Evolutionary history of the Maltese wall lizard Podarcis filfolensis: insights on the ‘Expansion–Contraction’ model of Pleistocene biogeography

The expansion–contraction (EC) model predicts demographic and range contraction of temperate species during Pleistocene glaciations as a consequence of climate‐related habitat changes, and provides a paradigm for explaining the high intraspecific diversity found in refugia in terms of long‐term demographic stability. However, recent evidence has revealed a weak predictive power of this model for terrestrial species in insular and coastal settings. We investigated the Pleistocene EC dynamics and their evolutionary consequences on temperate species using the Maltese archipelago and its endemic lizard Podarcis filfolensis as a model system. The evolutionary and demographic history of P. filfolensis as inferred from mitochondrial and nuclear sequences data does not conform to the EC model predictions, supporting (i) demographic and spatial stability or expansion, rather than contraction, of the northern and southern lineages during the last glacial period; and (ii) a major role for allopatric differentiation primed by sea‐level dynamics, rather than prolonged demographic stability, in the formation of the observed genetic diversity. When combined with evidence from other Mediterranean refugia, this study shows how the incorporation of Pleistocene sea‐level variations in the EC model accounts for a reverse demographic and range response of insular and coastal temperate biotas relative to continental ones. Furthermore, this cross‐archipelago pattern in which allopatric diversity is formed and shaped by EC cycles resembles that seen between isolated populations within mainland refugia and suggests that the EC model, originally developed to explain population fluctuations into and out‐of refugia, may be appropriate for describing the demographic and evolutionary dynamics driving the high genetic diversity observed in these areas.     

Tracing the evolutionary history of the mole,Talpa europaea,through mitochondrial DNA phylogeography and species distribution modelling

Our understanding of the effect of Pleistocene climatic changes on the biodiversity of European mammals mostly comes from phylogeographical studies of non‐subterranean mammals, whereas the influence of glaciation cycles on subterranean mammals has received little attention. The lack of data raises the question of how and to what extent the current amount and distribution of genetic variation in subterranean mammals is the result of Pleistocene range contractions/expansions. The common mole (Talpa europaea) is a strictly subterranean mammal, widespread across Europe, and represents one of the best candidates for studying the influence of Quaternary climatic oscillation on subterranean mammals. Cytochrome b sequences, as obtained from a sampling covering the majority of the distribution area, were used to evaluate whether Pleistocene climate change influenced the evolution of T. europaea and left a trace in the genetic diversity comparable to that observed in non‐subterranean small mammals. Subsequently, we investigated the occurrence of glacial refugia by comparing the results of phylogeographical analysis with species distribution modelling. We found three differentiated mitochondrial DNA lineages: two restricted to Spain and Italy and a third that was widespread across Europe. Phylogenetic inferences and the molecular clock suggest that the Spanish moles represent a highly divergent and ancient lineage, highlighting for the first time the paraphyly of T. europaea. Furthermore, our analyses suggest that the genetic break between the Italian and the European lineages predates the last glacial phase. Historical demography and spatial principal component analysis further suggest that the Last Glacial Maximum left a signature both in the Italian and in the European lineages. Genetic data combined with species distribution models support the presence of at least three putative glacial refugia in southern Europe (France, Balkan Peninsula and Black Sea) during thelast glacial maximum that likely contributed to post‐glacial recolonization of Europe. By contrast, the Italian lineage remained trapped in the Italian peninsula and, according to the pattern observed in other subterranean mammals, did not contribute to the recolonization of northern latitudes. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 495–512.     

Phylogeography and historical demography of the Lusitanian snail <Emphasis Type="Italic">Elona quimperiana</Emphasis> reveal survival in unexpected separate glacial refugia

Background  

Present day distributions of Palearctic taxa in northern latitudes mainly result from populations having survived in local patches during the Late Pleistocene and/or from recolonizing populations from southern temperate refugia. If well-studied Mediterranean and eastern European refugia are widely accepted, some recent biogeographical assumptions still remain unclear, such as the occurrence of multiple glacial refugia in Iberia and cryptic refugia in northern Europe during the last glaciations. The Lusitanian snail Elona quimperiana has a remarkably disjunct distribution, limited to northwestern France (Brittany), northwestern Spain and the Basque Country. By describing the phylogeographical structure of this species across its entire range, the present study attempts to identify refugia and subsequent recolonization routes.     

Interglacial genetic diversification of Moussonia deppeana (Gesneriaceae), a hummingbird‐pollinated,cloud forest shrub in northern Mesoamerica

Recent empirical work on cloud forest‐adapted species supports the role of both old divergences across major geographical areas and more recent divergences attributed to Pleistocene climate changes. The shrub Moussonia deppeana is distributed in northern Mesoamerica, with geographically disjunct populations. Based on sampling throughout the species range and employing plastid and nuclear markers, we (i) test whether the fragmented distribution is correlated with main evolutionary lineages, (ii) reconstruct its phylogeographical history to infer the history of cloud forest in northern Mesoamerica and (iii) evaluate a set of refugia/vicariance scenarios for the region and demographic patterns of the populations whose ranges expanded and tracked cloud forest conditions during the Last Glacial Maximum. We found a deep evolutionary split in M. deppeana about 6–3 Ma, which could be consistent with a Pliocene divergence. Comparison of variation in plastid and nuclear markers revealed several lineages mostly congruent with their isolated geographical distribution and restricted gene flow among groups. Results of species distribution modelling and coalescent simulations fit a model of multiple refugia diverging during interglacial cycles. The demographic history of M. deppeana is not consistent with an expanding–contracting cloud forest archipelago model during the Last Glacial Maximum. Instead, our data suggest that populations persisted across the geographical range throughout the glacial cycles, and experienced isolation and divergence during interglacial periods.     

Cryptic diversity of Italian bats and the role of the Apennine refugium in the phylogeography of the western Palaearctic

The Mediterranean Basin is typified by a high degree of species rarity and endemicity that reflects its position, geomorphology, and history. Although the composition and cryptic variation of the bat faunas from the Iberian and Balkan Peninsulas are relatively well studied, data from the Apennine Peninsula are still incomplete. This is a significant shortfall, given the presumed refugial role of this region in the context of Europe's Pleistocene phylogeography. It was thus our aim to supplement the phylogeographical information from the region, generating mitochondrial sequences and reviewing published data, with a focus on the dispersal and diversification patterns characterizing taxa with different life strategies. Site‐specific lineages were ascertained, especially in the genera Myotis and Plecotus and amongst the pipistrelloid bats, representing speciose radiations. It was possible to observe disjunct ranges with patches isolated south of the Alps in several species, corresponding with evolution of elevated genetic distance. The genetic subdivision within the continuous Italian range into northern and southern lineages in several taxa indicated the possible past substructure of the refugium. Several shared lineages between the Apennine and Ibero‐Maghrebian regions were observed, indicating connectivity between the Adriatic and Atlantic?Mediterranean refuges, and raising questions as to which region these clades originated from and what was the direction of faunal exchange between them. In contrast to Europe's other two main refugia, the Apennine Peninsula is a smaller region with simpler phylogeographical patterns. Nevertheless, our results support the idea that the region generated novel lineages. Whereas diversification in sedentary bats may have been driven through the generation of in situ adaptations, specialization, and niche differentiation, the emergence of species with a tramp strategy could have entailed the utilization of faunal drift and the taxon cycle. © 2015 The Linnean Society of London     

Living in a tilted world: climate change and geography limit speciation in Old World anchovies (Engraulis; Engraulidae)

Historical changes in the distributions of temperate species in response to Milankovitch climate cycles have been well documented in palaeontological studies and recently evaluated with phylogeographical methods. How these cycles influence biological diversity remains a matter of debate. Molecular surveys of terrestrial and freshwater fauna demonstrate glacial refugia in low latitudes and range expansions into high latitudes, but few genetic studies have assessed the corresponding impact on marine fauna. In the present study, mtDNA sequences (N = 84) are surveyed to understand the impact of long‐term climate oscillations on ‘Old World’ anchovies (genus Engraulis), a monophyletic group occurring in north and south temperate zones of the eastern Atlantic and the western Pacific. The analysis of a 521‐bp sequence of mtDNA cytochrome b indicates a late Miocene or Pliocene dispersal from the north‐eastern Pacific (California–Mexico) to the north‐western Pacific (Japan), followed by Pleistocene dispersal from the north‐western Pacific to Europe. Geography mandates that populations in southern Africa and Australia were stepping‐stones for this dispersal. However, neither population occupies an intermediate position in the mtDNA genealogy; both populations are more recently derived from their northern neighbours. Haplotype diversity is high (h = 0.93–0.97) in European, Australian, and Japanese anchovies, but low (h = 0.22) in the southern African population, where all haplotypes are more closely related to European specimens than to each other. These southern populations occupy a precarious position, lacking north–south coastlines that allow range shifts during climatic extremes. Recurring extinctions and episodic recolonizations from northern hemisphere populations are the likely results. In this case, ocean‐climatic changes retard rather than enhance opportunities for evolutionary radiations. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 88 , 673–689.     

Phylogeography of two cryptic species of African desert jerboas (Dipodidae: Jaculus)

The lesser Egyptian jerboa Jaculus jaculus is a desert dwelling rodent that inhabits a broad Arabian–Saharan arid zone. Recently, two distant sympatric lineages were described in North‐West Africa, based on morphometric and molecular data, which may correspond to two cryptic species. In the current study, phylogenetic relationships and phylogeographical structure among those lineages and geographical populations from North Africa and the Middle East were investigated. The phylogeographical patterns and genetic diversity of the cytochrome b gene (1110 bp) were addressed on 111 jerboas from 41 localities. We found that the variation in Africa is partitioned into two divergent mitochondrial clades (10.5% divergence relating to 1.65–4.92 Mya) that corresponds to the two cryptic species: J. jaculus and J. deserti. Diversifications within those cryptic species/clades were dated to 0.23–1.13 Mya, suggesting that the Middle Pleistocene climatic change and its environmental consequences affected the evolutionary history of African jerboas. The third distant clade detected, found in the Middle East region, most likely represents a distinct evolutionary unit, independent of the two African lineages. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ??, ??–??.     

Complex phylogeography in the Southern Smooth Snake (Coronella girondica) supported by mtDNA sequences

Palearctic reptiles with wide distribution through the Western Mediterranean are expected to display genetic substructuring because of the combining effects of current or past geographic barriers and climate fluctuations. We have examined this issue by sequencing cytochrome b and 16S rRNA mitochondrial fragments of 80 individuals of the snake Coronella girondica from 71 localities, covering the range of the species across Tunisia, Algeria, Morocco, Spain, Portugal, southern France and north‐western Italy. According to the obtained genealogy, C. girondica is structured into three divergent and well‐supported clades (north‐western Africa, Betic range and Iberia–France–Italy), which greatly match other phylogeographies already published for this region. Our estimations suggest that the divergence among the three clades took place approximately 1.4‐2.0 Ma, which roughly coincides with the Plio‐Pleistocene transition, characterized by an increase in climate variability. The existence of a clade in a narrow belt of south‐eastern Iberia represents another example of the high endemism rate of the region, with a key geographical situation and an important role in vicariant processes. Since the split among the three major lineages would be take place after the opening of the Strait of Gibraltar, overwater dispersal is here suggested. The subsequent genetic substructuring of these clades during the Pleistocene fits within the refugia‐within‐refugia model, highlighting the importance of the region as a scenario for multiple vicariant events.     

Glacial refugia influence plant diversity patterns in the Mediterranean Basin

Aim The aims of this study were to assess the distribution of putative Mediterranean refugia of plants, to compare the locations of refugia and those of regional hotspots of plant biodiversity, and to provide a critical analysis of the Mediterranean refugium paradigm. Furthermore, we consider how biogeographical and genetic results can be combined to guide global conservation strategies. Location The Mediterranean region. Methods We started from a detailed analysis of the scientific literature (1993–2007) in order to identify refugia in the Mediterranean region, based on intra‐specific phylogeographical studies of plant species. We used population locations together with gene‐pool identity to establish the database, comparing patterns of phylogeographical concordance with the locations of Mediterranean refugia. We then tested the biogeographical congruence between two biodiversity components, namely phylogeographical refugia and regional hotspots. Results We identified 52 refugia in the Mediterranean bioclimatic region and confirmed the role played by the three major peninsulas, with a shared total of 25 refugia. We emphasize the importance of areas that have previously been attributed a lesser role (large Mediterranean islands, North Africa, Turkey, Catalonia). Of the 52 refugia identified, 33 are situated in the western Mediterranean Basin and 19 in the eastern part. The locations of the phylogeographically defined refugia are significantly associated with the 10 regional hotspots of plant biodiversity, with 26 of these refugia (i.e. 50%) occurring within the hotspots. Main conclusions The locations of refugia are determined by complex historical and environmental factors, the cumulative effects of which need to be considered because they have occurred since the Tertiary, rather than solely during the last glacial period. Refugia represent climatically stable areas and constitute a high conservation priority as key areas for the long‐term persistence of species and genetic diversity, especially given the threat posed by the extensive environmental change processes operating in the Mediterranean region. The refugia defined here represent ‘phylogeographical hotspots’; that is, significant reservoirs of unique genetic diversity favourable to the evolutionary processes of Mediterranean plant species.     

Plastid and nuclear DNA polymorphism reveals historical processes of isolation and reticulation in the olive tree complex (Olea europaea)

Aim The olive tree is considered one of the best indicators of the Mediterranean climate. The species’ distribution is associated with geographical and bioclimatic factors, as well as being influenced by a long period of cultivation. Despite concerted efforts of different research groups, the origin of the Mediterranean olive tree still remains elusive. In the present study, relationships between taxa and populations covering the entire range of Olea europaea were investigated using both maternal (plastid genome) and biparental (nuclear genome) markers to disclose evolutionary patterns in the olive complex. Phylogenetic and phylogeographical results of the two‐genome analyses were interpreted in a biogeographical context. Location Mediterranean, temperate and subtropical floristic regions of the Old World. Methods Phylogeographical reconstructions of plastid DNA polymorphism were performed using microsatellites, restriction sites and indels on a wide sample of 185 representative trees across the Old World, including 28 herbarium specimens from remote areas. Additionally, the potential utility of one ITS‐1 pseudogene for phylogenetic analyses was explored using Bayesian and maximum parsimony approaches on a subsample of 38 olive trees. Results Forty plastid haplotypes were recognized and split into two lineages and seven sublineages. The analysis of ITS‐1 sequences also allowed the identification of seven well differentiated groups. Distribution of plastid and ribosomal DNA lineages was congruent, but particular cases of phylogenetic incongruence were disclosed (particularly in the Sahara and Madeira). Lastly, two divergent ITS‐1 copies were isolated from the same sample of four individuals of different subspecies. Main conclusions Phylogenetic congruence of both ITS‐1 and plastid lineages suggested an evolutionary scenario of predominant isolation during the Plio‐Pleistocene in Macaronesia, the Mediterranean, southern Africa, eastern Africa and Asia. The Saharan desert appeared to have played an important role of vicariant barrier between southern and northern African populations in early times. Incongruence of some plastid and nuclear results, as well as intermingled ITS‐1 copies of different lineages in single individuals, was interpreted as a result of recurrent reticulation events in the olive complex. We identified an ancient hybrid zone from the Sahara to north‐eastern African mountains, where divergent plastid and nuclear lineages still co‐exist. Results of this paper, and previous studies, suggest that the cultivated olive originated from a pre‐Quaternary Mediterranean ancestor, with no evidence for a recent hybrid origin. In contrast, a continuous process of olive domestication through local hybridization events of cultivated trees with natural populations may have brought about a remarkably high genomic diversity among cultivated trees across the Mediterranean.     

On glacial refugia,genetic diversity,and microevolutionary processes: deep phylogeographical structure in the endemic newt Lissotriton italicus1

We investigated the phylogeographical patterns of Lissotriton italcus, a newt endemic to the Italian peninsula, aiming to determine why hotspots of intraspecific diversity so ‘hot’. We found two main mitochindrial DNA lineages (net sequence divergence of 6.8% at two fragments of total length of 1897 bp): one restricted to part of the Calabrian peninsula (i.e the southernmost portion of the species range) and the other widespread throughout the rest of the species range. Both lineages, which had a parapatric distribution, showed evidence of further subdivisions, with an overall number of eight terminal haplogroups, most of whose times to the most recent common ancestors were estimated at the Late Pleistocene. Analysis of molecular variance suggested that partitioning populations according to the geographical distribution of these haplogroups can explain 97% of the observed genetic variation. These results suggest that L. italicus underwent repeated cycles of allopatric fragmentation throughout the Pleistocene, and that it likely survived the Late Pleistocene paleoenvironmental changes within eight separate refugia. Thus, the current hotspot of intraspecific diversity of L. italicus (within the Calabrian peninsula) has not been moulded by long‐term stability of large populations but rather by multiple events of allopatric fragmentation and divergence. When compared with the patterns recently identified in other species, these results suggest that the occurrence of phases of allopatric divergence (eventually followed by secondary admixture) could be a common, albeit probably underrated feature in the history of formation of hotspots of intraspecific diversity. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 42–55.     

Northern richness and southern poverty: contrasting genetic footprints of glacial refugia in the relictual tree Sciadopitys verticillata (Coniferales: Sciadopityaceae)

Sciadopitys verticillata is amongst the most relictual of all plants, being the last living member of an ancient conifer lineage, the Sciadopityaceae, and is distributed in small and disjunct populations in high rainfall regions of Japan. Although mega‐fossils indicate the persistence of the species within Japan through the Pleistocene glacial–interglacial cycles, how the species withstood the colder and drier climates of the glacials is not well known. The present study utilized phylogeography and palaeodistribution modelling to test whether the species survived within pollen‐based coastal temperate forest glacial refugia or within previously unidentified refugia close to its current range. Sixteen chloroplast haplotypes were found that displayed significant geographical structuring. Unexpectedly, northern populations in central Honshu most distant from coastal refugia had the highest chloroplast diversity and were differentiated from the south, a legacy of glacial populations possibly in inland river valleys close to its current northern range. By contrast, populations near putative coastal refugia in southern Japan, harboured the lower chloroplast diversity and were dominated by a single haplotype. Fragment size polymorphism at a highly variable and homoplasious mononucleotide repeat region in the trnT‐trnL intergenic spacer reinforced the contrasting patterns of diversity observed between northern and southern populations. The divergent histories of northern and southern populations revealed in the present study will inform the management of this globally significant conifer. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 108 , 263–277.     

Phylogeography of red deer (Cervus elaphus) in Europe

Aim To investigate the phylogeographical patterns of red deer (Cervus elaphus) in Europe, and to disentangle the influence of ancient (e.g. Pleistocene ice ages) from more recent processes (e.g. human translocations). Location Europe. Methods In this study we provide by far the most extensive analysis of genetic structure in European red deer, based on analyses of variation at two mitochondrial markers (cyt b and D‐loop) in a large number of individuals from 39 locations. Relationships of mitochondrial DNA haplotypes were determined using minimum spanning networks and phylogenetic analyses. Population structure was examined by analyses of molecular variance. Historical processes shaping the present patterns were inferred from nested clade analysis and nucleotide diversity statistics. Results Within Europe, we detected three deeply divergent mitochondrial DNA lineages. The three lineages displayed a phylogeographical pattern dividing individuals into western European, eastern European and Mediterranean (Sardinia, Spain and Africa) groups, suggesting contraction into three separate refugia during the last glaciation. Few haplotypes were shared among these three groups, a finding also confirmed by F_ST values. Calculations of divergence times suggest that the groups probably split during the Pleistocene. Main conclusions The observed pattern is interpreted to result from isolation in different refugia during the last glaciation. The western and eastern European lineages could be linked to an Iberian and Balkan refugium, respectively. The third lineage might originate from a Sardinian or African refugium. We link local phylogeographical patterns observed in Europe to the post‐glacial recolonization process, shaped by the geographical localization of refugia and barriers to gene flow. Regardless of the importance of red deer as a game species and the tradition of translocating red deer in Europe, we detected few individuals that did not match the trichotomous pattern, suggesting that translocations have occurred mainly at smaller spatial scales.     

One Species, Three Pleistocene Evolutionary Histories: Phylogeography of the Italian Crested Newt, Triturus carnifex

Phylogeographic patterns of temperate species from the Mediterranean peninsulas have been investigated intensively. Nevertheless, as more phylogeographies become available, either unique patterns or new lines of concordance continue to emerge, providing new insights on the evolution of regional biotas. Here, we investigated the phylogeography and evolutionary history of the Italian crested newt, Triturus carnifex, through phylogenetic, molecular dating and population structure analyses of two mitochondrial gene fragments (ND2 and ND4; overall 1273 bp). We found three main mtDNA lineages having parapatric distribution and estimated divergence times between Late Pliocene and Early Pleistocene. One lineage (S) was widespread south of the northern Apennine chain and was further geographically structured into five sublineages, likely of Middle Pleistocene origin. The second lineage (C) was widespread throughout the Padano-Venetian plain and did not show a clear phylogeographic structure. The third lineage (N) was observed in only two populations located on western Croatia/Slovenia. Results of analysis of molecular variance suggested that partitioning populations according to the geographic distribution of these lineages and sublineages explains 76% of the observed genetic variation. The phylogeographic structure observed within T. carnifex and divergence time estimates among its lineages, suggest that responses to Pleistocene environmental changes in this single species have been as diverse as those found previously among several codistributed temperate species combined. Consistent with the landscape heterogeneity, physiographic features, and palaeogeographical evolution of its distribution range, these responses encompass multiple refugia along the Apennine chain, lowland refugia in large peri-coastal plains, and a 'cryptic' northern refugium.     

Multiple periglacial refugia in the Patagonian steppe and post‐glacial colonization of the Andes: the phylogeography of Calceolaria polyrhiza

Aim We perform a phylogeographical study of an endemic Patagonian herbaceous plant to assess whether geographical patterns of genetic variation correspond to in situ Pleistocene survival or to glacial retreat and post‐glacial expansion. We also seek to determine the locations of potential glacial refugia and post‐glacial colonization routes. Location Southern Andes and Patagonian steppe. Methods We used Calceolaria polyrhiza, a widely distributed Patagonian herbaceous plant that occurs mainly in the understorey of Nothofagus rain forests and in the arid Patagonian steppe, as our model system. The chloroplast intergenic spacer trnH–psbA was sequenced for 590 individuals from 68 populations. Sequence data were analysed using phylogenetic (maximum parsimony, maximum likelihood and Bayesian inference) and population genetic (spatial analyses of molecular variance, mismatch distributions and neutrality tests) methods. Nested clade phylogeographic analyses, and divergence time estimates using a calibrated molecular clock, were also conducted. Results A total of 27 haplotypes identified in the present study clustered into four primary genealogical lineages, revealing three significant latitudinal phylogeographical breaks. The two high Andean lineages probably split first, during the late Miocene, and the Patagonian lineage split around 4 Ma, coincident with the establishment of the Patagonian steppe. Within each haplogroup, major diversification occurred in the Pleistocene. The Patagonian groups show a pattern consistent with a rapid post‐glacial expansion and colonization of the Andean flanks, achieved independently by four lineages. The highest haplotype diversity was found along a longitudinal transect that is remarkably congruent with the limit of the ice‐sheet extension during the Greatest Patagonian Glaciation. A north‐east expansion is evident, which is probably associated with the ‘Arid Diagonal’ fluctuations. Main conclusions Glacial climate fluctuations had a substantial impact on the diversification, distribution and demography of the study species. A scenario of multiple periglacial Pleistocene refugia and subsequent multiple recolonization routes, from eastern Patagonia to the Andean flanks, may explain the phylogeographical patterns observed. However, current genetic structure also preserves the imprints of older events that probably occurred in the Miocene and Pliocene, providing evidence that multiple processes, operating at different spatial and temporal scales, have moulded biodiversity in Patagonia.     

Population genetic structure of the bank vole Myodes glareolus within its glacial refugium in peninsular Italy

It is now well established that Southern European peninsulas have been major glacial refugia for temperate species during Pleistocene climatic oscillations. However, substantial environmental changes occurred also within these peninsulas throughout the Pleistocene, raising questions about the role and interplay of various microevolutionary processes in shaping patterns of intraspecific diversity within these areas. Here, we investigate the patterns of genetic variation in the bank vole Myodes glareolus within the Italian peninsula. By using a panel of 13 microsatellite loci, we found more intraspecific variation than expected based on previous assessments. Indeed, both Bayesian and ordination‐based clustering analyses of variation recovered five main geographic/genetic clusters along the peninsula, with three clusters geographically restricted to the southern portion of the peninsula. This clustering is supported by previous evidences of some morphological distinctiveness among these populations. This pattern can be explained by a refugia‐within‐refugia scenario, with the occurrence of multiple sub‐refugia for the bank vole within the Italian peninsula, likely promoted by the major palaeo‐environmental changes which affected forested habitats within this area during the Pleistocene. Moreover, our results support a scenario whereby the high levels of intraspecific diversity observed within major Pleistocene refugia are better explained by dynamic microevolutionary processes occurred within these areas, rather than by long‐term demographic stability of refugial population. Finally, the narrow and isolated distribution of some of the identified lineages suggests the need for future assessments of their conservation and taxonomic status.     

Phylogeography of a subalpine tall‐herb Ranunculus platanifolius (Ranunculaceae) reveals two main genetic lineages in the European mountains

A phylogeographical analysis of Ranunculus platanifolius, a typical European subalpine tall‐herb species, indicates the existence of two main genetic lineages based on amplified fragment length polymorphism (AFLP) markers. One group comprises populations from the Balkan Peninsula and the south‐eastern Carpathians and the other includes the remaining part of the range of the species, encompassing the western Carpathians, Sudetes, Alps, Pyrenees and Scandinavia. The main phylogeographical break observed in this species runs across the Carpathians and separates the main parts of this range (western and south‐eastern Carpathians), supporting a distinct glacial history of populations in these areas. The high genetic similarity of the Balkan Peninsula and south‐eastern Carpathian populations could indicate a common glacial refugium for these contemporarily isolated areas of species distribution. The western and northern part of the species range displays an additional weak differentiation into regional phylogeographical groups, which could have been shaped by isolation in glacial refugia or even by a postglacial isolation. The observed weak phylogeographical structure could also be linked with ecological requirements, allowing survival along streams in relatively low, forested mountain ranges. © 2013 The Linnean Society of London     

Phylogeography of an Italian endemic salamander (genus Salamandrina): glacial refugia,postglacial expansions,and secondary contact

The Italian endemic genus Salamandrina has been historically regarded as monotypic but, recently, studies based on both mitochondrial and nuclear markers have indicated the existence of two distinct species of spectacled salamanders: Salamandrina perspicillata, in central and northern Italy, and Salamandrina terdigitata, in southern Italy. We analyzed nucleotide variation at mitochondrial and nuclear genes [cytochrome b, 12S and 16S rRNA, recombination activating gene (RAG 1)] in 223 individuals from 56 locations, aiming to investigate their genetic structure and recent evolutionary histories. Phylogenetic and phylogeographical analyses revealed the existence of three and two genetically distinct groups of populations in northern and southern salamander, respectively. Historical demographic analyses led to the inference of range expansion for both species in the late Pleistocene. During the last glacial stage, each salamander survived in a single refugium, namely the southern in Calabria and the northern in central Italy. At the end of this period, both lineages expanded northward and established secondary contact. Spatial distribution of RAG 1 haplotype variation revealed two differentiated population groups corresponding to the major mitochondrial (mt)DNA clades. Nuclear pattern of introgressive hybridization was more extensive than the highly limited introgression of mtDNA markers. From a conservation standpoint, southern Latium and Calabria proved to be the major genetic diversity reservoirs, thus deserving particular conservation efforts. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 903–922.     

Population genetic structure and diversity of the Apennine endemic stream frog, Rana italica--insights on the Pleistocene evolutionary history of the Italian peninsular biota

For most species in the Western Palaearctic region, southern Mediterranean peninsulas have been identified as major Quaternary refugia and hotspots of intraspecific diversity, and thus, as areas of particular relevance for the conservation of the evolutionary potential. We analysed the patterns of geographical variation among 26 populations of the Italian stream frog, using both nuclear (allozymes) and mitochondrial (partial cytochrome b sequences) markers. Phylogenetic, phylogeographical and population genetic analyses suggested that the species survived the last glacial–interglacial cycles in two distinct refugia, one restricted to the tip of the Calabrian peninsula, at the extreme south of the species' range, the other spanning from central Calabria to central Apennines and showing evidences for further population subdivision therein. Historical demographic tests suggested a significant population expansion from the latter, which most likely began around the last pleniglacial. This expansion would have led to the rapid colonization of the northern Apennines to the north, and to a secondary contact and population admixture with the population from the southern refugium in southern central Calabria. A comparison of the evolutionary history inferred for the Italian stream frog with the data emerging for other codistributed species suggests: (i) the generality of a multiple-refugia scenario for the Italian peninsula, (ii) the possible occurrence of at least one suture zone in southern Italy, and (iii) that for most species, this Pleistocene refugium is not only a hotspot, but also a melting pot of intraspecific genetic diversity. Finally, the conservation implications of these results are also briefly highlighted.     

A multilocus sequencing approach reveals the cryptic phylogeographical history of Phyllodoce nipponica Makino (Ericaceae)

Discordant phylogeographical patterns among species with similar distributions may not only denote specific biogeographical histories of different species, but also could represent stochastic variance of genealogies in applied genetic markers. A multilocus investigation representing different genomes can be used to address the latter concern, allowing robust inference to biogeographical history. In the present study, we conducted a multilocus phylogeographical analysis to re‐examine the genetic structuring of Phyllodoce nipponica, in which chloroplast (cp)DNA markers exhibited a discordant pattern compared to those of other alpine plants. The geographical structure of sequence variation at five nuclear loci was not consistent with that of cpDNA and showed differentiation between the northern and southern parts of the range of this species. Its demographic history inferred from the isolation‐with‐migration model suggests that the north–south divergence originated from Pleistocene vicariance. In addition, the demographic parameters showed a lack of chloroplast‐specific gene flow, suggesting that stochastic variance in genealogy resulted in the discordant geographical structure. Thus, P. nipponica probably experienced Pleistocene vicariance between its southern and northern range parts in concordance with other alpine plants in the Japanese archipelago. The findings of the present study demonstrates the importance of using a multilocus approach for inferring population dynamics, as well as for reconciling discordant phylogeographical patterns among species. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 214–226.