The homogenous genetic structure and inferred unique history of range shifts during the Pleistocene climatic oscillations of <Emphasis Type="Italic">Arcterica nana</Emphasis> (Maxim.) Makino (Ericaceae)

Previous phylogeographic studies of alpine plants in Japan have inferred that populations in central Honshu persisted during the Pleistocene climatic oscillations and suggested interglacial survival in high mountains. However, Arcterica nana (Maxim.) Makino (Ericaceae) exhibits a homogenous genetic structure throughout Japan and may therefore have a unique phylogeographic history. This inconsistency could have resulted from insufficient resolution of previously analyzed chloroplast DNA sequences. Therefore, we conducted a phylogeographic investigation based on amplified fragment length polymorphisms. Using 176 individuals from 21 populations, the relationships among individuals and populations were determined by principal coordinate analysis and a neighbor-joining tree, respectively. In addition, genetic differentiation was estimated using analysis of molecular variance and spatial autocorrelation analysis. These analyses demonstrate a homogenous structure throughout the entire Japanese range, supporting the previous cpDNA phylogeography. Although this genetic structure is inconsistent with those of other alpine plants, it is difficult to postulate that pre-existing genetic differentiation was swamped exclusively within A. nana. Therefore, this homogenous genetic structure may have been caused by the distinct history of populations of A. nana. Specifically, the southern-ward migration and the subsequent continuous populations enabled gene flow throughout the Japanese archipelago during the last glacial period. Thus, our data suggest that alpine plants in the Japanese archipelago did not always experience a shared distribution change following climatic oscillations.     

Evolutionary history of a desert perennial Arnebia szechenyi (Boraginaceae): Intraspecific divergence,regional expansion and asymmetric gene flow

The complex interactions of historical, geological and climatic events on plant evolution have been an important research focus for many years. However, the role of desert formation and expansion in shaping the genetic structures and demographic histories of plants occurring in arid areas has not been well explored. In the present study, we investigated the phylogeography of Arnebia szechenyi, a desert herb showing a near-circular distribution surrounding the Tengger Desert in Northwest China. We measured genetic diversity of populations using three maternally inherited chloroplast DNA (cpDNA) fragments and seven bi-paternally inherited nuclear DNA (nDNA) loci that were sequenced from individuals collected from 16 natural populations across its range and modelled current and historical potential habitats of the species. Our data indicated a considerably high level of genetic variation within A. szechenyi and noteworthy asymmetry in historical migration from the east to the west. Moreover, two nuclear genetic groups of populations were revealed, corresponding to the two geographic regions separated by the Tengger Desert. However, analysis of cpDNA data did not show significant geographic structure. The most plausible explanation for the discrepancy between our findings based on cpDNA and nDNA data is that A. szechenyi populations experienced long periods of geographic isolation followed by range expansion, which would have promoted generalized recombination of the nuclear genome. Our findings further highlight the important role that the Tengger Desert, together with the Helan Mountains, has played in the evolution of desert plants and the preservation of biodiversity in arid Northwest China.     

High mountains of the Japanese archipelago as refugia for arctic–alpine plants: phylogeography of Loiseleuria procumbens (L.) Desvaux (Ericaceae)

According to previous phylogeographic studies, high mountains at low latitudes are important areas for the study of the evolutionary history of arctic–alpine plants in surviving the Pleistocene climatic oscillations. To evaluate this hypothesis, we elucidated the genetic structure of the arctic–alpine plant, Loiseleuria procumbens , in the Japanese archipelago, which corresponds to one of the southernmost limits of its distribution, using 152 individuals from 17 populations that covered the entire distribution of the Japanese archipelago and Sakhalin, in addition to samples from Sweden. Based on 854 bp of chloroplast DNA, we detected eight haplotypes. Along with haplotype distribution, strong genetic differentiation between populations in central and northern Japan was elucidated by a neighbour-joining tree (100%) and spatial analysis of molecular variance (79%), which is consistent with other alpine plants in Japan, regardless of the species' range. In addition, the southernmost populations from northern Japan showed specific genetic structure, although the remaining areas of northern Japan and Sakhalin harboured an homogenous genetic structure. Our results suggest that the populations in central Japan persisted for a long time during the Pleistocene climatic oscillation and that genetic divergence occurred in situ , supporting our hypothesis in conjunction with a previous study of another arctic–alpine plant, Diapensia lapponica subsp. obovata .  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 403–412.     

Phylogeography of <Emphasis Type="Italic">Achyranthes bidentata</Emphasis> (Amaranthaceae) in China’s Warm-Temperate Zone Inferred from Chloroplast and Nuclear DNA: Insights into Population Dynamics in Response to Climate Change During the Pleistocene

Previous phylogeographic studies of the warm-temperate zone in China focused on woody plants, but little attention was given to the climate-sensitive herbaceous plants. In this work, we implemented a phylogeographic survey on the perennial herb Achyranthes bidentata in China’s warm-temperate zone. The sequence variation of cpDNA and nDNA was examined across 209 individuals from 21 populations. A total of 11 chlorotypes and 26 ribotypes were identified. The cpDNA data showed weak population genetic differentiation and could not divide the 21 populations into different genetic groups. By contrast, the nDNA data revealed stronger genetic differentiation than cpDNA and could divide these populations into two genetic groups. The cpDNA and nDNA data both gave unambiguous signs of recent sudden population expansion. Based on the cpDNA and nDNA data, the estimated time of population expansion occurred at interglacial Marine Isotope Stage (MIS) 9 of the Penultimate Glaciation in China. The cpDNA and nDNA data suggested that the glaciation during this period deeply influenced the current distribution patterns and intraspecific divergence of A. bidentata. Our survey showed that A. bidentata tracked climatic oscillations by a large range of southward retreat into three main refugia during MIS 8, followed by the sudden northward expansion from these refugia during MIS 9.     

Latitudinal Environmental Niches and Riverine Barriers Shaped the Phylogeography of the Central Chilean Endemic Dioscorea humilis (Dioscoreaceae)

The effects of Pleistocene glaciations and geographical barriers on the phylogeographic patterns of lowland plant species in Mediterranean-climate areas of Central Chile are poorly understood. We used Dioscorea humilis (Dioscoreaceae), a dioecious geophyte extending 530 km from the Valparaíso to the Bío-Bío Regions, as a case study to disentangle the spatio-temporal evolution of populations in conjunction with latitudinal environmental changes since the Last Inter-Glacial (LIG) to the present. We used nuclear microsatellite loci, chloroplast (cpDNA) sequences and environmental niche modelling (ENM) to construct current and past scenarios from bioclimatic and geographical variables and to infer the evolutionary history of the taxa. We found strong genetic differentiation at nuclear microsatellite loci between the two subspecies of D. humilis, probably predating the LIG. Bayesian analyses of population structure revealed strong genetic differentiation of the widespread D. humilis subsp. humilis into northern and southern population groups, separated by the Maipo river. ENM revealed that the ecological niche differentiation of both groups have been maintained up to present times although their respective geographical distributions apparently fluctuated in concert with the climatic oscillations of the Last Glacial Maximum (LGM) and the Holocene. Genetic data revealed signatures of eastern and western postglacial expansion of the northern populations from the central Chilean depression, whereas the southern ones experienced a rapid southward expansion after the LGM. This study describes the complex evolutionary histories of lowland Mediterranean Chilean plants mediated by the summed effects of spatial isolation caused by riverine geographical barriers and the climatic changes of the Quaternary.     

Deciphering the global phylogeography of a coastal shrub (Scaevola taccada) reveals the influence of multiple forces on contemporary population structure

The phylogeography of coastal plant species is heavily influenced by past sealevel fluctuations, dispersal barriers, and life-history traits, such as long-distance dispersal ability of the propagules. Unlike the widely studied mangroves, phylogeographic patterns have remained mostly obscure for other coastal plant species. In this study, we sampled 42 populations of Scaevola taccada (Gaertn.) Roxb., a coastal shrub of the family Goodeniaceae, from 17 countries across its distribution range. We used five chloroplast DNA (cpDNA) and 14 nuclear microsatellite (simple sequence repeat [SSR]) markers to assess the influence of abiotic factors and population genetic processes on the phylogeographic pattern of the species. Geographical distribution of cpDNA haplotypes suggests that the species originated in Australia, followed by historical dispersal and expansion of its geographic range. Multiple abiotic factors, including the sealevel changes during the Pleistocene, the presence of landmasses like the Malay Peninsula, and contemporary oceanic circulation patterns, restricted gene flow between geographically distinct populations, thereby creating low haplotype diversity and a strong population structure. Population genetic processes acted on these isolated populations, leading to high nuclear genetic diversity and population differentiation, as revealed from analyzing the polymorphic SSR loci. Although genetic divergence was mostly concordant between cpDNA and SSR data, asymmetrical gene flow and ancestral polymorphism could explain the discordance in the detailed genetic structure. Overall, our findings indicate that abiotic factors and population genetic processes interactively influenced the evolutionary history and current phylogeographic pattern of S. taccada across its distribution range.     

The Historical Demography and Genetic Variation of the Endangered Cycas multipinnata (Cycadaceae) in the Red River Region,Examined by Chloroplast DNA Sequences and Microsatellite Markers

Cycas multipinnata C.J. Chen & S.Y. Yang is a cycad endemic to the Red River drainage region that occurs under evergreen forest on steep limestone slopes in Southwest China and northern Vietnam. It is listed as endangered due to habitat loss and over-collecting for the ornamental plant trade, and only several populations remain. In this study, we assess the genetic variation, population structure, and phylogeography of C. multipinnata populations to help develop strategies for the conservation of the species. 60 individuals from six populations were used for chloroplast DNA (cpDNA) sequencing and 100 individuals from five populations were genotyped using 17 nuclear microsatellites. High genetic differentiation among populations was detected, suggesting that pollen or seed dispersal was restricted within populations. Two main genetic clusters were observed in both the cpDNA and microsatellite loci, corresponding to Yunnan China and northern Vietnam. These clusters indicated low levels of gene flow between the regions since their divergence in the late Pleistocene, which was inferred from both Bayesian and coalescent analysis. In addition, the result of a Bayesian skyline plot based on cpDNA portrayed a long history of constant population size followed by a decline in the last 50,000 years of C. multipinnata that was perhaps affected by the Quaternary glaciations, a finding that was also supported by the Garza-Williamson index calculated from the microsatellite data. The genetic consequences produced by climatic oscillations and anthropogenic disturbances are considered key pressures on C. multipinnata. To establish a conservation management plan, each population of C. multipinnata should be recognized as a Management Unit (MU). In situ and ex situ actions, such as controlling overexploitation and creating a germplasm bank with high genetic diversity, should be urgently implemented to preserve this species.     

Phylogeography and genetic structure of the red-legged partridge (Alectoris rufa): more evidence for refugia within the Iberian glacial refugium

The Pleistocene climatic oscillations promoted the diversification in avian species during the last glacial period. The red‐legged partridge (Alectoris rufa, Family Phasianidae) has a large natural distribution extending from the Mediterranean to humid temperate zones. However, the genetic structure for this species is unknown. The present study investigates the phylogeography, genetic structure and demographic history of A. rufa across its distribution, employing both mitochondrial DNA control region sequences and nuclear microsatellite loci. Our results propose that this species was greatly affected by Pleistocene glaciations. The mismatch analyses suggest that the current populations resulted from post‐glacial expansion and subsequent differentiation resulting in five diagnosable genetic clusters: Southwestern, Central‐eastern, Northwestern, Balearic and French and Italian. Further, we found evidence of three glacial refugia within the currently recognized Iberian glacial refugium. The intraspecific structure revealed by both maternal and biparental phylogeographic analyses was not resolved in the phylogenetic analyses. Based on all considerations, we recommended that five management units be recognized.     

Phylogeography of the black fly Simulium tani (Diptera: Simuliidae) from Thailand as inferred from mtDNA sequences

Intraspecific phylogeography has been used widely as a tool to infer population history. However, little attention has been paid to Southeast Asia despite its importance in terms of biodiversity. Here we used the cytochrome oxidase I gene of mitochondrial DNA (mtDNA) for a phylogeographic study of 147 individuals of the black fly Simulium tani from Thailand. The mtDNA revealed high genetic differentiation between the major geographical regions of north, east and central/south Thailand. Mismatch distributions indicate population expansions during the mid-Pleistocene and the late Pleistocene suggesting that current population structure and diversity may be due in part to the species' response to Pleistocene climatic fluctuations. The genealogical structure of the haplotypes, high northern diversity and maximum-likelihood inference of historical migration rates, suggest that the eastern and central/southern populations originated from northern populations in the mid-Pleistocene. Subsequently, the eastern region had had a largely independent history but the central/southern population may be largely the result of recent (c. 100,000 years ago) expansion, either from the north again, or from a relictual population in the central region. Cytological investigation revealed that populations from the south and east have two overlapping fixed chromosomal inversions. Since these populations also share ecological characteristics it suggests that inversions are involved in ecological adaptation. In conclusion both contemporary and historical ecological conditions are playing an important role in determining population genetic structure and diversity.     

The phylogeography of Fagus hayatae (Fagaceae): genetic isolation among populations

The beech species Fagus hayatae is an important relict tree species in subtropical China, whose biogeographical patterns may reflect floral responses to climate change in this region during the Quaternary. Previous studies have revealed phylogeography for three of the four Fagus species in China, but study on F. hayatae, the most sparsely distributed of these species, is still lacking. Here, molecular methods based on eight simple sequence repeat (SSR) loci of nuclear DNA (nDNA) and three chloroplast DNA (cpDNA) sequences were applied for analyses of genetic diversity and structure in 375 samples from 14 F. hayatae populations across its whole range. Both nDNA and cpDNA indicated a high level of genetic diversity in this species. Significant fixation indexes and departures from the Hardy–Weinberg equilibrium, with a genetic differentiation parameter of R_st of 0.233, were detected in nDNA SSR loci among populations, especially those on Taiwan Island, indicating strong geographic partitioning. The populations were classified into two clusters, without a prominent signal of isolation‐by‐distance. For the 15 haplotypes detected in the cpDNA sequence fragments, there was a high genetic differentiation parameter (G_st = 0.712) among populations. A high G_st of 0.829 was also detected outside but not within the Sichuan Basin. Consistent with other Fagus species in China, no recent population expansion was detected from tests of neutrality and mismatch distribution analysis. Overall, genetic isolation with limited gene flow was prominent for this species and significant phylogeographic structures existed across its range except for those inside the Sichuan Basin. Our study suggested long‐term geographic isolation in F. hayatae with limited population admixture and the existence of multiple refugia in the mountainous regions of the Sichuan Basin and southeast China during the Quaternary. These results may provide useful information critical for the conservation of F. hayatae and other Chinese beech species.     

Some butterflies do not care much about topography: a single genetic lineage of Erebia euryale (Nymphalidae) along the northern Iberian mountains

The phylogeography of montane species often reveals strong genetic differentiation among mountain ranges. Both classic morphological and genetic studies have indicated distinctiveness of Pyrenean populations of the butterfly Erebia euryale. This hypothesis remained inconclusive until data from the westernmost populations of the distribution area (Cantabrian Mountains) were analysed. In the present study, we set out to describe the population structure of Erebia euryale in western Cantabria, where the species occurs in scattered localities. For this goal, we estimate the genetic diversity and differentiation found in 218 individuals from six Cantabrian (North Spain) localities genotyped by 17 allozyme loci. We also sequence 816 bp of the cytochrome oxidase subunit I mitochondrial gene in 49 individuals from Cantabrian localities and 41 specimens from five other European sites. Mitochondrial data support the recognition of four major genetic groups previously suggested for the European populations based on allozyme polymorphisms. Both mitochondrial and nuclear markers reveal genetic distinctiveness of a single Pyrenean–Cantabrian lineage of E. euryale. The lack of geographical structure and the star‐like topology displayed by the mitochondrial haplotypes indicate a pattern of demographic expansion in northern Iberia, probably related to Upper Pleistocene climatic oscillations. By contrast, within the Pyrenean–Cantabrian lineage, Cantabrian samples are genetically structured in nuclear datasets. In particular, San Isidro is significantly differentiated from the other five populations, which cluster into two groups. We recognize an evolutionary significant unit for Pyrenean–Cantabrian populations of Erebia euryale. Our results also illustrate that the evolutionary history of a species may be shaped by processes undetectable by using mtDNA alone.     

Diversity and demography in Beringia: multilocus tests of paleodistribution models reveal the complex history of arctic ground squirrels

To assess effects of historical climate change on northern species, we quantified the population history of the arctic ground squirrel (Spermophilus parryii), an arctic-adapted rodent that evolved in Beringia and was strongly influenced by climatic oscillations of the Quaternary. Competing hypotheses for the species' population history were derived from patterns of mitochondrial (mtDNA) structure and a bioclimatic envelope model (BEM). Hypotheses invoked (1) sequential isolation of regional populations beginning with the Arctic, (2) deep isolation only across central Alaska, and (3) widespread panmixia, and were tested using coalescent methods applied to eight nuclear (nDNA) loci. The data rejected strict interpretations of all three hypotheses, but perspectives underlying each encompassed aspects of the species' history. Concordance between mtDNA and nDNA geographic structure revealed three semi-independently evolving phylogroups, whereas signatures of gene flow at nDNA loci were consistent with a historical contact between certain populations as inferred by the BEM. Demographic growth was inferred for all regions despite expectations of postglacial habitat contraction for parts of Beringia. Our results highlight the complementary perspectives on species' histories that multiple lines of evidence provide, and underscore the utility of multilocus data for resolving complex population histories relevant to understanding effects of climate change.     

Distinct Phylogeographic Structures of Wild Radish (Raphanus sativus L. var. raphanistroides Makino) in Japan

Coastal plants with simple linear distribution ranges along coastlines provide a suitable system for improving our understanding of patterns of intra-specific distributional history and genetic variation. Due to the combination of high seed longevity and high dispersibility of seeds via seawater, we hypothesized that wild radish would poorly represent phylogeographic structure at the local scale. On the other hand, we also hypothesized that wild radish populations might be geographically differentiated, as has been exhibited by their considerable phenotypic variations along the islands of Japan. We conducted nuclear DNA microsatellite loci and chloroplast DNA haplotype analyses for 486 samples and 144 samples, respectively, from 18 populations to investigate the phylogeographic structure of wild radish in Japan. Cluster analysis supported the existence of differential genetic structures between the Ryukyu Islands and mainland Japan populations. A significant strong pattern of isolation by distance and significant evidence of a recent bottleneck were detected. The chloroplast marker analysis resulted in the generation of eight haplotypes, of which two haplotypes (A and B) were broadly distributed in most wild radish populations. High levels of variation in microsatellite loci were identified, whereas cpDNA displayed low levels of genetic diversity within populations. Our results indicate that the Kuroshio Current would have contributed to the sculpting of the phylogeographic structure by shaping genetic gaps between isolated populations. In addition, the Tokara Strait would have created a geographic barrier between the Ryukyu Islands and mainland Japan. Finally, extant habitat disturbances (coastal erosion), migration patterns (linear expansion), and geographic characteristics (small islands and sea currents) have influenced the expansion and historical population dynamics of wild radish. Our study is the first to record the robust phylogeographic structure in wild radish between the Ryukyu Islands and mainland Japan, and might provide new insight into the genetic differentiation of coastal plants across islands.     

Phylogeography of East Asian <Emphasis Type="Italic">Lespedeza buergeri</Emphasis> (Fabaceae) based on chloroplast and nuclear ribosomal DNA sequence variations

The dynamic changes in land configuration during the Quaternary that were accompanied by climatic oscillations have significantly influenced the current distribution and genetic structure of warm-temperate forests in East Asia. Although recent surveys have been conducted, the historical migration of forest species via land bridges and, especially, the origins of Korean populations remains conjectural. Here, we reveal the genetic structure of Lespedeza buergeri, a warm-temperate shrub that is disjunctively distributed around the East China Sea (ECS) at China, Korea, and Japan. Two non-coding regions (rpl32-trnL, psbA-trnH) of chloroplast DNA (cpDNA) and the internal transcribed spacer of nuclear ribosomal DNA (nrITS) were analyzed for 188 individuals from 16 populations, which covered almost all of its distribution. The nrITS data demonstrated a genetic structure that followed geographic boundaries. This examination utilized AMOVA, comparisons of genetic differentiation based on haplotype frequency/genetic mutations among haplotypes, and Mantel tests. However, the cpDNA data showed contrasting genetic pattern, implying that this difference was due to a slower mutation rate in cpDNA than in nrITS. These results indicated frequent migration by this species via an ECS land bridge during the early Pleistocene that then tapered gradually toward the late Pleistocene. A genetic isolation between western and eastern Japan coincided with broad consensus that was suggested by the presence of other warm-temperate plants in that country. For Korean populations, high genetic diversity indicated the existence of refugia during the Last Glacial Maximum on the Korean Peninsula. However, their closeness with western Japanese populations at the level of haplotype clade implied that gene flow from western Japanese refugia was possible until post-glacial processing occurred through the Korea/Tsushima Strait land bridge.     

Contrasting patterns of mitochondrial and microsatellite genetic structure among Western European populations of tawny owls (Strix aluco)

A recent study of mitochondrial phylogeography of tawny owls (Strix aluco) in western Europe suggested that this species survived the Pleistocene glaciations in three allopatric refugia located in Iberia, Italy, and the Balkans, and the latter was likely the predominant source of postglacial colonization of northern Europe. New data from seven microsatellite loci from 184 individual owls distributed among 14 populations were used to assess the genetic congruence between nuclear and mitochondrial DNA (mtDNA) markers. Microsatellites corroborated the major phylogeographical conclusions reached on the basis of the mtDNA sequences, but also showed important differences leading to novel inferences. Microsatellites corroborated the three major refugia and supported the Balkan origin of northern populations. When corrected for differences in effective population size, microsatellites and mtDNA yielded generally congruent overall estimates of population structure (N*ST=0.12 vs. RST=0.16); however, there was substantial heterogeneity in the RST among the seven nuclear loci that was not correlated with heterozygosity. Populations representing the Balkans postglacial expansion interact with populations from the other two refugia forming two clines near the Alps and the Pyrenees. In both cases, the apparent position of the contact zones differed substantially between markers due to the genetic composition of populations sampled in northern Italy and Madrid. Microsatellite data did not corroborate the lower genetic diversity of northern, recently populated regions as was found with mtDNA; this discrepancy was taken as evidence for a recent bottleneck recovery. Finally, this study suggests that congruence among genetic markers should be more likely in cases of range expansion into new areas than when populations interact across contact zones.     

Climatic Factors Drive Population Divergence and Demography: Insights Based on the Phylogeography of a Riparian Plant Species Endemic to the Hengduan Mountains and Adjacent Regions

Quaternary climatic factors have played a significant role in population divergence and demography. Here we investigated the phylogeography of Osteomeles schwerinae, a dominant riparian plant species of the hot/warm-dry river valleys of the Hengduan Mountains (HDM), Qinling Mountains (QLM) and Yunnan-Guizhou Plateau (YGP). Three chloroplast DNA (cpDNA) regions (trnD-trnT, psbD-trnT, petL-psbE), one single copy nuclear gene (glyceraldehyde 3-phosphate dehydrogenase; G3pdh), and climatic data during the Last Interglacial (LIG; c. 120–140 ka), Last Glacial Maximum (LGM; c. 21 ka), and Current (c. 1950–2000) periods were used in this study. Six cpDNA haplotypes and 15 nuclear DNA (nDNA) haplotypes were identified in the 40 populations of O. schwerinae. Spatial Analysis of Molecular Variance, median-joining networks, and Bayesian phylogenetic trees based on the cpDNA and nDNA datasets, all suggested population divergence between the QLM and HDM-YGP regions. Our climatic analysis identified significant heterogeneity of the climatic factors in the QLM and HDM-YGP regions during the aforementioned three periods. The divergence times based on cpDNA and nDNA haplotypes were estimated to be 466.4–159.4 ka and 315.8–160.3 ka, respectively, which coincide with the time of the weakening of the Asian monsoons in these regions. In addition, unimodal pairwise mismatch distribution curves, expansion times, and Ecological Niche Modeling suggested a history of population expansion (rather than contraction) during the last glaciation. Interestingly, the expansion times were found being well consistent with the intensification of the Asian monsoons during this period. We inferred that the divergence between the two main lineages is probably caused by disruption of more continuous distribution because of weakening of monsoons/less precipitation, whilst subsequent intensification of the Asian monsoons during the last glaciation facilitated the expansion of O. schwerinae populations.     

Isolation and introgression in the Intermountain West: contrasting gene genealogies reveal the complex biogeographic history of the American pika (Ochotona princeps)

Aim We studied the history of colonization, diversification and introgression among major phylogroups in the American pika, Ochotona princeps (Lagomorpha), using comparative and statistical phylogeographic methods. Our goal was to understand how Pleistocene climatic fluctuations have shaped the distribution of diversity at mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) loci in this alpine specialist. Location North America’s Intermountain West. Methods We accumulated mtDNA sequence data (c. 560–1700 bp) from 232 pikas representing 64 localities, and sequenced two nuclear introns (mast cell growth factor, c. 550 bp, n = 148; protein kinase C iota, c. 660 bp, n = 139) from a subset of individuals. To determine the distribution of major mtDNA lineages, we conducted a phylogenetic analysis on the mtDNA sequence data, and we calculated divergence times among the lineages using a Bayesian Markov chain Monte Carlo approach. Relationships among nuclear alleles were explored with minimum spanning networks. Finally, we conducted coalescent simulations of alternative models of population history to test for congruence between nDNA and mtDNA responses to Pleistocene glacial cycles. Results We found that: (1) all individuals could be assigned to one of five allopatric mtDNA lineages; (2) lineages are associated with separate mountain provinces; (3) lineages originated from at least two rounds of differentiation; (4) nDNA and mtDNA markers exhibited overall phylogeographic congruence; and (5) introgression among phylogroups has occurred at nuclear loci since their initial isolation. Main conclusions Pika populations associated with different mountain systems have followed separate but not completely independent evolutionary trajectories through multiple glacial cycles. Range expansion associated with climate cooling (i.e. glaciations) promoted genetic admixture among populations within mountain ranges. It also permitted periodic contact and introgression between phylogroups associated with different mountain systems, the record of which is retained at nDNA but not mtDNA loci. Evidence for different histories at nuclear and mtDNA loci (i.e. periodic introgression versus deep isolation, respectively) emphasizes the importance of multilocus perspectives for reconstructing complete population histories.     

Phylogeography reveals latitudinal population structure in the common herb Plantago coronopus

The increase in gene diversity from high to low latitudes is a widely recognized biogeographical pattern, often shaped by differential effects of Late Quaternary climatic changes. Here, we evaluate the effects of Pleistocene climatic changes from northern Europe to North Africa and their implications on the population differentiation of the widespread, short‐lived herb Plantago coronopus. We used amplified fragment length polymorphism to investigate the population structure and phylogeography of P. coronopus in 273 individuals from 29 populations covering its complete latitudinal range. Although Bayesian clustering, principal coordinates analysis and a consensus UPGMA tree were not fully congruent, two well‐supported clades, associated with distinct latitudinal zones (northern Europe and the Mediterranean region), were revealed as a general pattern. Moreover, populations from the western Atlantic edge and, to a lesser extent, the central Mediterranean region exhibited signs of admixture, suggesting secondary contacts. The admixed populations in the western Atlantic and central Mediterranean are geographically intermediate between the northern and southern lineages. The northernmost lineage exhibited low genetic diversity, a clear sign of a recent colonization. In contrast, populations from the southernmost part of the range showed the highest level of genetic diversity, indicating possible refugia for the species during the Quaternary ice ages. Overall, our study allows spatial structure of the genetic variation of a widespread herb across its latitudinal range to be disentangled and provides insights into how past climatic history influences present genetic patterns. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 618–634.     

Diversification in subtropical mountains: phylogeography, Pleistocene demographic expansion, and evolution of polyphenic mandibles in Taiwanese stag beetle, Lucanus formosanus

Pleistocene glacial oscillations have had profound impacts on the historical population dynamics of extant species. However, the genetic consequences of past climatic changes depend largely on the latitude and topography of the regions in question. This study investigates the effect of Pleistocene glacial periods and the Central Mountain Range on the phylogeography, historical demography, and phenotypic differentiation of a montane forest-dwelling stag beetle, Lucanus formosanus (Coleoptera: Lucanidae), which exhibits extensive mandible variations across mountain ranges in subtropical Taiwan. Analyses of mitochondrial (cox1) and nuclear (wg) loci reveal that L. formosanus originated nearly 1.6 million years ago (Mya) in the early Pleistocene period and consisted of geographically overlapping Alishan and Widespread clades. A drastic population expansion starting approximately 0.2 Mya in the Widespread clade likely resulted from altitudinal range shift of the temperate forests, which was closely tied to the arrival of the Riss glacial period in the late Middle Pleistocene. A ring-like pattern of historical gene flow among neighboring populations in the vicinity of the Central Mountain Range indicates that the mountains constitute a strong vicariant barrier to the east-west gene flow of L. formosanus populations. A geographic cline of decreasing mandible size from central to north and south, and onto southeast of Taiwan is inconsistent with the low overall phylogeographic structures. The degree of mandible variation does not correlate with the expected pattern of neutral evolution, indicating that the evolutionary diversification of this morphological weapon is most likely subject to sexual or natural selection. We hypothesize that the adaptive evolution of mandibles in L. formosanus is shaped largely by the habitat heterogeneity.     

Genetic variation of oaks (<Emphasis Type="Italic">Quercus</Emphasis> spp.) in Switzerland. 3. Lack of impact of postglacial recolonization history on nuclear gene loci

Quercus petraea, Quercus pubescens and Quercus robur are closely related and interfertile white oaks native to Switzerland. The three species are known to share identical cpDNA haplotypes, which are indicative of the postglacial recolonization history of populations. Only two haplotypes are common in Switzerland. We compared variation of cpDNA and of isozymes in 28 oak populations from Switzerland in order to assess the impact of the postglacial population history on current genetic structures of nuclear controlled isozyme gene loci. Species delineation was based on Principal Component Analysis of leaf morphological traits. The species status of populations was reflected at isozyme gene loci, but differentiation between populations with different cpDNA haplotypes and hence different recolonization history was very low at enzyme gene loci for all species. Thus, glacial and postglacial population history was not reflected at nuclear gene loci on the temporal and spatial scale covered by the present study. Extensive gene flow through pollen among populations is likely to have blurred a previously existing genetic differentiation at biparentally inherited gene loci that possibly evolved in the different glacial refugia of the above mentioned cpDNA haplotypes.