The role of topography in structuring the demographic history of the pine processionary moth,Thaumetopoea pityocampa (Lepidoptera: Notodontidae)

Aim We investigated the Quaternary history of the pine processionary moth, Thaumetopoea pityocampa, an oligophagous insect currently expanding its range. We tested the potential role played by mountain ranges during the post‐glacial recolonization of western Europe. Location Western Europe, with a focus on the Pyrenees, Massif Central and western Alps. Methods Maternal genetic structure was investigated using a fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene. We analysed 412 individuals from 61 locations and performed maximum likelihood and maximum parsimony phylogenetic analyses and hierarchical analysis of molecular variance, and we investigated signs of past expansion. Results A strong phylogeographic pattern was found, with two deeply divergent clades. Surprisingly, these clades were not separated by the Pyrenees but rather were distributed from western to central Iberia and from eastern Iberia to the Italian Peninsula, respectively. This latter group consisted of three shallowly divergent lineages that exhibited strong geographic structure and independent population expansions. The three identified lineages occurred: (1) on both sides of the Pyrenean range, with more genetically diverse populations in the east, (2) from eastern Iberia to western France, with a higher genetic diversity in the south, and (3) from the western Massif Central to Italy. Admixture areas were found at the foot of the Pyrenees and Massif Central. Main conclusions The identified genetic lineages were geographically structured, but surprisingly the unsuitable high‐elevation areas of the main mountainous ranges were not responsible for the spatial separation of genetic groups. Rather than acting as barriers to dispersal, mountains appear to have served as refugia during the Pleistocene glaciations, and current distributions largely reflect expansion from these bottlenecked refugial populations. The western and central Iberian clade did not contribute to the northward post‐glacial recolonization of Europe, yet its northern limit does not correspond to the Pyrenees. The different contributions of the identified refugia to post‐glacial expansion might be explained by differences in host plant species richness. For example, the Pyrenean lineage could have been trapped elevationally by tracking montane pines, while the eastern Iberian lineage could have expanded latitudinally by tracking thermophilic lowland pine species.     

Imprints of multiple glacial refugia in the Pyrenees revealed by phylogeography and palaeodistribution modelling of an endemic spider

Mediterranean mountain ranges harbour highly endemic biota in islandlike habitats. Their topographic diversity offered the opportunity for mountain species to persist in refugial areas during episodes of major climatic change. We investigate the role of Quaternary climatic oscillations in shaping the demographic history and distribution ranges in the spider Harpactocrates ravastellus, endemic to the Pyrenees. Gene trees and multispecies coalescent analyses on mitochondrial and nuclear DNA sequences unveiled two distinct lineages with a hybrid zone around the northwestern area of the Catalan Pyrenees. The lineages were further supported by morphological differences. Climatic niche‐based species distribution models (SDMs) identified two lowland refugia at the western and eastern extremes of the mountain range, which would suggest secondary contact following postglacial expansion of populations from both refugia. Neutrality test and approximate Bayesian computation (ABC) analyses indicated that several local populations underwent severe bottlenecks followed by population expansions, which in combination with the deep population differentiation provided evidence for population survival during glacial periods in microrefugia across the mountain range, in addition to the main Atlantic and Mediterranean (western and eastern) refugia. This study sheds light on the complexities of Quaternary climatic oscillations in building up genetic diversity and local endemicity in the southern Europe mountain ranges.     

Population genetic structure of rock ptarmigan in the 'sky islands' of French Pyrenees: implications for conservation

Expected consequences of global warming include habitat reduction in many cool climate species. Rock ptarmigan is a Holarctic grouse that inhabits arctic and alpine tundra. In Europe, the Pyrenean ptarmigan inhabits the southern edge of the species' range and since the last glacial maximum its habitat has been severely fragmented and is restricted to high-alpine zones or 'sky islands'. A recent study of rock ptarmigan population genetic in Europe found that the Pyrenean ptarmigan had very low genetic diversity compared with that found in the Alps and Scandinavia. Habitat fragmentation and reduced genetic diversity raises concerns about the viability of ptarmigan populations in the Pyrenees. However, information on population structuring and gene flow across the Pyrenees, which is essential for designing a sound management plan, is absent. In this study, we use seven microsatellites and mitochondrial control region sequences to investigate genetic variation and differentiation among five localities across the Pyrenees. Our analyses reveal the presence of genetic differentiation among all five localities and a significant isolation-by-distance effect that is likely the result of short dispersal distances and high natal and breeding philopatry of Pyrenean ptarmigan coupled with severe habitat fragmentation. Furthermore, analysis of molecular variance, principal component analysis and Bayesian analysis of genetic structuring identified the greatest amount of differentiation between the eastern and main parts of the Pyrenean chain separated by the Sègre Valley. Our data also show that the Canigou massif may host an isolated population and requires special conservation attention. We propose a management plan which includes the translocation of birds. If a sky island structure affects genetic divergence in rock ptarmigan, it may also affect the genetic structure of other sky island species having low dispersal abilities.     

Multiple glacial refugia and contemporary dispersal shape the genetic structure of an endemic amphibian from the Pyrenees

Historical factors (colonization scenarios, demographic oscillations) and contemporary processes (population connectivity, current population size) largely contribute to shaping species’ present‐day genetic diversity and structure. In this study, we use a combination of mitochondrial and nuclear DNA markers to understand the role of Quaternary climatic oscillations and present‐day gene flow dynamics in determining the genetic diversity and structure of the newt Calotriton asper (Al. Dugès, 1852), endemic to the Pyrenees. Mitochondrial DNA did not show a clear phylogeographic pattern and presented low levels of variation. In contrast, microsatellites revealed five major genetic lineages with admixture patterns at their boundaries. Approximate Bayesian computation analyses and linear models indicated that the five lineages likely underwent separate evolutionary histories and can be tracked back to distinct glacial refugia. Lineage differentiation started around the Last Glacial Maximum at three focal areas (western, central and eastern Pyrenees) and extended through the end of the Last Glacial Period in the central Pyrenees, where it led to the formation of two more lineages. Our data revealed no evidence of recent dispersal between lineages, whereas borders likely represent zones of secondary contact following expansion from multiple refugia. Finally, we did not find genetic evidence of sex‐biased dispersal. This work highlights the importance of integrating past evolutionary processes and present‐day gene flow and dispersal dynamics, together with multilocus approaches, to gain insights into what shaped the current genetic attributes of amphibians living in montane habitats.     

Genetic structure of montane isolates of Pinus sylvestris L. in a Mediterranean refugial area

Aim This work investigates the population genetic effects of periodic altitudinal migrations and interstadial fragmentation episodes in long‐term Scots pine (Pinus sylvestris L.) populations at a regional scale. Location The study focuses on Scots pine populations in the northern Meseta and peripheral mountain chains, central and north‐western Iberian Peninsula. The ample macrofossil record in the area shows that this 60,000‐km² region represent a glacial refugium for Scots pine. The species occupied large areas on the Meseta plains during glacial cold stages, but it has periodically sheltered at high elevation in the surrounding mountain chains during warm episodes, conforming to a fragmented pattern similar to its present‐day distribution. Methods We perform a fine‐scale chloroplast microsatellite (cpSSR) survey to assess the genetic structure of 13 montane Scots pine isolates in the northern Meseta (total N = 322 individuals). Using a hierarchical analysis of molecular variance (amova ), we test the hypothesis of genetic isolation among disjunct mountain areas. We use a standard coalescence model to estimate genealogical relationship among populations, investigating the potential role of the regional relief as a factor influencing historic gene exchange among Scots pine populations. Results Population haplotypic diversity was high among Scots pine populations (H_e = 0.978), greater than values reported for other more thermophilic pine species in the Iberian Peninsula. The amova revealed low (but significant) differentiation among populations (Φ_ST = 0.031, P = 0.010), showed that the disjoint montane distribution could not account for the genetic divergence among areas (Φ_CT = 0.012, P = 0.253), and that there was non‐trivial subdivision among populations within the same mountain region (Φ_SC = 0.021, P = 0.012). The genealogical relationships among populations showed that Scots pine isolates growing on disjoint mountain blocks, but on slopes flowing to the same basin, were genetically closer than populations growing on different slopes of the same mountain chain, flowing to different basins. Main conclusions The observed genetic structure for Scots pine is consistent with its population history, inferred from the palaeobotanical record, with vertical migrations throughout climatic pulses and with the drainage basins and large long‐term population sizes connecting different mountain blocks during the cooler glacial periods. Overall, the results suggest that, despite periodic interstadial fragmentation episodes, Scots pine biology provides for the long‐term maintenance of high within‐population and low among‐population genetic diversity at neutral genetic markers.     

Contrasting phylogeographies inferred for the two alpine sister species Cardamine resedifolia and C. alpina (Brassicaceae)

Aim We use Cardamine alpina and C. resedifolia as models to address the detailed history of disjunctions in the European alpine system. These species grow on siliceous bedrock: C. alpina in the Alps and Pyrenees, and C. resedifolia in several mountain ranges from the Sierra Nevada to the Balkans. We explore differentiation among their disjunct populations as well as within the contiguous Alpine and Pyrenean ranges, and compare the phylogeographical histories of these diploid sister species. We also include samples of the closely related, arctic diploid C. bellidifolia in order to explore its origin and post‐glacial establishment. Location European alpine system, Norway and Iceland. Methods We employed amplified fragment length polymorphisms (AFLPs). AFLP data were analysed using principal coordinates analysis, neighbour joining and Bayesian clustering, and measures of diversity and differentiation were computed. Results For the snow‐bed species C. alpina (27 populations, 203 plants) we resolved two strongly divergent lineages, corresponding to the Alps and the Pyrenees. Although multiple glacial refugia were invoked in the Pyrenees, we inferred only a single one in the Maritime Alps – from which rapid post‐glacial colonization of the entire Alps occurred, accompanied by a strong founder effect. For C. resedifolia (33 populations, 247 plants), which has a broader ecological amplitude and a wider distribution, the genetic structuring was rather weak and did not correspond to the main geographical disjunctions. This species consists of two widespread and largely sympatric main genetic groups (one of them subdivided into four geographically more restricted groups), and frequent secondary contacts exist between them. Main conclusions The conspicuously different histories of these two sister species are likely to be associated with their different ecologies. The more abundant habitats available for C. resedifolia may have increased the probability of its gradual migration during colder periods and also of successful establishment after long‐distance dispersal, whereas C. alpina has been restricted by its dependence on snow‐beds. Surprisingly, the arctic C. bellidifolia formed a very divergent lineage with little variation, contradicting a scenario of recent, post‐glacial migration from the Alps or Pyrenees.     

Southern isolation and northern long‐distance dispersal shaped the phylogeography of the widespread,but highly disjunct,European high mountain plant Artemisia eriantha (Asteraceae)

We investigated the range dynamics of Artemisia eriantha, a widespread, but rare, mountain plant with a highly disjunct distribution in the European Alpine System. We focused on testing the roles of vicariance and long‐distance dispersal in shaping the current distribution of the species. To this end, we collected AFLP and plastid DNA sequence data for 17 populations covering the entire distributional range of the species. Strong phylogeographical structure was found in both datasets. AFLP data suggested that almost all populations were genetically strongly differentiated, with 58% of the overall genetic variation partitioned among populations. Bayesian clustering identified five groups of populations: Balkans, Pyrenees, Central Apennines, one southwestern Alpine population and a Widespread cluster (eastern Pyrenees, Alps, Carpathians). Major groups were supported by neighbor‐joining and NeighbourNet analyses. Fourteen plastid haplotypes were found constituting five strongly distinct lineages: Alps plus Pyrenees, Apennines, Balkans, southern Carpathians, and a Widespread group (eastern Pyrenees, northern Carpathians, Mt. Olympus). Plastid DNA data suggested that A. eriantha colonized the European Alpine System in a westward direction. Although, in southern Europe, vicariant differentiation among the Iberian, Italian and Balkan Peninsulas predominated, thus highlighting their importance as glacial refugia for alpine species, in temperate mountain ranges, long‐distance dispersal prevailed. This study emphasizes that currently highly disjunct distributions can be shaped by both vicariance and long‐distance dispersal, although their relative importance may be geographically structured along, for instance, latitude, as in A. eriantha. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 174 , 214–226.     

Contrasting patterns of nuclear microsatellite genetic structure of Fraxinus mandshurica var. japonica between northern and southern populations in Japan

Aim The aim of this study is to detect extant patterns of population genetic structure of Fraxinus mandshurica var. japonica in Japan, and to provide insights into the post‐glacial history of this species during the Holocene. Location Hokkaido and Honshu islands, Japan (including the Oshima and Shimokita peninsulas). Methods We examined nine polymorphic nuclear microsatellite loci to assess genetic variation within and among 15 populations across almost the entire range of the species in Japan. Extant patterns of geographical structure were analysed using Bayesian clustering, Monmonier’s algorithm, analysis of molecular variance, Mantel tests and principal coordinates analysis. Recent bottlenecks within populations and regional genetic variation were also assessed. Results Northern populations (Hokkaido Island and the Shimokita Peninsula) formed a single homogeneous deme, maintaining the highest level of allelic diversity on the Oshima Peninsula. By contrast, southern populations (Honshu Island) demonstrated strong substructure on both coasts. Specifically, populations on the Pacific side of Honshu exhibited significant bottlenecks and erosion of allelic diversity but preserved distinct subclusters diverging from widespread subclusters on the Japan Sea side of this island. Main conclusions Genetic evidence and life history traits suggest that F. mandshurica occupied cryptic northern refugia on the Oshima Peninsula during the Last Glacial Maximum, which is reflected in the species’ extant northern distribution. Strong geographical structure in southern populations, in agreement with fossil pollen records, suggests geographical isolation by mountain ranges running north–south along Honshu. Given that this tree species is cold‐adapted and found in riparian habitats, populations on the Pacific side of Honshu probably contracted into higher‐elevation swamps during warm post‐glacial periods, leading to a reduction of effective population sizes and rare allelic richness.     

The molecular population structure of the tall forb Cicerbita alpina (Asteraceae) supports the idea of cryptic glacial refugia in central Europe

There is an ongoing debate about the glacial history of non‐arctic species in central and northern Europe. The two main hypotheses are: (1) postglacial colonization from refugia outside this region; (2) glacial survival in microclimatically favourable sites within the periglacial areas. In order to clarify the glacial history of a boreo‐montane tall forb, we analysed AFLPs from populations of Cicerbita alpina through most of its range (Scandinavia, the mountains of central Europe, the Alps, the Pyrenees and the Balkan Peninsula). We found a major differentiation between the Pyrenean population and all others, supported by principal coordinate, neighbour joining and STRUCTURE analyses. Furthermore, three populations from the central and north‐eastern Alps were genetically distinct from the bulk of populations from Scandinavia, central Europe, the Alps and the Balkan Peninsula. Most populations, including those from central and northern Europe, had moderate to high levels of genetic diversity (mean Shannon index H_Sh = 0.292, mean percentage of polymorphic loci P = 54.1%, mean Nei's gene diversity H = 0.195). The results indicate separate glacial refugia in the Pyrenean region and the Italian Alps. Furthermore, they provide evidence of glacial persistence in cryptic refugia north of the Alps, from where Scandinavia and most of the Alps are likely to have been colonized following deglaciation. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 164 , 142–154.     

Molecules and models indicate diverging evolutionary effects from parallel altitudinal range shifts in two mountain Ringlet butterflies

Quaternary climatic oscillations caused severe range expansions and retractions of European biota. During the cold phases, most species shifted to lower latitudes and altitudes, and expanded their distribution range northwards and to higher elevations during the warmer interglacial phases. These range shifts produced contrasting distribution dynamics, forming geographically restricted distribution patterns but also panmictic distributions, strongly dependent on the ecologic demands of the species. The two closely related butterfly species Erebia ottomana Herrich‐Schäffer, 1847 and Erebia cassioides (Reiner & Hohenwarth, 1792) show subalpine and alpine distribution settings, respectively. Erebia ottomana is found up to the treeline (1400–2400 m a.s.l.), whereas E. cassioides reaches much higher elevations (from about 1800 m a.s.l. in the Retezat Mountains, in Romania, to 2800 m a.s.l.). Thus, both species cover diverging climatic niches, and thus might also have been distributed differently during the cold glacial stages. Individuals of these two species were sampled over the mountain areas of the Balkan Peninsula and genetically analysed using allozyme electrophoresis. Additionally, we performed species distribution models (SDMs) to simulate the distribution patterns of both species in the past (i.e. during the Last Glacial Maximum and the Atlanticum). Our genetic data show contrasting structures, with comparatively low genetic differentiation but high genetic diversity found in E. ottomana, and with stronger genetic differentiation and a lower level of genetic diversity, including many endemic alleles, occurring restricted to single mountain massifs in E. cassioides. The SDMs support a downhill shift during glacial periods, especially for E. ottomana, with possible interconnection among mountain regions. We conclude that during the cold glacial phases, both species are assumed to shift downhill, but persisted at different elevations, with E. ottomana reaching the foothills and spreading over major parts of the Balkan Peninsula. In contrast, E. cassioides (the truly alpine species) survived in the foothills, but did not reach and spread over lowland areas. This more widespread distribution at the Balkan Peninsula of E. ottomana compared with E. cassioides is strongly supported by our distribution models. As a consequence, long‐term geographic restriction to distinct mountain massifs in E. cassioides versus panmixia in E. ottomana produced two contrasting evolutionary scenarios. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112 , 569–583.     

Divergence and diversity: lessons from an arctic-alpine distribution (Pardosa saltuaria group, Lycosidae)

The relationship of interpopulation genetic divergence and within-population diversity has been studied for many temperate species in Europe, but not for the cold-adapted fauna. Here we present the first European-wide phylogeographical study of an arctic-alpine distribution in invertebrates, focusing on wolf spiders of the Pardosa saltuaria group. One hundred twenty-seven (127) specimens from 14 populations were examined. Within Europe, these populations were distributed among six high mountain ranges and Scandinavia. We sequenced the whole 921 base pair mitochondrial (mt) ND1 gene. The resulting 55 unique haplotypes form three monophyletic phylogroups of deep divergence: a Pyrenean, a Balkan and a 'northern' clade. Genetic distances (3.6-4.0%) between the major clades indicate that the arctic-alpine range disjunction was initiated by vicariance events, which precede the four major Alpine glaciations. However, low divergence and incomplete lineage sorting within the 'northern clade' suggest a late Pleistocene separation of the Alpine, Scandinavian, Carpathian and Sudetian populations. Thus, we provide evidence for a multiglacial origin of arctic-alpine distributions in Europe, i.e. the current disjunction results from range fragmentation in several glacial cycles. The pattern of genetic diversity within populations seems predominantly determined by historical factors, but is modified by contemporary aspects. Overall, diversity and divergence are negatively correlated. We suggest that low diversity values might result from (i) ancient bottlenecking during warm interglacial periods, as seen in the Pyrenees and Balkans; (ii) recent bottlenecking in small modern areas, as seen in the Giant Mountains and Bohemian Forest; and (iii) dispersal bottlenecking in northern Scandinavia.     

Pyrenean ptarmigans decline under climatic and human influences through the Holocene

In Europe, the Quaternary is characterized by climatic fluctuations known to have led to many cycles of contraction and expansion of species geographical ranges. In addition, during the Holocene, historical changes in human occupation such as colonization or abandonment of traditional land uses can also affect habitats. These climatically or anthropically induced geographic range changes are expected to produce considerable effective population size change, measurable in terms of genetic diversity and organization. The rock ptarmigan (Lagopus muta) is a small-bodied grouse occurring throughout Northern hemispheric arctic and alpine tundra. This species is not considered threatened at a continental scale, but the populations in the Pyrenees are of concern because of their small population size, geographical isolation and low genetic diversity. Here, we used 11 microsatellites to investigate genetic variations and differentiations and infer the overall demographic history of Pyrenean rock ptarmigan populations. The low genetic variability found in these populations has been previously thought to be the result of a bottleneck that occurred following the last glacial maximum (i.e., 10 000 years ago) or more recently (i.e., during the last 200 years). Our results clearly indicate a major bottleneck affecting the populations in the last tenth of the Holocene. We discuss how this decline can be explained by a combination of unfavorable and successive events that increased the degree of habitat fragmentation.     

Local and regional founder effects in lake zooplankton persist after thousands of years despite high dispersal potential

We reconstructed the genetic structure of a planktonic crustacean Daphnia longispina living in high mountain lakes and ponds in the Pyrenees to investigate whether it was shaped by persistent founder effects originating shortly after the last glacial maximum or by ongoing dispersal and effective migration (gene flow). We found that the genetic structure can largely be explained by a single colonization event following gradual deglaciation of the Pyrenees ~10 000–15 000 years ago. Nuclear genetic diversity declined steeply from southeast to northwest, suggestive of serial colonization of available habitats with advancing deglaciation. The spatial genetic structure suggests that founder effects were major determinants of the present‐day diversity, both at the catchment level and at the level of individual water bodies, further supporting extremely low effective migration rates. This study reveals a prime example of a founder effect that is both long lasting and maintained at small spatial scales. Our data suggest a process of isolation by colonization as a result of strong priority effects and monopolization. We found evidence for the spread of haplotypes with Pyrenean ancestry across the Palaearctic over distances up to 5500 km, although the local genetic structure after colonization was hardly influenced by contemporary dispersal. Finally, our data also suggest that mitochondrial mutation rates in the studied populations were seven times higher than typically assumed. Overall, we show that founder effects can persist for centuries even at small spatial scales at which the potential for dispersal is high.     

Congruent signals of population history but radically different patterns of genetic diversity between mitochondrial and nuclear markers in a mountain lizard

Historical factors, current population size, population connectivity and selective processes at linked loci contribute to shaping contemporary patterns of neutral genetic diversity. It is now widely acknowledged that nuclear and mitochondrial markers react differently to current demography as well as to past history, so the use of both types of markers is often advocated to gain insight on both historical and contemporary processes. We used 12 microsatellite loci genotyped in 13 populations of a mountain lizard (Iberolacerta bonnali) to test whether the historical scenario favoured by a previous mitochondrial study was also supported by nuclear markers and thereby evaluated the consequences of postglacial range movements on nuclear diversity. Congruent signals of recent history were revealed by nuclear and mitochondrial markers using an Approximate Bayesian computation approach, but contemporary patterns of mtDNA and nuclear DNA diversity were radically different. Although dispersal in this species is probably highly restricted at all spatial scales, colonization abilities have been historically good, suggesting capability for reestablishment of locally extinct populations except in fully disconnected habitats.     

Signature of mid‐Pleistocene lineages in the European silver fir (Abies alba Mill.) at its geographic distribution margin

In a conservation and sustainable management perspective, we identify the ecological, climatic, and demographic factors responsible for the genetic diversity patterns of the European silver fir (Abies alba Mill.) at its southwestern range margin (Pyrenees Mountains, France, Europe). We sampled 45 populations throughout the French Pyrenees and eight neighboring reference populations in the Massif Central, Alps, and Corsica. We genotyped 1,620 individuals at three chloroplast and ten nuclear microsatellite loci. We analyzed within‐ and among‐population genetic diversity using phylogeographic reconstructions, tests of isolation‐by‐distance, Bayesian population structure inference, modeling of demographic scenarios, and regression analyses of genetic variables with current and past environmental variables. Genetic diversity decreased from east to west suggesting isolation‐by‐distance from the Alps to the Pyrenees and from the Eastern to the Western Pyrenees. We identified two Pyrenean lineages that diverged from a third Alpine–Corsica–Massif Central lineage 0.8 to 1.1 M years ago and subsequently formed a secondary contact zone in the Central Pyrenees. Population sizes underwent contrasted changes, with a contraction in the west and an expansion in the east. Glacial climate affected the genetic composition of the populations, with the western genetic cluster only observed in locations corresponding to the coldest past climate and highest elevations. The eastern cluster was observed over a larger range of temperatures and elevations. All demographic events shaping the current spatial structure of genetic diversity took place during the Mid‐Pleistocene Transition, long before the onset of the Holocene. The Western Pyrenees lineage may require additional conservation efforts, whereas the eastern lineage is well protected in in situ gene conservation units. Due to past climate oscillations and the likely emergence of independent refugia, east–west oriented mountain ranges may be important reservoir of genetic diversity in a context of past and ongoing climate change in Europe.     

Effects of population size and isolation on the genetic structure of the East African mountain white‐eye Zosterops poliogaster (Aves)

Habitat size, quality and isolation determine the genetic structure and diversity of populations and may influence their evolutionary potential and vulnerability to stochastic events. Small and isolated populations are subject to strong genetic drift and can lose much of their genetic diversity due to stochastic fixation and loss of alleles. The mountain white‐eye Zosterops poliogaster, a cloud forest bird species, is exclusively found in the high mountains of East Africa. We analysed 13 polymorphic microsatellites for 213 individuals of this species that were sampled at different points in time in three mountain massifs differing in habitat size, isolation and habitat degradation. We analysed the genetic differentiation among mountain populations and estimated the effective population sizes. Our results indicate three mountain‐specific genetic clusters. Time cohorts did not show genetic divergences, suggesting that populations are large enough to prevent strong drift effects. Effective population sizes were higher in larger and geographically interconnected habitat patches. Our findings underline the relevance of ecological barriers even for mobile species and show the importance of investigating different estimators of population size, including both approaches based on single and multiple time‐points of sampling, for the inference of the demographic status of a population. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 828–836.     

Geography determines genetic relationships between species of mountain pine (Pinus mugo complex) in western Europe

Aim Our aims were to test whether morphological species of mountain pines were genetically supported in the western part of the distribution range of the Pinus mugo species complex (Pinus mugo Turra sensu lato), to resolve genetically homogeneous clusters of populations, to determine historical demographic processes, and to assess the potential hybridization of mountain pines with Scots pine, Pinus sylvestris L. Location Populations were sampled in the Iberian System, the Pyrenees, the French Mont Ventoux, Vosges and Jura mountains, the German Black Forest and throughout the Alps. This corresponded to a range‐wide sampling for mountain pine sensu stricto (Pinus uncinata Ram.) and to a sampling of the western parts of the ranges of dwarf mountain pine (Pinus mugo Turra sensu stricto) and bog pine/peatbog pine [Pinus rotundata Link/Pinus × pseudopumilio (Willk.) Beck]. Methods In total, 786 individuals of P. mugo sensu lato from 29 natural populations, and 85 individuals of P. sylvestris from four natural populations were genotyped at three chloroplast microsatellites (cpSSRs). Populations were characterized for standard genetic diversity statistics and signs of demographic expansion. Genetic structure was explored using analysis of molecular variance, differentiation statistics and Bayesian analysis of population structure (BAPS). Results One hundred haplotypes were identified in P. mugo sensu lato. There was a stronger differentiation between geographical regions than between morphologically identified taxa (P. mugo sensu stricto, P. uncinata and P. rotundata/P. ×pseudopumilio). Overall genetic differentiation was weak (G_ST = 0.070) and displayed a clear phylogeographic structure [N_ST = 0.263, N_ST > N_ST (permuted), P < 0.001]. BAPS identified a Pyrenean and an Alpine gene pool, along with several smaller genetic clusters corresponding to peripheral populations. Main conclusions The core regions of the Pyrenees and Alps were probably recolonized, respectively by P. uncinata and P. uncinata/P. mugo sensu stricto, from multiple glacial refugia that were well connected by pollen flow within the mountain chains. Pinus rotundata/P. × pseudopumilio populations from the Black Forest, Vosges and Jura mountains were probably recolonized from various glacial populations that kept their genetic distinctiveness despite late glacial and early Holocene expansion. Marginal P. uncinata populations from the Iberian System are compatible with elevational shifts and long‐term isolation. The causes of haplotype sharing between P. mugo sensu lato and P. sylvestris require further research.     

Low genetic diversity of a high mountain burnet moth species in the Pyrenees

The burnet moth Zygaena anthyllidis, endemic to the high elevations of the Pyrenees, is vulnerable to land-use. In order to identify conservation priorities based on an assessment of genetic diversity within populations and gene flow among populations, we examined Z. anthyllidis’ genetic variability and differentiation based on allozyme electrophoresis from seven populations scattered across its entire range. In comparison to other mountain Lepidoptera, the populations studied exhibit a low level of genetic diversity. Remarkable between-population differentiation (F _ST = 0.053), the presence of private alleles, and the lack of significant isolation-by-distance pattern characterises the genetic make-up of the species. We interpreted the pattern of genetic differentiation as a consequence of low dispersal power in combination with insufficient landscape connectivity. Ongoing land-use change might reinforce genetic differentiation due to habitat fragmentation and additionally affect negatively allozyme variability at shifting range margins, i.e. the capacity to adapt to changing environments. We therefore suggest creating a network of suitable habitats at the landscape scale to facilitate genetic exchange and to conserve the species’ overall genetic variability.     

Phylogeography and genetic differentiation along the distributional range of the orchid Epidendrum fulgens: a Neotropical coastal species not restricted to glacial refugia

Aim Phylogeographical studies in the Brazilian Atlantic Forest (BAF) have mostly included species associated with forest habitats, whereas taxa associated with grassland and sand‐dune plant communities have so far been largely overlooked. This study examines the phylogeography of the orchid Epidendrum fulgens, which occurs on coastal sand dunes and granitic outcrops, in order to identify major genetic divergences or disjunctions across the range of the species and to investigate the genetic signatures of past range contractions and expansions. Location Southern and south‐eastern seashore vegetation along the BAF biome, and granitic and arenitic outcrops that occur in the subtropical grassland plant communities located south of the BAF. Methods Nine nuclear and four plastid microsatellite loci were used to genotype 424 individuals from 16 populations across the distributional range of E. fulgens. For both sets of markers, we estimated genetic diversity and population differentiation, testing for a north–south gradient of genetic diversity. The plastid haplotype network and a Bayesian assignment analysis of nuclear markers were used to infer population structure. Past demographic changes were investigated using a coalescence approach. Results A deep disjunction was found between northern populations within the BAF and southern populations outside the BAF that occur on granitic and arenitic outcrops. Recent demographic reductions were detected in northern populations on coastal sands. Such demographic changes were not expected for those populations, as previous studies with forest species had found evidence of population expansion in the same areas. Higher genetic diversity was found in southern populations on granite, in contrast to patterns observed in previous studies of forest species. Main conclusions The results are consistent with the long‐term persistence of E. fulgens. Bottlenecks were detected in populations from areas where population expansion events have been detected in other plant (and animal) species, suggesting that forest expansion after the Last Glacial Maximum played a role in the population fragmentation and decrease in genetic diversity in E. fulgens. A substantial genetic division in E. fulgens corresponds to the ‘Portal de Torres’, a region that demarcates the northern limits of subtropical grassland plant communities and the southern limits of the BAF.     

Long-distance dispersal vs vicariance: the origin and genetic diversity of alpine plants in the Spanish Sierra Nevada

Here, we investigated the origin and genetic diversity of four alpine plant species co-occurring in the Spanish Sierra Nevada and other high mountains in south-western Europe by analysis of amplified fragment length polymorphisms (AFLPs). In Kernera saxatilis, Silene rupestris and Gentiana alpina we found intraspecific phylogroups corresponding to mountain regions as predicted by the vicariance hypothesis. Moreover, genetic distances between Sierra Nevada and Pyrenees populations were always higher than those between populations from the Pyrenees and the south-western Alps/Massif Central. This suggests successive disruption of gene exchange between mountain ranges as postglacial climatic warming proceeded from south to north. In Papaver alpinum, our data indicate that a central Pyrenean population arose via long-distance dispersal from the Sierra Nevada, and that vicariant separation events between the Sierra Nevada and the Pyrenees and between the Pyrenees and the south-western Alps occurred simultaneously. Overall, Sierra Nevada populations of all species investigated here preserve unexpectedly high (or not exceptionally reduced) genetic diversity. This testifies to the important influence of long-term isolation, i.e. vicariance, on genetic diversity through fostering the accumulation of new mutations and/or the fixation of ancestral ones.