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     

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.     

Phylogeography of Pulsatilla vernalis (L.) Mill. (Ranunculaceae): chloroplast DNA reveals two evolutionary lineages across central Europe and Scandinavia

Aim The aim of this study was to test hypotheses regarding some of the main phylogeographical patterns proposed for European plants, in particular the locations of glacial refugia, the post‐glacial colonization routes, and genetic affinities between southern (alpine) and northern (boreal) populations. Location The mountains of Europe (Alps, Balkans, Carpathians, Central Massif, Pyrenees, Scandinavian chain, Sudetes), and central European/southern Scandinavian lowlands. Methods As our model system we used Pulsatilla vernalis, a widely distributed European herbaceous plant occurring both in the high‐mountain environments of the Alps and other European ranges and in lowlands north of these ranges up to Scandinavia. Based on a distribution‐wide sampling of 61 populations, we estimated chloroplast DNA (cpDNA) variation along six regions using polymerase chain reaction–restriction fragment‐length polymorphisms (PCR–RFLPs) (trnH–trnK, trnK–trnK, trnC–trnD, psbC–trnS, psaA–trnS, trnL–trnF) and further sequencing of trnL–trnF and trnH–psbA. In addition, 11 samples of other European species of Pulsatilla were sequenced to survey the genus‐scale cpDNA variation. Results Eleven PCR–RFLP polymorphisms were detected in P. vernalis, revealing seven haplotypes. They formed two distinct genetic groups. Three haplotypes representing both groups dominated and were widely distributed across Europe, whereas the others were restricted to localized regions (central Alps, Tatras/Sudetes mountains) or single populations. Sequencing analysis confirmed the reliability of PCR–RFLPs and homology of haplotypes across their distribution. The chloroplast DNA variation across the section Pulsatilla was low, but P. vernalis did not share haplotypes with other species. Main conclusions The genetic distinctiveness of P. vernalis populations from the south‐western Alps with respect to other Alpine populations, as well as the affinities between the former populations and those from the eastern Pyrenees, is demonstrated, thus providing support for the conclusions of previous studies. Glacial refugia in the Dolomites are also suggested. Isolation is inferred for the high‐mountain populations from the Tatras and Sudetes; this is in contrast to the case for the Balkans, which harboured the common haplotype. Specific microsatellite variation indicates the occurrence of periglacial lowland refugia north of the Alps, acting as a source for the post‐glacial colonization of Scandinavia. The presence of different fixed haplotypes in eastern and western Scandinavia, however, suggests independent post‐glacial colonization of these two areas, with possible founder effects.     

Genetic structure of Hypochaeris uniflora (Asteraceae) suggests vicariance in the Carpathians and rapid post-glacial colonization of the Alps from an eastern Alpine refugium

Aim The range of the subalpine species Hypochaeris uniflora covers the Alps, Carpathians and Sudetes Mountains. Whilst the genetic structure and post‐glacial history of many high‐mountain plant taxa of the Alps is relatively well documented, the Carpathian populations have often been neglected in phylogeographical studies. The aim of the present study is to compare the genetic variation of the species in two major European mountain systems – the Alps and the Carpathians. Location Alps and Carpathians. Methods The genetic variation of 77 populations, each consisting of three plants, was studied using amplified fragment length polymorphism (AFLP). Results Neighbour joining and principal coordinate analyses revealed three well‐supported phylogeographical groups of populations corresponding to three disjunct geographical regions – the Alps and the western and south‐eastern Carpathians. Moreover, two further clusters could be distinguished within the latter mountain range, one consisting of populations from the eastern Carpathians and the second consisting of populations from the southern Carpathians. Populations from the Apuseni Mountains had an intermediate position between the eastern and southern Carpathians. The genetic clustering of populations into four groups was also supported by an analysis of molecular variance, which showed that most genetic variation (almost 46%) was found among these four groups. By far the highest within‐population variation was found in the eastern Carpathians, followed by populations from the southern and western Carpathians. Generally, the populations from the Alps were considerably less variable and displayed substantially fewer region‐diagnostic markers than those from the south‐eastern Carpathians. Although no clear geographical structure was found within the Alps, based on neighbour joining or principal coordinate analyses, some trends were obvious: populations from the easternmost part were genetically more variable and, together with those from the south‐western part, exhibited a higher proportion of rare AFLP fragments than populations in other areas. Moreover, the total number of AFLP fragments per population, the percentage of polymorphic loci and the proportion of rare AFLP fragments significantly decreased from east to west. Main conclusions Deep infraspecific phylogeographical gaps between the populations from the Alps and the western and south‐eastern Carpathians suggest the survival of H. uniflora in three separate refugia during the last glaciation. Our AFLP data provide molecular evidence for a long‐term geographical disjunction between the eastern and western Carpathians, previously suggested from the floristic composition at the end of 19th century. It is likely that Alpine populations survived the Last Glacial in the eastern part of the Alps, from where they rapidly colonized the rest of the Alps after the ice sheet retreated. Multiple founder effects may explain a gradual loss of genetic variation during westward colonization of the Alps.     

High genetic differentiation in the alpine plant Campanula alpina Jacq. (Campanulaceae): evidence for glacial survival in several Carpathian regions and long-term isolation between the Carpathians and the Alps

A survey of amplified fragment length polymorphism (AFLP) and chloroplast DNA (cpDNA) variation was conducted to elucidate the phylogeography of Campanula alpina , a key species of silicicolous alpine grasslands in the Carpathians with a disjunct distribution in the Eastern European Alps. The Carpathians experienced a different glacial history from the Alps: local glaciers were present only in the highest massifs, while alpine habitats extended over larger areas related to their present distribution in this region. We asked: (i) whether in the Carpathians a high-mountain plant exhibits a complex phylogeographical structure or rather signatures of recent migrations, and (ii) whether the disjunct part of the species' distribution in the Alps resulted from a recent colonization from the Carpathians or from a restricted expansion from separate Eastern Alpine refugia. Our study revealed a clear phylogeographical pattern in AFLPs supported by congruent groups of distinct cpDNA haplotypes. Highest genetic differentiation was observed between the Alps and the Carpathians, indicating a long-term isolation between populations from these two mountain ranges. Further genetic division within the Carpathians suggests that current species' distribution is composed of several groups which have been isolated from each other for a long period. One genetic break separates Western from Southeastern Carpathian material, which is in line with a classical biogeographical boundary. A further, strongly supported genetic group was identified at the southwestern edge of the Carpathian arch. In the Eastern Alps, genetic traces of glacial survival in separate refugial areas in the calcareous northern part and the siliceous central part were found.     

Post-glacial history of the dominant alpine sedge Carex curvula in the European Alpine System inferred from nuclear and chloroplast markers

The alpine sedge Carex curvula ssp. curvula is a clonal, dominant graminoid found in the European Alps, the Carpathians, the Pyrenees and in some of the Balkan Mountains. It is a late-successional species of acidophilous alpine meadows that occurs on sites that were covered by ice during the last glacial maximum (LGM). By applying the amplified fragment length polymorphism (AFLP) fingerprinting and chloroplast DNA (cpDNA) sequencing, we attempted to identify the recolonization routes followed by the species after the last ice retreat. We relied on the genetic diversity of 37 populations covering the entire distributional range of the species. As a wind-pollinated species, C. curvula is characterized by a low level of population genetic differentiation. Nuclear and chloroplast data both support the hypothesis of a long-term separation of Eastern (Balkans and Carpathians) and Western (Alps and Pyrenees) lineages. In the Alps, a continuum of genetic depauperation from the east to the west may be related to a recolonization wave originating in the eastern-most parts of the chain, where the main glacial refugium was likely located. The Pyrenean populations are nested within the western Alps group and show a low level of genetic diversity, probably due to recent long-distance colonization. In contrast to the Alps, we found no phylogeographical structure in the Carpathians. The combination of reduced ice extension during the Würm period and the presence of large areas of siliceous substrate at suitable elevation suggest that in contrast to populations in the Alps, the species in the Carpathians underwent a local vertical migration rather than extinction and recolonization over long distance.     

Amplified fragment length polymorphism (AFLP) suggests old and recent immigration into the Alps by the arctic-alpine annual Comastoma tenellum (Gentianaceae)

Aim This study aims to elucidate the phylogeography of the arctic‐alpine annual Comastoma tenellum (Rottb.) Toyok. (Gentianaceae) and to unravel the history of its immigration into the Alps. Location Although samples from Alaska and Central Asia were also included, our study focusses on Europe, especially on the Alps. Methods We applied amplified fragment length polymorphism (AFLP) fingerprinting on 37 populations (162 individuals) of C. tenellum and analysed the results phenetically. Results As C. tenellum is mainly inbreeding, there is typically little to no intrapopulational genetic variation. Two populations from Alaska and Altai are strongly separated from all other accessions. The majority of the populations from the Alps group together with high bootstrap support. They fall into an unsupported Alps I group (northwards of Gran Paradiso) and a well‐supported Alps II group (south‐western Alps). The remaining European populations form a weakly‐supported branch constituting accessions from the Carpathians, Scandinavia and two populations from the Eastern Alps. Main conclusions Comastoma tenellum reached the Alps at least twice. The first immigration event resulted in a lineage that is clearly separated from the other European accessions. The immigration must have occurred well before the last glaciation because this lineage shows further phylogeographical structuring into two groups (Alps II in the south‐western Alps and Alps I in the rest of the Alps). This pattern is presumably due to isolation in different glacial refugia. In addition to the old immigration event, the species reached the Alps in recent times either from Scandinavia or from the Carpathians via long‐distance dispersal. These immigrations resulted in (at least) two populations that are spatially small and poor in individuals.     

The crested newt Triturus cristatus recolonized temperate Eurasia from an extra‐Mediterranean glacial refugium

We assess the role of the Carpathians as an extra‐Mediterranean glacial refugium for the crested newt Triturus cristatus. We combine a multilocus phylogeography (one mitochondrial protein‐coding gene, three nuclear introns, and one major histocompatibility complex gene) with species distribution modelling (projected on current and Last Glacial Maximum climate layers). All genetic markers consistently show extensive genetic variation within and genetic depletion outside the Carpathians. The species distribution model suggests that most of the current range was unsuitable at the Last Glacial Maximum, but a small suitable area remained in the Carpathians. Triturus cristatus dramatically expanded its postglacial range, colonizing much of temperate Eurasia from a glacial refugium in the Carpathians. Within the Carpathians, T. cristatus persisted in multiple geographically discrete regions, providing further support for a Carpathian ‘refugia within refugia’ scenario. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 574–587.     

Haplotype richness in refugial areas: phylogeographical structure of <Emphasis Type="Italic">Saxifraga callosa</Emphasis>

This paper illustrates the phylogeographical structure of Saxifraga callosa in order to describe its genetic richness in refugial areas and to reconstruct its glacial history. S. callosa is a species spread throughout south-east France and Italy with a high distribution in the Maritime Alps. Four chloroplast microsatellite and AFLP markers were analyzed in populations of S. callosa. The size variants of all tested loci amount to 11 different haplotypes. Intrapopulational haplotype variation was found in two of the populations analyzed: on the Mt. Toraggio in the Maritime Alps, and in the Apuan Alps. On the other hand, no intrapopulational variation was found in 25 populations, most of which were sampled from isolated areas. Analysis of the haplotype distribution showed that population subdivision across all populations was high (G _ST = 0.899). Moreover, its genetic structure was studied using AMOVA and STRUCTURE analysis. The study legitimated inferred conclusions about the phylogeographical structure of the species and identified centers of diversity. Considerations concerning genetic structure and divergence among three major clades (Maritime Alps, Apuan Alps and Apennines), the patchy distribution of haplotypes, and the high number of private haplotypes support the proposal that S. callosa survived in some refugia within the Italian Peninsula refugium, and that mainly northern populations of refugia were involved in postglacial recolonization.     

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.     

Cochlearia macrorrhiza (Brassicaceae): A bridging species between Cochlearia taxa from the Eastern Alps and the Carpathians?

Cochlearia macrorrhiza is one of the most highly endangered species in Central Europe and less than five individuals survived at its natural stand in a lowland area between the Eastern Alps and the Carpathians. Amplified fragment length polymorphisms (AFLPs) confirmed the status of C. macrorrhiza as a distinct taxon. Lowland C. macrorrhiza does not bridge the distribution of montainous and alpine Cochlearia species from the Eastern Alps and the Carpathians genetically, and C. macrorrhiza represents a separate lineage which evolved from diploid Cochlearia as C. excelsa in East Austrian high alpine regions did. Another species considered in this study, the Romanian C. borzaeana is more closely related to C. tatrae from the High Tatra mountains than to C. pyrenaica from Slovakia or Austria and the AFLP results suggest a single origin of alpine 2n=42 taxa. Genetic differentiation within and between populations is highly structured geographically, and the AFLP data favour a former widespread distribution of C. pyrenaica in mountainous regions and a parallel evolution of high alpine taxa in the Eastern Alps and the Carpathians, respectively.     

Phylogeography of the Japanese giant flying squirrel, Petaurista leucogenys (Rodentia: Sciuridae): implication of glacial refugia in an arboreal small mammal in the Japanese Islands

To test the association between temperate forest dynamics and glacial refugia for arboreal small mammals, we studied the phylogeography of the Japanese giant flying squirrel ( Petaurista leucogenys ) using complete mitochondrial cytochrome b gene sequences (1140 bp). This squirrel is endemic to three of Japan's main islands: Honshu, Shikoku, and Kyushu. We examined 58 specimens of P. leucogenys collected from 40 localities in Japan. Additionally, two individuals with unknown sampling localities were included in phylogenetic analyses. There were 54 haplotypes of P. leucogenys. We found five major phylogroups (Northern, Central, South-eastern, South-western, and Southern). These phylogroups may have originated from glacial refugia during the Late Pleistocene. After the last glaciation, the Northern phylogroup, widely distributed in eastern Japan, could have extensively expanded northward from its refugia. By contrast, in western Japan, population expansion was restricted to western Japan. All members of four phylogroups existed in western Japan during glaciations. The complicated phylogeographical pattern of P. leucogenys populations originating from western Japan may have resulted from the long history.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 98 , 47–60.     

Multiple introgression events and range shifts in Schizocodon (Diapensiaceae) during the Pleistocene

Range shifts during the Pleistocene shaped the unique phylogeographical structures of numerous species. Accompanying species migration, sister taxa may have experienced multiple introgression events. Here, we report the signature of introgression events in multiple areas in Schizocodon, herbs endemic to Japan, using amplified fragment length polymorphism (AFLP) fingerprinting and plastid DNA haplotyping in 48 populations. Although the present distributions of S. soldanelloides and S. ilicifolius are mainly allopatric, the species share plastid DNA haplotypes in each region (north‐eastern, north‐central, south‐central and south‐western Japan); in contrast, the specific groups were highly supported by AFLP analyses. These results support the occurrence of multiple introgression events in Schizocodon. Notably, the disjunct plastid haplotypes found only in S. ilicifolius var. intercedens suggest complete plastid DNA replacement at local areas from S. soldanelloides into S. ilicifolius var. ilicifolius. Furthermore, we found that S. soldanelloides experienced range contraction and expansion during glacial and interglacial cycles based on mismatch distribution analysis and ecological niche modelling. Based on several pieces of evidence, our study supports the idea that historical range shifts associated with Pleistocene climatic oscillations favoured multiple and regional introgression events in Schizocodon. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 173 , 46–63.     

The role of disjunction and postglacial population expansion on phylogeographical history and genetic diversity of the circumboreal plant Chamaedaphne calyculata

In the last decade a number of studies has illustrated quite different phylogeographical patterns amongst plants with a northern present‐day geographical distribution, spanning the entire circumboreal region and/or circumarctic region and southern mountains. These works, employing several marker systems, have brought to light the complex evolutionary histories of this group. Here I focus on one circumboreal plant species, Chamaedaphne calyculata (leatherleaf), to unravel its phylogeographical history and patterns of genetic diversity across its geographical range. A survey of 29 populations with combined analyses of chloroplast DNA (cpDNA), internal transcribed spacer (ITS) and AFLP markers revealed structuring into two groups: Eurasian/north‐western North American, and north‐eastern North American. The present geographical distribution of C. calyculata has resulted from colonization from two putative refugial areas: east Beringia and south‐eastern North America. The variation of chloroplast DNA (cpDNA) and ITS sequences strongly indicated that the evolutionary histories of the Eurasian/north‐western North American and the north‐eastern North American populations were independent of each other because of a geographical disjunction in the distribution area and ice‐sheet history between north‐eastern and north‐western North America. Mismatch analysis using ITS confirmed that the present‐day population structure is the result of rapid expansion, probably since the last glacial maximum. The AFLP data revealed low genetic diversity of C. calyculata (P = 19.5%, H = 0.085) over the whole geographical range, and there was no evidence of loss of genetic diversity within populations in the continuous range, either at the margins or in formerly glaciated and nonglaciated regions. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 761–775.     

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.     

Disjunct distribution of Hypericum nummularium L. (Hypericaceae): molecular data suggest bidirectional colonization from a single refugium rather than survival in distinct refugia

Hypericum nummularium has a strongly disjunct, bi‐areal distribution in Europe: it is abundant in the Pyrenees and grows in a very restricted part of the Alps, more than 1000 km away. My aim was to estimate the genetic divergence between these areas and to identify the factors responsible for the disjunction: glacial relicts, bidirectional colonization from a common refugium, long‐distance dispersal and/or human introduction? Internal transcribed spacers (ITS) sequencing (680 bp) and amplified fragment length polymorphism (AFLP) fingerprinting (104 polymorphic markers) showed very low differentiation between populations in the Alps and the Pyrenees, indicating that H. nummularium probably survived in a single refugium. Moreover, levels of genetic diversity were similar in the two areas, making human introduction and long‐distance dispersal unlikely. Thus, the species probably survived in one refugium, subsequently colonizing both areas more or less simultaneously. The comparison of genetic and geographical distances suggested a step by step migration in the Alps (isolation by distance), whereas random dispersal events were more likely in the Pyrenees. Finally, I discuss possible causes for the restricted distribution area of H. nummularium in the Alps (e.g. unsuitable habitat, low dispersal capacities) and conclude that strong human disturbance is probably the major limit to the expansion of the species in this region. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 87 , 437–447.     

<Emphasis Type="Italic">Eleocharis mamillata</Emphasis> — Distribution and infraspecific differentiation

Eleocharis mamillata is a widespread species in the temperate zone of Eurasia and North America. Populations in mountainous areas of Europe and Asia (the Pyrenees, Alps, Carpathians, Balkans, Ural, Caucasus, Altai) can be separated as subspeciesaustriaca differing mainly by the stylopodium shape from the nominate subspecies. Clear morphological criteria to create a separate infraspecific taxon in East Asia could not be found.     

Phylogeographical Analysis of mtDNA Data Indicates Postglacial Expansion from Multiple Glacial Refugia in Woodland Caribou (Rangifer tarandus caribou)

Glacial refugia considerably shaped the phylogeographical structure of species and may influence intra-specific morphological, genetic, and adaptive differentiation. However, the impact of the Quaternary ice ages on the phylogeographical structure of North American temperate mammalian species is not well-studied. Here, we surveyed ∼1600 individuals of the widely distributed woodland caribou (Rangifer tarandus caribou) using mtDNA control region sequences to investigate if glacial refugia contributed to the phylogeographical structure in this subspecies. Phylogenetic tree reconstruction, a median-joining network, and mismatch distributions supported postglacial expansions of woodland caribou from three glacial refugia dating back to 13544–22005 years. These three lineages consisted almost exclusively of woodland caribou mtDNA haplotypes, indicating that phylogeographical structure was mainly shaped by postglacial expansions. The putative centres of these lineages are geographically separated; indicating disconnected glacial refugia in the Rocky Mountains, east of the Mississippi, and the Appalachian Mountains. This is in congruence with the fossil record that caribou were distributed in these areas during the Pleistocene. Our results suggest that the last glacial maximum substantially shaped the phylogeographical structure of this large mammalian North American species that will be affected by climatic change. Therefore, the presented results will be essential for future conservation planning in woodland caribou.     

Phylogeography of two sympatric giant flying squirrel subspecies,Petaurista alborufus lena and P. philippensis grandis (Rodentia: Sciuridae), in Taiwan

To test the association between Pleistocene forest dynamics relative to elevation and the population dynamics of arboreal small mammals, we examined the phylogeographical predictions for the genetic structure of the red and white giant flying squirrel (Petaurista alborufus lena) and the Indian giant flying squirrel (P. philippensis grandis) using complete mitochondrial control region sequences. Both giant flying squirrels are endemic subspecies to Taiwan and are sympatric in much of their range. In the phylogenetic analyses, we included 35 specimens of P. alborufus lena collected from 20 localities and five specimens with unknown sampling localities. Also, we phylogenetically examined 32 specimens of P. philippensis grandis from 18 localities and three specimens with unknown sampling localities. We identified 36 haplotypes of P. alborufus lena and 33 haplotypes of P. philippensis grandis. Although we did not recognize major phylogroups, we found several minor phylogroups in both subspecies, suggesting similar evolutionary histories. Phylogeographical and demographic tests showed distributions of these two subspecies expanded into coniferous and mixed forests that developed during glaciation in Taiwan's lowlands and middle lands. This suggests that these two Petaurista subspecies shifted elevation from mountainous areas to lowlands during glaciation. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 404–419.     

Humans and other animals and the plants they ingest

Primula allionii is endemic to a tiny area of the Maritime Alps and has one of the narrowest distribution ranges in this hotspot of biodiversity. Phylogeographical patterns in P. allionii were studied using plastid DNA markers and dominantly inherited markers (AFLP and ISSR) to verify any admixture between P. allionii and the sympatric P. marginata and to detect the phylogeographical history of the species. Morphometric measurements of flowers and admixture analysis support the hypothesis that hybridization occurs in nature. Species distribution models using two climate models (CCSM and MIROC) suggested a reduction in habitat suitability during cold periods. Phylogeographical analysis suggested an old allopatric divergence during the mid‐Pleistocene transition (about 0.8 Mya) without recolonization/contraction cycles. The Alps watershed does not act as a strong barrier between the two main areas of the distribution range, and moderate gene flow by pollen seems to create the admixture recorded among the stands. According to our results, the persistence of P. allionii throughout the Ice Age appears to be linked to the capacity of the Maritime Alps to provide a wide diversity of microhabitats consistent with the recent biogeographical pattern proposed for the Mediterranean Basin. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 173 , 637–653.