Intervarietal and intravarietal genetic structure in Douglas‐fir: nuclear SSRs bring novel insights into past population demographic processes,phylogeography, and intervarietal hybridization

Douglas‐fir (Pseudotsuga menziesii) is one of numerous wide‐range forest tree species represented by subspecies/varieties, which hybridize in contact zones. This study examined the genetic structure of this North American conifer and its two hybridizing varieties, coastal and Rocky Mountain, at intervarietal and intravarietal level. The genetic structure was subsequently associated with the Pleistocene refugial history, postglacial migration and intervarietal hybridization/introgression. Thirty‐eight populations from the USA and Canada were genotyped for 13 nuclear SSRs and analyzed with simulations and traditional population genetic structuring methods. Eight genetic clusters were identified. The coastal clusters embodied five refugial populations originating from five distinct refugia. Four coastal refugial populations, three from California and one from western Canada, diverged during the Pleistocene (56.9–40.1 ka). The three Rocky Mountain clusters reflected distinct refugial populations of three glacial refugia. For Canada, ice covered during the Last Glacial Maximum, we present the following three findings. (1) One refugial population of each variety was revealed in the north of the distribution range. Additional research including paleodata is required to support and determine whether both northern populations originated from cryptic refugia situated south or north of the ice‐covered area. (2) An interplay between intravarietal gene flow of different refugial populations and intervarietal gene flow by hybridization and introgression was identified. (3) The Canadian hybrid zone displayed predominantly introgressants of the Rocky Mountain into the coastal variety. This study provides new insights into the complex Quaternary dynamics of this conifer essential for understanding its evolution (outside and inside the native range), adaptation to future climates and for forest management.     

Biogeography and evolution of Abies (Pinaceae) in the Mediterranean Basin: the roles of long‐term climatic change and glacial refugia

Aim The genus Abies exemplifies plant diversification related to long‐term climatic, geological and evolutionary changes. Today, the Mediterranean firs comprise nine species, one natural hybrid and several varieties. Here I summarize current knowledge concerning the origin and evolution of the genus Abies in the Mediterranean Basin and propose a comprehensive hypothesis to explain the isolation and speciation pattern of Mediterranean firs. Location The Mediterranean Basin. Methods The literature on Abies was reviewed, focusing on the morphology, fossil records, molecular ecology, phytosociology and biogeography of the genus in the Mediterranean Basin. Results Abies fossils from the western Mediterranean indicate a wide Tertiary circum‐Mediterranean distribution of the Abies ancestor. Palaeogeographical data also suggest a single eastern Mediterranean Tertiary ancestor. Following the Miocene to Pliocene climate crisis and marine transgressions, the ancestor of the northern Mediterranean firs is hypothesized to have separated into two eastern groups, one on the Balkan Peninsula and the other in Asia Minor. However, land bridges may have permitted gene flow at times. A southward migration of A. alba to refugia, where older fir species may have remained isolated since the Miocene, could explain recent findings indicating that morphologically distant species are more closely related than expected based on such morphological classification. Main conclusions The Abies genus appears to have undergone significant morphological differentiation that does not necessarily imply reproductive isolation. That is, long‐term Mediterranean Basin dryness along a south‐eastern to north‐western gradient may have caused an initial Miocene–Pliocene speciation sequence. Pleistocene glacial cycles probably forced migrations to occur, leading to repeated contact between fir species in glacial refugia.     

Phylogeography of spruce beetles (Dendroctonus rufipennis Kirby) (Curculionidae: Scolytinae) in North America

Tree-feeding insects that are widespread in north temperate regions are excellent models for studying how past glaciations have impacted differentiation and speciation. We used mitochondrial DNA (mtDNA) sequences and allele frequencies at nine microsatellite loci to examine genetic population structure across the current range of the spruce beetle (Dendroctonus rufipennis), an economically important insect in North America. Two major haplotype groups occur across northern North America, from Newfoundland to Alaska, on white spruce (Picea glauca), and a third distinctive haplotype group occurs throughout the Rocky Mountains on Engelmann spruce (Picea engelmannii). The two mtDNA lineages found in northern populations are 3-4% divergent from each other and from the lineages found in the Rocky Mountains. Analyses of microsatellite data also suggest the existence of major population groupings associated with different geographical regions. In the Pacific Northwest, concordant contact zones for genetically distinct populations of spruce beetles and their principal hosts appear to reflect recent secondary contact. Although we could detect no evidence of historical mtDNA gene flow between allopatric population groups, patterns of variation in the Pacific Northwest suggest recent hybridization and introgression. Together with the pollen record for spruce, they also suggest that beetles have spread from at least three glacial refugia. A minimum estimate of divergence time between the Rocky Mountain and northern populations was 1.7 Myr (million years), presumably reflecting the combined effects of isolation during multiple glacial cycles.     

Phylogeography of the tailed frog (Ascaphus truei): implications for the biogeography of the Pacific Northwest

Tailed frogs are distributed in high-gradient streams within the disjunct mesic forests of the Pacific Northwest and represent the basal lineage of the anurans. We sequenced 1,530 nucleotides of the mitochondrial cytochrome b and NADH dehydrogenase subunit two genes from 23 populations and used parsimony, maximum-likelihood, and nested-clade analyses to estimate relationships among populations and infer evolutionary processes. We found two divergent haplotype clades corresponding with inland Rocky Mountain populations and coastal populations and separated by up to 0.133 substitutions per site. Within the coastal assemblage, haplotypes formed clades by mountain range with 0.010-0.024 substitutions per site divergence among populations. Inland haplotypes exhibited minimal genetic structure, with the exception of 0.021 substitutions per site distance between populations from the East Fork of the South Fork of the Salmon River and all other inland haplotypes. The magnitude of divergence between inland and coastal populations, as well as the paleobotanical record, suggest isolation of these lineages occurred during the late Miocene to early Pliocene, probably in response to the rise of the Cascade Mountains. Genetic structure within coastal and inland populations is consistent with isolation in refugia during the late Pliocene and early Pleistocene. Closely related inland haplotypes reflect range expansion following glaciation. The depth of divergence between inland and coastal populations supports the persistence of mesic forests within the inland Pacific Northwest throughout the Pleistocene and is congruent with patterns found in several other mesic forest species. Based on mitochondrial divergence and previous allozyme and morphological data, we recommend recognition of inland populations as a distinct species, Ascaphus montanus.     

Identification of glacial refugia in south-eastern North America by phylogeographical analyses of a forest understorey plant, Trillium cuneatum

Aim We examine several hypotheses emerging from biogeographical and fossil records regarding glacial refugia of a southern thermophilic plant species. Specifically, we investigated the glacial history and post‐glacial colonization of a forest understorey species, Trillium cuneatum. We focused on the following questions: (1) Did T. cuneatum survive the Last Glacial Maximum (LGM) in multiple refugia, and (if so) where were they located, and is the modern genetic structure congruent with the fossil record‐based reconstruction of refugia for mesic deciduous forests? (2) What are the post‐glacial colonization patterns in the present geographical range? Location South‐eastern North America. Methods We sampled 45 populations of T. cuneatum throughout its current range. We conducted phylogeographical analyses based on maternally inherited chloroplast DNA (cpDNA haplotypes) and used TCS software to reconstruct intraspecific phylogeny. Results We detected six cpDNA haplotypes, geographically highly structured into non‐overlapping areas. With one exception, none of the populations had mixed haplotype composition. TCS analysis resulted in two intraspecific cpDNA lineages, with one clade subdivided further by shallower diversification. Main conclusions Our investigation revealed that T. cuneatum survived the LGM in multiple refugia, belonging to two (western, eastern) genealogical lineages geographically structured across south‐eastern North America. The western clade is confined to the south‐western corner of T. cuneatum’s modern range along the Lower Mississippi Valley, where fossil records document a major refugium of mesic deciduous forest. For the eastern clade, modern patterns of cpDNA haplotype distribution suggest cryptic vicariance, in the form of forest contractions and subsequent expansions associated with Pleistocene glacial cycles, rather than simple southern survival and subsequent northward colonization. The north–south partitioning of cpDNA haplotypes was unexpected, suggesting that populations of this rather southern thermophilic species may have survived in more northern locations than initially expected based on LGM climate reconstruction, and that the Appalachian Mountains functioned as a barrier to the dispersal of propagules originating in more southern refugia. Furthermore, our results reveal south‐west to north‐east directionality in historical migration through the Valley and Ridge region of north‐west Georgia.     

Multiple glacial refugia for cool‐temperate deciduous trees in northern East Asia: the Mongolian oak as a case study

In East Asia, temperate forests are predicted to have retracted southward to c. 30° N during the last glacial maximum (LGM) based on fossil pollen data, whereas phylogeographic studies have often suggested glacial in situ survival of cool‐temperate deciduous trees in their modern northern ranges. Here we report a study of the genetic diversity and structure of 29 natural Mongolian oak (Quercus mongolica) populations using 19 nuclear simple sequence repeat (nSSR) loci and four chloroplast DNA fragments. Bayesian clustering analysis with nSSRs revealed five groups, which were inferred by approximate Bayesian computation (ABC) to have diverged in multiple refugia through multiple glacial–interglacial cycles. Analysis of chloroplast DNA variation revealed four lineages that were largely but incompletely geographically disjunct. Ecological niche modelling (ENMs) indicated a southward range shift of the oak's distribution at the LGM, although high suitability scores were also evident in the Changbai Mts. (Northeast China), the Korean Peninsula, areas surrounding the Bohai Sea, and along the coast of the Russian Far East. In addition, endemic chloroplast DNA haplotypes and nuclear lineages occurred in high‐latitude northern areas where the ENM predicted no suitable habitat. The combined evidence from nuclear and chloroplast DNA, and the results of the ENM clearly demonstrate that multiple northern refugia, including cryptic ones, were maintained across the current distributional range of the Mongolian oak during the LGM or earlier glacial periods. Though spatially limited, postglacial expansions from these refugia have led to a pattern of decreased genetic diversity with increasing latitude.     

Phylogeography of maritime pine inferred with organelle markers having contrasted inheritance

Range-wide variation of maritime pine was studied at maternally inherited and paternally inherited markers (mitochondrial DNA and chloroplast DNA). While chloroplast DNA exhibits the highest diversity, phylogeographic inferences from this marker are blurred by homoplasy and extensive pollen flow. In contrast, the only three mitochondrial haplotypes found provide a clear picture of nonoverlapping areas colonized from different refugia, with no single population having a mixed composition (GST = 1). Comparison of the genetic structure inferred from both organelle genomes allows the investigation of differential seed and pollen dispersal, pointing to pollen, but not seed, dispersal across the Strait of Gibraltar (from Morocco into Iberia). A comparison with already available genetic information, especially that of one of the maritime pine's most threatening insect pests, the bast scale Matsucoccus feytaudi, further completes the picture.     

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

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

Chloroplast evidence for geographic stasis of the Australian bird‐dispersed shrub Tasmannia lanceolata (Winteraceae)

Few chloroplast‐based genetic studies have been undertaken for plants of mesic temperate forests in the southern hemisphere and fossil‐based models have provided evidence of vegetation history only at the broadest scales in this region. This study investigates the chloroplast DNA phylogeography of Tasmannia lanceolata (Winteraceae), a fleshy‐fruited, bird‐dispersed shrub that is widespread in the mountains of southeastern Australia and Tasmania. Thirty haplotypes were identified after sequencing 3206 bp of chloroplast DNA in each of 244 individuals collected across the species’ range. These haplotypes showed unexpectedly strong phylogeographic structuring, including a phylogeographic break within a continuous part of the species’ range, with the distribution of four major clades mostly not overlapping, and geographic structuring of haplotypes within these clades. This strong geographic patterning of chloroplast DNA provided evidence for the survival of T. lanceolata in multiple putative wet forest refugia as well as evidence for additional wet forest species refugia in southeastern Australia. In western Tasmania lower haplotype diversity below the LGM tree line compared to above the LGM tree line suggests that glacial refugia at high altitudes may have been important for T. lanceolata. The level of geographic structuring in T. lanceolata is similar to gravity dispersed southern hemisphere plants such as Nothofagus and Eucalyptus. Behavioural traits of the birds transporting seed may have had a strong bearing on the limited transport of T. lanceolata seed, although factors limiting establishment, possibly including selection, may also have been important.     

Marked genetic divergence among sky island populations of Sedum lanceolatum (Crassulaceae) in the Rocky Mountains

Climate change during the Quaternary played an important role in the differentiation and evolution of plants. A prevailing hypothesis is that alpine and arctic species survived glacial periods in refugia at the periphery of glaciers. Though the Rocky Mountains, south of the southernmost extent of continental ice, served as an important glacial refuge, little is known about how climate cycles influenced populations within this region. We inferred the phylogeography of Sedum lanceolatum (Crassulaceae) within the Rocky Mountain refugium to assess how this high-elevation plant responded to glacial cycles. We sequenced 884 base pairs (bp) of cpDNA intergenic spacers (tRNA-L to tRNA-F and tRNA-S to tRNA-G) for 333 individuals from 18 alpine populations. Our highly variable markers allowed us to infer that populations persisted across the latitudinal range throughout the climate cycles, exhibited significant genetic structure, and experienced cycles of range expansion and fragmentation. Genetic differentiation in S. lanceolatum was most likely a product of short-distance elevational migration in response to climate change, low seed dispersal, and vegetative reproduction. To the extent that Sedum is a good model system, paleoclimatic cycles were probably a major factor preserving genetic variation and promoting divergence in high-elevation flora of the Rocky Mountains.     

Population genomic evidence for multiple Pliocene refugia in a montane‐restricted harvestman (Arachnida,Opiliones, Sclerobunus robustus) from the southwestern United States

The integration of ecological niche modelling into phylogeographic analyses has allowed for the identification and testing of potential refugia under a hypothesis‐based framework, where the expected patterns of higher genetic diversity in refugial populations and evidence of range expansion of nonrefugial populations are corroborated with empirical data. In this study, we focus on a montane‐restricted cryophilic harvestman, Sclerobunus robustus, distributed throughout the heterogeneous Southern Rocky Mountains and Intermontane Plateau of southwestern North America. We identified hypothetical refugia using ecological niche models (ENMs) across three time periods, corroborated these refugia with population genetic methods using double‐digest RAD‐seq data and conducted population‐level phylogenetic and divergence dating analyses. ENMs identify two large temporally persistent regions in the mid‐latitude highlands. Genetic patterns support these two hypothesized refugia with higher genetic diversity within refugial populations and evidence for range expansion in populations found outside hypothesized refugia. Phylogenetic analyses identify five to six genetically divergent, geographically cohesive clades of S. robustus. Divergence dating analyses suggest that these separate refugia date to the Pliocene and that divergence between clades pre‐dates the late Pleistocene glacial cycles, while diversification within clades was likely driven by these cycles. Population genetic analyses reveal effects of both isolation by distance (IBD) and isolation by environment (IBE), with IBD more important in the continuous mountainous portion of the distribution, while IBE was stronger in the populations inhabiting the isolated sky islands of the south. Using model‐based coalescent approaches, we find support for postdivergence migration between clades from separate refugia.     

Imprints of glacial refugia in the modern genetic diversity of Pinus sylvestris

Aim To understand the impact of glacial refugia and migration pathways on the modern genetic diversity of Pinus sylvestris. Location The study was carried out throughout Europe. Methods An extended set of data of pollen and macrofossil remains was used to locate the glacial refugia and reconstruct the migrating routes of P. sylvestris throughout Europe. A vegetation model was used to simulate the extent of the potential refugia during the last glacial period. At the same time a genetic survey was carried out on this species. Results The simulated distribution of P. sylvestris during the last glacial period is coherent with the observed fossil data, which showed a patchy distribution of the refugia between c. 40° N and 50° N. Several migrational fronts were detected within the Iberian and the Italian peninsulas, and outside the Hungarian plain and around the Alps. The modern mitochondrial DNA depicted three different haplotypes for P. sylvestris. Two distinct haplotypes were restricted to northern Spain and Italy, and the third haplotype dominated most of the present‐day remaining distribution range of P. sylvestris in Europe. Main conclusions During the last glacial period P. sylvestris was constrained under severe climatic conditions to survive in scattered and restricted refugial areas. Combining palaeoenvironmental data, vegetation modelling and the genetic data, we have shown that the long‐term isolation in the glacial refugia and the migrational process during the Holocene have played a major role in shaping the modern genetic diversity of P. sylvestris in Europe.     

Revisiting tree-migration rates: Abies alba (Mill.), a case study

At northern temperate latitudes trees have adjusted their ranges substantially in response to changing climates during the Holocene. Results from dispersal model simulations suggest that postglacial migration rates may have been over-estimated from fossil pollen data. As a contribution to this debate, we infer the migration rates of Abies alba (Mill.), silver fir, as a case-study species, by using a spatially explicit approach based on fossil pollen but taking into account its modern genetic diversity pattern. Maximum estimates of migration rates from fossil pollen data alone are higher than 700 m yr^?1 during the Holocene. Considering the potential refugia as suggested from all the fossil data but restricting the area over which silver fir expanded from each glacial refugium using data on the current haplotype distribution, the estimated maximum migration rates of silver fir are less than 250 m yr^?1. Genetic information may allow for (1) the exclusion of those refugial areas where the species may have survived during the last glacial period but from which it did not spread or spread only very locally and (2) the delineation of the areas over which the species spread from each glacial refugium. The estimated rates in the present study are generally consistent with rates suggested from modelling approaches. This study shows that integrating fossil pollen records can improve simulations of dispersal processes and, thus, allow for better predictions of future changes in tree species’ ranges.     

Admixture of genetic lineages of different glacial origin: a case study of <Emphasis Type="Italic">Abies alba</Emphasis> Mill. in the Carpathians

Genetic exchange between divergent lineages of silver fir (Abies alba Mill.) was studied in the Ukrainian Carpathians where two expanding populations originating from different glacial refugia meet. The study included 33 silver fir populations from Ukraine, Romania and Slovakia which were investigated using the maternally inherited mitochondrial nad5-4 marker and biparentally inherited nuclear microsatellites. The boundary between mitochondrial lineages is very sharp; only six populations containing a mixture of different haplotypes were found. Bayesian analysis of population structure based on seven nSSR loci revealed the existence of two clusters which coincided fairly well with mitochondrial lineages. Both haplotype frequencies and proportions of clusters identified by the Bayesian analysis exhibited a clinal transition over the contact zone, with cline widths of 17.6 km for mitochondrial haplotype frequencies (reflecting gene flow by seeds) and 119.6 km for Bayesian clusters based on nSSR (reflecting gene flow by pollen). Allelic richness and gene diversity differ significantly between mitochondrial lineages, the Balkan group being more variable, but an increase in gene diversity towards the boundary between lineages was observed only within the Balkan lineage. The observed patterns are suggested to reflect the postglacial colonization and historical gene flow. They demonstrated that in silver fir as a wind-dispersed species, the colonization front is quite continuous, and the survival of migrant seeds in already established populations is low. The relative contribution of pollen-mediated gene flow to genetic exchange between divergent lineages associated with glacial refugia is much higher than in the case of seeds, but pollen dispersal distance is lower than suggested by earlier studies.     

The geographical distribution of genetic variation of silver fir (Abies alba,Pinaceae) in relation to its migration history

Silver fir presently occurs in many mountainous regions of eastern, western, southern and Central Europe. In order to elucidate the biogeographic history of fir populations in different European areas, the distribution of area-specific alleles at eight enzyme loci and the allele frequency distributions at seven polymorphic enzyme loci were investigated in seed or bud samples from 48 provenances comprising 98 single stands. Due to great genetic divergence among different populations located near the ancient glacial retreats, it was concluded that silver fir survived in five refugia during the last glaciation but migrated from only three refugia to its present natural range. The occurrence of unique alleles in particular fir areas indicated its migratory routes to the north and the existence of a few introgression zones where silver fir from different refugia has met during its expansion.     

Less Pollen-Mediated Gene Flow for More Signatures of Glacial Lineages: Congruent Evidence from Balsam Fir cpDNA and mtDNA for Multiple Refugia in Eastern and Central North America

The phylogeographic structure and postglacial history of balsam fir (Abies balsamea), a transcontinental North American boreal conifer, was inferred using mitochondrial DNA (mtDNA) and chloroplast DNA (cpDNA) markers. Genetic structure among 107 populations (mtDNA data) and 75 populations (cpDNA data) was analyzed using Bayesian and genetic distance approaches. Population differentiation was high for mtDNA (dispersed by seeds only), but also for cpDNA (dispersed by seeds and pollen), indicating that pollen gene flow is more restricted in balsam fir than in other boreal conifers. Low cpDNA gene flow in balsam fir may relate to low pollen production due to the inherent biology of the species and populations being decimated by recurrent spruce budworm epidemics, and/or to low dispersal of pollen grains due to their peculiar structural properties. Accordingly, a phylogeographic structure was detected using both mtDNA and cpDNA markers and population structure analyses supported the existence of at least five genetically distinct glacial lineages in central and eastern North America. Four of these would originate from glacial refugia located south of the Laurentide ice sheet, while the last one would have persisted in the northern Labrador region. As expected due to reduced pollen-mediated gene flow, congruence between the geographic distribution of mtDNA and cpDNA lineages was higher than in other North American conifers. However, concordance was not complete, reflecting that restricted but nonetheless detectable cpDNA gene flow among glacial lineages occurred during the Holocene. As a result, new cpDNA and mtDNA genome combinations indicative of cytoplasmic genome capture were observed.     

Molecular and palaeoecological evidence for multiple glacial refugia for evergreen oaks on the Iberian Peninsula

Aim  A multiple glacial refugia hypothesis for Mediterranean plant species was tested with the evergreen Quercus complex ( Quercus suber L., Quercus ilex L. and Quercus coccifera L.) from the Iberian Peninsula, using molecular and palaeobotanical data.
Location  The Iberian Peninsula, which is an ecologically and physiographically complex area located on the western edge of the Mediterranean Basin.
Methods  We sampled 1522 individuals from 164 populations of Q. suber , Q. ilex and Q. coccifera . A review of the recent literature on fossil pollen and charcoal records and a nested clade analysis on chloroplast DNA polymerase chain reaction-restriction fragment length polymorphism was carried out to infer demographic and historical processes.
Results  The analysis indicates at least one glacial refugium for Q. suber in south-western Iberia. Extensive introgression of Q. suber with Q. ilex indicates several potential refugia in eastern Iberia. Past fragmentation was followed by a restricted range flow/range expansion, suggesting multiple refugia for Q. ilex–Q. coccifera elsewhere in central and northern Iberia and multiple areas of secondary contact. This finding is consistent with fossil records.
Main conclusions  The predicted multiple refugia during glacial periods indicates the existence of secondary post-glaciation contact areas. These areas contained complex diversity patterns resulting mainly from range expansions followed by isolation by distance. To a lesser degree, traces of restricted and long-distance dispersal were also found.     

Chloroplast DNA variation and postglacial recolonization of common ash (Fraxinus excelsior L.) in Europe

We used chloroplast polymerase chain reaction-restriction-fragment length polymorphism (PCR-RFLP) and chloroplast microsatellites to assess the structure of genetic variation and postglacial history across the entire natural range of the common ash (Fraxinus excelsior L.), a broad-leaved wind-pollinated and wind-dispersed European forest tree. A low level of polymorphism was observed, with only 12 haplotypes at four polymorphic microsatellites in 201 populations, and two PCR-RFLP haplotypes in a subset of 62 populations. The clear geographical pattern displayed by the five most common haplotypes was in agreement with glacial refugia for ash being located in Iberia, Italy, the eastern Alps and the Balkan Peninsula, as had been suggested from fossil pollen data. A low chloroplast DNA mutation rate, a low effective population size in glacial refugia related to ash's life history traits, as well as features of postglacial expansion were put forward to explain the low level of polymorphism. Differentiation among populations was high (GST= 0.89), reflecting poor mixing among recolonizing lineages. Therefore, the responsible factor for the highly homogeneous genetic pattern previously identified at nuclear microsatellites throughout western and central Europe (Heuertz et al. 2004) must have been efficient postglacial pollen flow. Further comparison of variation patterns at both marker systems revealed that nuclear microsatellites identified complex differentiation patterns in south-eastern Europe which remained undetected with chloroplast microsatellites. The results suggest that data from different markers should be combined in order to capture the most important genetic patterns in a species.     

Rethinking long‐term vegetation dynamics: multiple glacial refugia and local expansion of a species complex

Evidence is accumulating that some arcto‐boreal plant taxa persisted through the last glacial maximum (LGM) in Alaska and adjacent Canada. However, the spatial patterns of glacial persistence and associated postglacial colonization remain largely unknown. In this study, we investigated the LGM refugia of an alder (Alnus) species complex (n = 3 taxa) and assess the spatiotemporal dynamics of Alnus in this vast region. Specifically, we conducted high‐throughput DNA sequencing (ddRADseq) on Alnus foliar samples collected from a dense population network to investigate patterns of genetic structure and infer the presence of glacial lineages. Species distribution modeling (SDM) was used to investigate the probability and possible locations of glacial persistence. These analyses were integrated and then compared with fossil pollen data to identify the locations of refugial populations and spatial patterns of postglacial colonization. Our genetic analyses revealed two glacial lineages with separate geographic origins for each Alnus taxon, suggesting that the genus persisted in multiple LGM refugia. Non‐overlapping hindcast distributions based on SDMs further support the presence of multiple, spatially distinct refugia. These ddRADseq and SDM results, in conjunction with reassessment of fossil pollen records, suggest that Alnus expanded from several population nuclei that existed during the LGM and coalesced during the Holocene to form its present range. These results challenge the unidirectional model for postglacial vegetation expansion, implying that climate buffering associated with landscape heterogeneity and adaptation to millennial‐scale environmental variability played important roles in driving late‐Quaternary population dynamics.     

Chloroplast DNA phylogeography of Alnus glutinosa (L.) Gaertn.

Traditionally, information on the postglacial history of plant species has been gained from the analysis of fossil pollen data. More recently, surveys of present patterns of genetic variation have given valuable insights into species phylogeography. The genus Alnus , based on fossil data, is known to have had at least four glacial refugia. A survey of chloroplast DNA (cpDNA) diversity in populations of black alder ( A. glutinosa ) was undertaken in order to gain more insight into its postglacial history. This revealed a high degree of structuring of 13 cpDNA haplotypes on a European scale which indicated that most of northern and central Europe was colonized from a refuge in the Carpathian Mountains. Based on the distribution of two common cpDNA haplotypes, colonization routes from this refuge can be determined. The locations of other previously identified refugia are confirmed and two formerly unconfirmed refugial areas for alder (southern Spain and Turkey) are proposed.