we studied the butterfly Maniola jurtina as a model for this group. The species has two major genetic lineages (mean genetic distance between lineages: 0.033; F _CT: 0.052), most probably evolving in glacial differentiation centres in the western and eastern Mediterranean. The onset of this differentiation might have been the beginning of the last glacial stage maximum some 40 kyr bp . A hybrid zone between these two lineages exists in western Central Europe. No genetic substructures have been found within the two lineages ( F _SC: 0.017) and average genetic distances are very small. Therefore, it is highly probable that postglacial expansion was of the phalanx type. There is, at most, very limited differentiation at regional and local scales. However, the genetic diversity within populations is high (means: A : 2.68; H _E: 17.2%; P : 78%), as would be predicted for such a common species. Comparison of these results with a published allozyme analysis revealed a similar phylogeographical pattern, but lower genetic diversity in the latter. Morphological patterns of wings and genitalia show similar geographical patterns as allozyme data.   © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 85 , 419–431.     

Geographical and Ecological Drivers of Mitonuclear Genetic Divergence in a Mediterranean Grasshopper

The study of the neutral and/or selective processes driving genetic variation in natural populations is central to determine the evolutionary history of species and lineages and understand how they interact with different historical and contemporary components of landscape heterogeneity. Here, we combine nuclear and mitochondrial data to study the processes shaping genetic divergence in the Mediterranean esparto grasshopper (Ramburiella hispanica). Our analyses revealed the presence of three main lineages, two in Europe that split in the Early-Middle Pleistocene and one in North Africa that diverged from the two European ones after the Messinian. Lineage-specific potential distribution models and tests of environmental niche differentiation suggest that the phylogeographic structure of the species was driven by allopatric divergence due to the re-opening of the Gibraltar strait at the end of the Messinian (Europe–Africa split) and population fragmentation in geographically isolated Pleistocene climatic refugia (European split). Although we found no evidence for environment as an important driver of genetic divergence at the onset of lineage formation, our analyses considering the spatial distribution of populations and different aspects of landscape composition suggest that genetic differentiation at mitochondrial loci was largely explained by environmental dissimilarity, whereas resistance-based estimates of geographical distance were the only predictors of genetic differentiation at nuclear markers. Overall, our study shows that although historical factors have largely shaped concordant range-wide patterns of mitonuclear genetic structure in the esparto grasshopper, different contemporary processes (neutral gene flow vs. environmental-based selection) seem to be governing the spatial distribution of genetic variation in the two genomes.     

Genetically diverse but with surprisingly little geographical structure: the complex history of the widespread herb Carex nigra (Cyperaceae)

Aim Based on extensive range‐wide sampling, we address the phylogeographical history of one of the most widespread and taxonomically complex sedges in Europe, Carex nigra s. lat. We compare the genetic structure of the recently colonized northern areas (front edge) and the long‐standing southern areas (rear edge), and assess the potential genetic basis of suggested taxonomic divisions at the rank of species and below. Location Amphi‐Atlantic, central and northern Europe, circum‐Mediterranean mountain ranges, central Siberia, Himalayas. Methods A total of 469 individuals sampled from 83 populations, covering most of the species’ range, were analysed with amplified fragment length polymorphism (AFLP) and chloroplast DNA (cpDNA) markers. Bayesian clustering, principal coordinates analysis, and estimates of diversity and differentiation were used for the analysis of AFLP data. CpDNA data were analysed with statistical parsimony networks and maximum parsimony and Bayesian inference of phylogenetic trees. Results Overall genetic diversity was high, but differentiation among populations was limited. Major glacial refugia were inferred in the Mediterranean Basin and in western Russia; in addition, there may have been minor refugia in the North Atlantic region. In the southern part of the range, we found high levels, but geographically quite poorly structured genetic diversity, whereas the levels of genetic diversity varied among different areas in the north. North American populations were genetically very similar to the European populations. Main conclusions The data are consistent with extensive gene flow, which has obscured the recent history of the taxon. The limited differentiation in the south probably results from the mixing of lineages expanding from several local refugia. Northward post‐glacial colonization resulted in a leading‐edge pattern of low diversity in the Netherlands, Belgium, Scotland and Iceland, whereas the observed high diversity levels in Fennoscandia suggest broad‐fronted colonization from the south as well as from the east. The patterns found in the American populations are consistent with post‐glacial colonization, possibly even with anthropogenic introduction from Europe. Our data also suggest that the tussock‐forming populations of C. nigra, often referred to as a distinct species (Carex juncella), represent an ecotype that has originated repeatedly from different populations with creeping rhizomes.     

Rangewide phylogeography of a bird-dispersed Eurasian shrub: contrasting Mediterranean and temperate glacial refugia

We studied the phylogeography of alder buckthorn (Frangula alnus), a bird-dispersed shrub or small tree distributed over most of Europe and West Asia and present in three of the four main refugia of West Palaearctic temperate woody plants: the Iberian Peninsula, the Balkans and Anatolia. A total of 78 populations from 21 countries were analysed for chloroplast DNA variation using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), and 21 different haplotypes were distinguished. We found a very strong overall population differentiation (GST = 0.81) and phylogeographical structure, and a sharp contrast between the haplotype-rich refugia and the almost completely uniform area of postglacial colonization. The haplotype network comprises three lineages made up of haplotypes from the Iberian Peninsula, Anatolia with the Caucasus, and temperate Europe. The Iberian and the Anatolian branches represent parts of a major lineage that spans over the whole northern Mediterranean Basin and some neighbouring areas and probably dates back to the Tertiary. Many haplotypes of this lineage are distributed locally and most populations are fixed for a single haplotype; these populations have apparently been very stable since their establishment, experiencing negligible gene flow and few mutations. The temperate European lineage consists of one very widespread and abundant plus six locally distributed haplotypes. Four of them are located in Southeast Europe, the putative refugium of all extant temperate European populations. Contrary to populations from Iberia and Anatolia, F. alnus populations from the southeastern European refugium have most genetic variation within populations. Bird-mediated seed dispersal has apparently allowed not only a very rapid postglacial expansion of F. alnus but also subsequent regular seed exchanges between populations of the largely continuous species range in temperate Europe. In contrast, the disjunct F. alnus populations persisting in Mediterranean mountain ranges seem to have experienced little gene flow and have therefore accumulated a high degree of differentiation, even at short distances. Populations from the southern parts of the glacial refugia have contributed little to the postglacial recolonization of Europe, but their long-term historical continuity has allowed them to maintain a unique store of genetic variation.     

Genetic diversity and phylogeography of the European roe deer: the refuge area theory revisited

The extant taxa of central and northern Europe are commonly believed to derive from Pleistocene ancestors, who moved to the north from three separate glacial refugia: the Iberian and Italian peninsulae, as well as the southern Balkans. The issue of postglacial dispersal patterns was addressed through the investigation of population structure and phylogeography of the European roe deer, Capreolus capreolus . The genetic diversity in 376 individuals representing 14 allegedly native populations across their European range was assessed, using ten autosomal microsatellite loci and restriction fragment length polymorphisms of the mitochondrial D-loop and NADH dehydrogenase 1 gene segments. Our results suggest the existence of three major genetic lineages of roe deer in Europe. One comprises populations in the south-western limit of the species' distribution (i.e. Iberia), where an internal substructure splits a northern from a southern sublineage. A second lineage includes populations of southern and eastern Europe, as well as a separate sublineage sampled in central-southern Italy, where the existence of the subspecies Capreolus c. italicus was supported. In central-northern Europe, a third lineage is present, which appeared genetically rather homogeneous, although admixed, and equally divergent from both the eastern and western lineages. Current patterns of intraspecific genetic variation suggest that postglacial recolonization routes of this cervid to northern Europe could be due to range expansion from one or more refugia in central-eastern Europe, rather than proceeding from the Mediterranean areas.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 85–100.