Extensive range persistence in peripheral and interior refugia characterizes Pleistocene range dynamics in a widespread Alpine plant species (Senecio carniolicus, Asteraceae)

Recent evidence suggests that survival of arctic-alpine organisms in peripheral or interior glacial refugia are not mutually exclusive and may both be involved in shaping an organism's Pleistocene history, yet potentially at different time levels. Here, we test this hypothesis in a high-mountain plant (diploid lineage of Senecio carniolicus, Asteraceae) from the Eastern European Alps, in which patterns of morphological variation and current habitat requirements suggest survival in both types of refugia. To this end, we used AFLPs, nuclear and plastid DNA sequences and analysed them, among others, within a graph theoretic framework and using novel Bayesian methods of phylogeographic inference. On the basis of patterns of genetic diversity, occurrence of rare markers, distribution of distinct genetic lineages and patterns of range connectivity both interior refugia in the formerly strongly glaciated central Alps and peripheral refugia along the southern margin of the Alps were identified. The presence of refugia congruently inferred by markers resolving at different time levels suggests that these refugia acted as such throughout several glacial cycles. The high degree of range persistence together with gradual range expansion, which contrasts with the extent of range shifts implied for other Alpine species, is likely responsible for incipient lineage differentiation evident from the genetic data. Replacing a simplistic peripheral vs. interior refugia dualism by more complex models involving both types of refugia and considering different time levels will help identifying common phylogeographic patterns with respect to, for instance, location of refugia and colonization routes and elucidating their underlying genetic and/or ecological causes. DNA sequences have been deposited in GenBank under accession nos. FR796701–FR797793 and nos. HE614296–HE614583.     

Glacial history of Saxifraga paniculata (Saxifragaceae): molecular biogeography of a disjunct arctic-alpine species from Europe and North America

The molecular biogeography of the disjunctly distributed and morphologically highly variable species Saxifraga paniculata Mill. was analysed using amplified fragment length polymorphism (AFLP) and chloroplast microsatellites. The study comprised 77 samples from mountain regions in Europe and North America throughout the complete range of distribution. AFLP data revealed clear genetic differentiation between samples from the Arctic, the Caucasus, and the eastern European mountains. Samples from the Alps were divided into two groups. One group clustered with the samples from central Europe and the Pyrenees, whereas another group with individuals from southern Norway. AFLP diversity was lowest in the Arctic and highest in the Alps. Chloroplast microsatellite analysis revealed eight haplotypes but no unequivocal phylogeographical pattern. However, haplotype diversity was highest in the Alps and central Europe whereas, in the Arctic, only few widespread haplotypes could be found. The results indicate in situ survival of S. paniculata in the Caucasus, the eastern European mountains, and the Alps. The Arctic has presumably been colonized postglacially from North American refugia south of the ice shield. Southern Norway and the Pyrenees have most likely been colonized from two phylogeographically different groups in the Alps. The origin of the central European samples remains ambiguous. In situ survival seems to be as possible as several postglacial recolonization events from the Alps. The obtained molecular data clearly support the subdivision of S. paniculata into three subspecies: ssp. cartilaginea from the Caucasus, ssp. laestadii from northern Norway, Iceland, and North America, and ssp. paniculata from the other geographical regions.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 385–398.     

Molecular evidence for polyploid origins in Saxifraga (Saxifragaceae): the narrow arctic endemic S. svalbardensis and its widespread allies

The recently described polyploid Saxifraga svalbardensis is endemic to the arctic archipelago of Svalbard. We investigated relationships among four closely related species of Saxifraga in Svalbard and tested three previously proposed hypotheses for the origin of S. svalbardensis: (1) differentiation from the morphologically and chromosomally variable polyploid S. cernua; (2) hybridization between the diploid S. hyperborea and S. cernua; and (3) hybridization between the tetraploid S. rivularis and S. cernua. Fifteen populations were analyzed using random amplified polymorphic DNAs (RAPDs) and nucleotide sequences of the chloroplast gene matK and the internal transcribed spacers (ITS) of nuclear ribosomal DNA (rDNA). RAPD and matK data suggest that S. svalbardensis has originated from a hybrid with S. rivularis as the maternal parent and S. cernua as the paternal parent, possibly a single time, whereas ITS data could not be used to discriminate among the hypotheses. The data also suggest that the diploid S. hyperborea is a progenitor of the tetraploid S. rivularis. The four populations examined of S. svalbardensis were virtually identical for RAPD and ITS markers, whereas S. cernua showed high levels of variation, suggesting that the latter polyploid either has formed recurrently or has undergone considerable differentiation since its origin.     

Promiscuity in populations of the cushion plant Saxifraga oppositifolia in the Swiss Alps as inferred from random amplified polymorphic DNA (RAPD)

Overviews on patterns of genetic variation within and among plant populations show that widespread, outcrossing species should have a high proportion of the total genetic variation within populations and a low proportion among populations, which results in little population differentiation. However, in Alpine areas, large–scale distribution barriers as well as small-scale habitat heterogeneity could lead to geographical and temporal isolation, respectively. We investigated the genetic variation of Saxifraga oppositifolia from 10 populations of the Alps in southeastern Switzerland using random amplified polymorphic DNA (RAPD). Based on the banding patterns of four RAPD primers, 84 polymorphic markers identified all 189 sampled individuals as being genetically different. The genetic variation was mainly found within populations (95%), whereas less than 5% was found among populations and among regions. Analyses of molecular variance ( AMOVA ) suggested that population differentiation was highly significant. However, grouping populations differently into regions did not appear to result in a clear correspondence of genetic and geographical relatedness. Genetic variation did not significantly differ between populations of two elevational levels. This coincides with results of former pollination experiments that revealed a breeding system of S. oppositifolia which remains the same irrespective of the elevation. We assume that the high outcrossing rate, rare clonal reproduction, and some long-distance dispersal even among topographically separated populations are the crucial determinants for the pattern of genetic variation found in the investigated area.     

The impact of Pleistocene climate change on an ancient arctic-alpine plant: multiple lineages of disparate history in Oxyria digyna

The ranges of arctic-alpine species have shifted extensively with Pleistocene climate changes and glaciations. Using sequence data from the trnH-psbA and trnT-trnL chloroplast DNA spacer regions, we investigated the phylogeography of the widespread, ancient (>3 million years) arctic-alpine plant Oxyria digyna (Polygonaceae). We identified 45 haplotypes and six highly divergent major lineages; estimated ages of these lineages (time to most recent common ancestor, T(MRCA)) ranged from ～0.5 to 2.5 million years. One lineage is widespread in the arctic, a second is restricted to the southern Rocky Mountains of the western United States, and a third was found only in the Himalayan and Altai regions of Asia. Three other lineages are widespread in western North America, where they overlap extensively. The high genetic diversity and the presence of divergent major cpDNA lineages within Oxyria digyna reflect its age and suggest that it was widespread during much of its history. The distributions of individual lineages indicate repeated spread of Oxyria digyna through North America over multiple glacial cycles. During the Last Glacial Maximum it persisted in multiple refugia in western North America, including Beringia, south of the continental ice, and within the northern limits of the Cordilleran ice sheet. Our data contribute to a growing body of evidence that arctic-alpine species have migrated from different source regions over multiple glacial cycles and that cryptic refugia contributed to persistence through the Last Glacial Maximum.     

Late Neogene history of the laurel tree (Laurus L., Lauraceae) based on phylogeographical analyses of Mediterranean and Macaronesian populations

Aim The post‐glacial range dynamics of many European plant species have been widely investigated, but information rapidly diminishes as one moves further back in time. Here we infer the historical range shifts of Laurus, a paradigmatic tree of the Tethyan flora that has covered southern Eurasia since the Oligo‐Miocene, by means of phylogenetic and phylogeographical analyses. Location Mediterranean Basin, Black Sea and Macaronesian archipelagos (Azores, Madeira, Canary Islands). Methods We analysed plastid DNA (cpDNA) sequence (trnK–matK, trnD–trnT) variation in 57 populations of Laurus and three Lauraceae genera. Phylogenetic methods (maximum parsimony and Bayesian inference) and statistical parsimony networks were used to reconstruct relationships among haplotypes. These results were contrasted with the fossil record and bioclimatic niche‐based model predictions of past distributions to infer the migration routes and location of refugia. Results The phylogenetic tree revealed monophyly for Laurus. Overall sequence variability was low within Laurus, but six different haplotypes were distinguished and a single network retrieved, portraying three lineages primarily related to geography. A strongly divergent eastern lineage occupied Turkey and the Near East, a second clade was located in the Aegean region and, lastly, a western clade grouped all Macaronesian and central and western Mediterranean populations. A close relationship was observed between the Macaronesian populations of L. azorica and the western populations of L. nobilis. Main conclusions The phylogeographical structure of Laurus preserves the imprints of an ancient contraction and break‐up of the range that resulted in the evolution of separate cpDNA lineages in its western‐ and easternmost extremes. Intense range dynamics in the western Mediterranean and multiple glacial refugia contributed to the generation and long‐term conservation of this phylogeographical pattern, as shown by the fit between the haplotype ranges and past suitable areas inferred from bioclimatic models. Finally, our results challenge the taxonomic separation of Laurus into two distinct species.     

Phylogeography of Potentilla fruticosa (Rosaceae) in the Qinghai-Tibetan Plateau revisited: a reappraisal and new insights

Background: Most empirical studies to date have suggested that alpine plants in the central Qinghai-Tibetan Plateau (QTP) originated from the south-eastern QTP. However, previous phylogeographcial analysis of Potentilla fruticosa suggested that it diversified in the central QTP, which has also been assumed to have been a glacial refugium, and expanded to the north-eastern regions during the mid-Holocene period.

Aim: We reappraise this claim in the light of information acquired from sampling, haplotyping and analysing additional populations.

Methods: We sequenced the chloroplast trnT-L intergenic spacer of 346 individuals collected from 52 populations. We reconstructed phylogenetic relationships among haplotypes through Bayesian and Network analysis, and used several methods for demographic analysis.

Results: Some common and highly divergent haplotypes were distributed in the central, western and south-eastern QTP. Mismatch and other population genetic analyses applied to our data suggested that a distinct range expansion had occurred between approximately 30,000 and 325,000 years ago (kya).

Conclusions: Besides the possible postglacial expansion in the north-eastern QTP, our results further suggested that the range of the species radically expanded across the whole Plateau before the last glacial maximum (around 18 kya) and the south-eastern, western and central QTP regions had together provided important refugia during recent glacial stages. These findings, in contrast to the previous conclusions, highlight the importance of adequate sampling strategies in phylogeographical studies.     

Phylogeography and refugia of the Japanese endemic alpine plant, Phyllodoce nipponica Makino (Ericaceae)

Aim  This study aims to elucidate the phylogeography of the Japanese endemic alpine plant, Phyllodoce nipponica Makino (Ericaceae) and to infer the location of refugia of alpine plants in Japan during climatic oscillations.
Location  Alpine zone in the Japanese archipelago.
Methods  We determined the chloroplast (cp) DNA haplotypes of 155 individuals (22 populations) based on sequence data from the trnL-F and trnT-L intergenic spacers and the trnL intron, whose phylogenetic relationships were analysed using the program tcs . To examine the genetic structure, analysis of molecular variance ( amova ) was carried out and the population differentiation was shown by the parameters G _ST and N _ST.
Results  The haplotype composition and the results of amova showed that populations in the Japanese Central Mountain Region (JCMR) and in the westernmost region were highly divergent (18.8%). The diversity within populations was very high in the JCMR ( h _S = 0.421); less variation was found within populations located in other regions at lower elevations.
Main conclusions  Phyllodoce nipponica survived climatic changes during the Quaternary in the JCMR and the westernmost region. Most of the distribution range was colonized during only one range expansion. The source location from which the range expansion occurred was unclear.     

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.     

Understanding population history for conservation purposes: population genetics of Saxifraga aizoides (Saxifragaceae) in the lowlands and lower mountains north of the Alps

Several alpine species have outlying populations in the lowlands and lower mountains north of the Alps. These small, isolated populations are usually described as either (1) glacial relics, (2) descendants from populations living on forelands and moraines during the ice ages, or (3) populations founded by long-distance dispersal after glaciation. A floristic survey of the historic and present distributions and an allozyme investigation were performed on one of these relic species, Saxifraga aizoides. The species was historically more abundant and had more stations in more regions of northeastern Switzerland. The former population structures within regions, nowadays destroyed, were still reflected in distinct and high regional genetic diversity and variation. There was weak evidence of increased inbreeding in outlying populations, but populations did not deviate from Hardy-Weinberg equilibrium. No geographic pattern of genetic variation above the regional scale (>10 km) was found. Based on the spatial and genetic structures found, it was not possible to discriminate between the abovementioned hypotheses. Nevertheless, the study shows how a thorough evaluation of distribution and abundance data aids the interpretation of genetic data with respect to population history, biogeography, and conservation biology.     

Molecular data and species distribution models reveal the Pleistocene history of the mayfly Ameletus inopinatus (Ephemeroptera: Siphlonuridae)1

1. We investigated the Pleistocene and Holocene history of the rare mayfly Ameletus inopinatus EATON 1887 (Ephemeroptera: Siphlonuridae) in Europe. We used A. inopinatus as a model species to explore the phylogeography of montane, cold‐tolerant aquatic insects with arctic–alpine distributions. 2. Using species distribution models, we developed hypotheses about the species demographic history in Central Europe and the recolonisation history of Fennoscandia. We tested these hypotheses using mitochondrial cytochrome oxidase I (mtCOI) sequence data and compared our genetic results with previously generated microsatellite data to explore genetic diversity distributions of A. inopinatus. 3. We observed old lineages, deep splits and almost complete lineage sorting of mtCOI sequences among mountain ranges. These results support a periglacial survival, i.e. persistence at the periphery of Pleistocene glaciers in Central Europe. 4. There was strong differentiation between the Fennoscandian and all other populations, indicating that Fennoscandia was recolonised from a refugium not accounted for in our sampling. High degrees of population genetic structure within the northern samples suggest that Fennoscandia was recolonised by more than one lineage. However, this structure was not apparent in previously published microsatellite data, consistent with secondary contact without sexual incompatibility or with sex‐biased dispersal. 5. Our demographic analyses indicate that (i) the separation of northern and Central European lineages occurred during the early Pleistocene; (ii) Central European populations have persisted independently throughout the Pleistocene and (iii) the species extended its range about 150 000 years ago.     

Inferring the past to predict the future: climate modelling predictions and phylogeography for the freshwater gastropod Radix balthica (Pulmonata, Basommatophora)

Understanding the impact of past climatic events on species may facilitate predictions of how species will respond to future climate change. To this end, we sampled populations of the common pond snail Radix balthica over the entire species range (northwestern Europe). Using a recently developed analytical framework that employs ecological niche modelling to obtain hypotheses that are subsequently tested with statistical phylogeography, we inferred the range dynamics of R. balthica over time. A Maxent modelling for present-day conditions was performed to infer the climate envelope for the species, and the modelled niche was used to hindcast climatically suitable range at the last glacial maximum (LGM) c . 21 000 years ago. Ecological niche modelling predicted two suitable areas at the LGM within the present species range. Phylogeographic model selection on a COI mitochondrial DNA data set confirmed that R. balthica most likely spread from these two disjunct refuges after the LGM. The match observed between the potential range of the species at the LGM given its present climatic requirements and the phylogeographically inferred refugial areas was a clear argument in favour of niche conservatism in R. balthica , thus allowing to predict the future range. The subsequent projection of the potential range under a global change scenario predicts a moderate pole-ward shift of the northern range limits, but a dramatic loss of areas currently occupied in France, western Great Britain and southern Germany.     

Phylogeography and palaeodistribution modelling of Nassauvia subgenus Strongyloma (Asteraceae): exploring phylogeographical scenarios in the Patagonian steppe

The Patagonian steppe is an immense, cold, arid region, yet phylogeographically understudied. Nassauvia subgen. Strongyloma is a characteristic element of the steppe, exhibiting a continuum of morphological variation. This taxon provides a relevant phylogeographical model not only to understand how past environmental changes shaped the genetic structure of its populations, but also to explore phylogeographical scenarios at the large geographical scale of the Patagonian steppe. Here, we (1) assess demographic processes and historical events that shaped current geographic patterns of haplotypic diversity; (2) analyze hypotheses of isolation in refugia, fragmentation of populations, and/or colonization of available areas during Pleistocene glaciations; and (3) model extant and palaeoclimatic distributions to support inferred phylogeographical patterns. Chloroplast intergenic spacers, rpl32–trnL and trnQ–5′rps16, were sequenced for 372 individuals from 63 populations. Nested clade analysis, analyses of molecular variance, and neutrality tests were performed to assess genetic structure and range expansion. The present potential distribution was modelled and projected onto a last glacial maximum (LGM) model. Of 41 haplotypes observed, ten were shared among populations associated with different morphological variants. Populations with highest haplotype diversity and private haplotypes were found in central‐western and south‐eastern Patagonia, consistent with long‐term persistence in refugia during Pleistocene. Palaeomodelling suggested a shift toward the palaeoseashore during LGM; new available areas over the exposed Atlantic submarine platform were colonized during glaciations with postglacial retraction of populations. A scenario of fragmentation and posterior range expansion may explain the observed patterns in the center of the steppe, which is supported by palaeomodelling. Northern Patagonian populations were isolated from southern populations by the Chubut and the Deseado river basins during glaciations. Pleistocene glaciations indirectly impacted the distribution, demography, and diversification of subgen. Strongyloma through decreased winter temperatures and water availability in different areas of its range.     

Contemporary patterns in a historical context: phylogeographic history of the pipevine swallowtail,Battus philenor (Papilionidae)

Abstract We examined mitochondrial DNA (mtDNA) variation in pipevine swallowtail butterflies ( Battus philenor ) from throughout its extant range to provide a historical, phylogeographical context for ecological studies of the disjunct population in California. We evaluate current hypotheses regarding host plant use, behavior, and mimetic relationships of B. philenor populations and generate alternative hypotheses. Compared to populations throughout the rest of the species' range, California populations are ecologically distinct in that they lack mimics, lay significantly larger clutches of eggs, and exclusively use a unique, endemic larval host plant. Analysis of molecular variance, tests of population differentiation, and nested clade analysis of mtDNA variation indicate that, despite low levels of population genetic structure across the species' range, there is evidence of recent range expansion from presumed Pleistocene refuge(s) in southeastern North America. Colonization of California appears to have been a recent event. This phylogeographic investigation also suggests that the evolution of life-history adaptations to a novel larval host has occurred rapidly in California and the lack of mimics in California may be attributable to the recency of colonization.     

Phylogeography of the bigeye chub Hybopsis amblops (Teleostei: Cypriniformes): early Pleistocene diversification and post‐glacial range expansion

The bigeye chub, Hybopsis amblops, is a member of the Central Highlands ichthyofauna of eastern North America. Phylogenetic analyses of the H. amblops species group based on a 1059 bp fragment of the mitochondrial DNA cytochrome b gene did not recover a monophyletic group. The inclusion of Hybopsis hypsinotus in the species complex is questionable. Within H. amblops, five strongly supported clades were identified; two clades containing haplotypes from the Ozark Highlands and three clades containing haplotypes from the Eastern Highlands and previously glaciated regions of the Ohio and Wabash River drainages. Estimates of the timing of divergence indicated that prior to the onset of glaciation, vicariant events separated populations east and west of the Mississippi River. East of the Mississippi River glacial cycles associated with the blocking and rerouting of the Teays River system caused populations to be pushed southward into refugia of the upper Ohio River. Following the most recent Wisconsinan glaciation, populations expanded northward into previously glaciated regions and southward into the Cumberland River drainage. In the Ozarks, west of the Mississippi River, isolation of clades appears to be maintained by the lack of stream capture events between the upper Arkansas and the White River systems and a barrier formed by the Arkansas River.