History and evolution of alpine plants endemic to the Qinghai-Tibetan Plateau: Aconitum gymnandrum (Ranunculaceae)

How Quaternary climatic oscillations affected range distributions and intraspecific divergence of alpine plants on the Qinghai‐Tibetan Plateau (QTP) remains largely unknown. Here, we report a survey of chloroplast DNA (cpDNA) and nuclear ribosomal internal transcribed spacer (ITS) DNA variation aimed at exploring the phylogeographical history of the QTP alpine endemic Aconitum gymnandrum. We sequenced three cpDNA fragments (rpl20–rps12 intergenic spacer, the trnV intron and psbA‐trnH spacer) and also the nuclear (ITS) region in 245 individuals from 23 populations sampled throughout the species’ range. Two distinct lineages, with eastern and western geographical distributions respectively, were identified from a phylogenetic analysis of ITS sequence variation. Based on a fast substitution rate, these were estimated to have diverged from each other in the early Pleistocene approximately 1.45 Ma. The analysis of cpDNA variation identified nine chlorotypes that clustered into two major clades that were broadly congruent in geographical distribution with the two ITS lineages. The east–west split of cpDNA divergence was supported by an amova which partitioned approximately half of the total variance between these two groups of populations. Analysis of the spatial distribution of chlorotypes showed that each clade was subdivided into two groups of populations such that a total of four population groups existed in the species. It is suggested that these different groups derive from four independent glacial refugia that existed during the Last Glacial Maximum (LGM), and that three of these refugia were located at high altitude on the QTP platform itself at that time. Coalescent simulation of chlorotype genealogies supported both an early Pleistocene origin of the two main cpDNA clades and also the ‘four‐refugia’ hypothesis during the LGM. Two previous phylogeographical studies of QTP alpine plants indicated that such plants retreated to refugia at the eastern/south‐eastern plateau edge during the LGM and/or previous glacial maxima. However, the results for A. gymnandrum suggest that at least some of these cold‐tolerant species may have also survived centrally on the QTP platform throughout the Quaternary.     

The Quaternary evolutionary history,potential distribution dynamics,and conservation implications for a Qinghai–Tibet Plateau endemic herbaceous perennial,Anisodus tanguticus (Solanaceae)

Various hypotheses have been proposed about the Quaternary evolutionary history of plant species on the Qinghai–Tibet Plateau (QTP), yet only a handful of studies have considered both population genetics and ecological niche context. In this study, we proposed and compared climate refugia hypotheses based on the phylogeographic pattern of Anisodus tanguticus (three plastid DNA fragments and nuclear internal transcribed spacer regions from 32 populations) and present and past species distribution models (SDMs). We detected six plastid haplotypes in two well‐differentiated lineages. Although all haplotypes could be found in its western (sampling) area, only haplotypes from one lineage occurred in its eastern area. Meanwhile, most genetic variations existed between populations (F_ST = 0.822). The SDMs during the last glacial maximum and last interglacial periods showed range fragmentation in the western area and significant range contraction in the eastern area, respectively, in comparison with current potential distribution. This species may have undergone intraspecific divergence during the early Quaternary, which may have been caused by survival in different refugia during the earliest known glacial in the QTP, rather than geological isolation due to orogenesis events. Subsequently, climate oscillations during the Quaternary resulted in a dynamic distribution range for this species as well as the distribution pattern of its plastid haplotypes and nuclear genotypes. The interglacial periods may have had a greater effect on A. tanguticus than the glacial periods. Most importantly, neither genetic data nor SDM alone can fully reveal the climate refugia history of this species. We also discuss the conservation implications for this important Tibetan folk medicine plant in light of these findings and SDMs under future climate models. Together, our results underline the necessity to combine phylogeographic and SDM approaches in future investigations of the Quaternary evolutionary history of species in topographically complex areas, such as the QTP.     

Range expansion during the Pleistocene drove morphological radiation of the fir genus (Abies,Pinaceae) in the Qinghai‐Tibet Plateau and Himalayas

Range expansion caused by climate oscillations in the past probably promoted morphological radiation in a few plant groups. In this study, we aim to test this hypothesis through phylogeographical analysis of the cold‐tolerant fir genus (Abies) in the Qinghai‐Tibet Plateau (QTP) and Himalayas, where it comprises 12 described species. We examined sequence variation in two maternally inherited mitochondrial (mt) DNA fragments (nad5‐4 and nad7‐1) and two paternally inherited plastid DNA fragments (trnS‐G and trnL‐F) for 733 individuals from 75 populations of the species in a monophyletic group. Only six mtDNA haplotypes were recovered, but five were shared between multiple species and one occurred at a high frequency, providing strong evidence of range expansion. Forty‐three plastid DNA haplotypes were detected, 19 of which were shared between species and three occurred at high frequency. Network, mismatch and Bayesian skyline plot analyses of all plastid DNA haplotypes from this clade clearly suggested range expansion. This expansion was dated as having occurred during the longest and most extensive glaciation in the Pleistocene. Our results therefore supported the range expansion hypothesis for this clade of Abies during the Pleistocene; expansion probably drove the morphological radiation of the clade in the QTP and Himalayas, although it remains unclear whether the different morphotypes should be acknowledged as independent, reproductively isolated species. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 444–453.     

Complex fine‐scale phylogeographical patterns in a putative refugial region for Fagus sylvatica (Fagaceae)

Broad‐scale plastid (chloroplast) DNA studies of beech (Fagus sylvatica) populations suggest the existence of glacial refugia and introgression zones in south‐eastern Europe. We choose a possible refugium of beech in northern Greece, Mt. Paggeo, which hosts a private plastid haplotype for beech, to conduct a fine‐scale genetic study. We attempt to confirm or reject the hypothesis of the existence of a small‐scale refugium and to gain an understanding of the ecological and topographical factors affecting the spatial distribution of plastid haplotypes in the area. Our results reveal a high haplotype diversity on Mt. Paggeo, but the overall distribution of haplotypes shows no significant correlation with the ecological characteristics of the beech forests. However, the private haplotype is found at high frequencies in beech forests located in or near ravines, having a high spatial overlap with a relict vegetation type occurring in ecological conditions found mainly in ravines. This result emphasizes the importance of topography in the existence of glacial refugia in the wider area. Furthermore, haplotypes originating from two more widespread beech lineages in Greece are found on Mt. Paggeo, indicating a possible mixing of populations originating from a local refugium with populations from remote refugia that possibly migrated into the area after the last glaciation. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 174 , 516–528.     

Phylogeography of the genus Dasiphora (Rosaceae) in the Qinghai‐Tibetan Plateau: divergence blurred by expansion

Plateau uprisings and climatic oscillations are considered to have caused extensive allopatric divergences that account for the rich species diversity of the Qinghai‐Tibetan Plateau (QTP). However, secondary contact during range shifts in the Quaternary glacial cycles or inter‐uplift stages may have restored the gene flow between species and so counteracted these divergences, particularly in rapidly‐adapting dominant elements. We tested this hypothesis by determining the phylogeographical history of Dasiphora (Rosaceae), a genus of two species that are widely distributed on the QTP and co‐exist in numerous localities. We sequenced two chloroplast DNA fragments (rbcL, trnT‐L) for 559 individuals from 87 populations. Bayesian methods were used to identify phylogenetic relationships and to estimate divergence times. Demographic histories were inferred using neutrality tests, mismatch distribution analysis, and coalescent simulation. A total of 112 haplotypes that clustered into three major groups were identified. The formation of these groups and their subgroups was dated to between the Pliocene and the late Pleistocene. In addition, we found that some groups underwent multiple extensive expansions. Species‐specific haplotypes were identified for each species, although these haplotypes phylogenetically intermixed. These results suggest that recent plateau uplifts and climatic oscillations might have caused the deep divergences observed within this genus. However, later range expansions probably blurred these divergences and possible species boundaries. Our results shed new light on the complex evolutionary history of the QTP alpine plants. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 777–788.     

Multiple refugia and barriers explain the phylogeography of the Valais shrew,Sorex antinorii (Mammalia: Soricomorpha)

The aim of the present study was to investigate the genetic structure of the Valais shrew (Sorex antinorii) by a combined phylogeographical and landscape genetic approach, and thereby to infer the locations of glacial refugia and establish the influence of geographical barriers. We sequenced part of the mitochondrial cytochrome b (cyt b) gene of 179 individuals of S. antinorii sampled across the entire species' range. Six specimens attributed to S. arunchi were included in the analysis. The phylogeographical pattern was assessed by Bayesian molecular phylogenetic reconstruction, population genetic analyses, and a species distribution modelling (SDM)‐based hindcasting approach. We also used landscape genetics (including isolation‐by‐resistance) to infer the determinants of current intra‐specific genetic structure. The phylogeographical analysis revealed shallow divergence among haplotypes and no clear substructure within S. antinorii. The starlike structure of the median‐joining network is consistent with population expansion from a single refugium, probably located in the Apennines. Long branches observed on the same network also suggest that another refugium may have existed in the north‐eastern part of Italy. This result is consistent with SDM, which also suggests several habitable areas for S. antinorii in the Italian peninsula during the LGM. Therefore S. antinorii appears to have occupied disconnected glacial refugia in the Italian peninsula, supporting previous data for other species showing multiple refugia within southern refugial areas. By coupling genetic analyses and SDM, we were able to infer how past climatic suitability contributed to genetic divergence of populations. The genetic differentiation shown in the present study does not support the specific status of S. arunchi. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 864–880.     

Phylogeography and the origins of range disjunctions in a north temperate fish,the pygmy whitefish (Prosopium coulterii), inferred from mitochondrial and nuclear DNA sequence analysis

Aim To investigate the degree of phylogeographical divergence within pygmy whitefish (Prosopium coulterii) and to test hypotheses concerning the origin of disjunct populations within North America. Location North America from western Alaska to Lake Superior. Methods Mitochondrial (ATPase subunit VI) and nuclear (ITS‐1, ITS‐2) DNA sequence variation was assessed across the species’ North American range to test for the existence of distinct phylogeographical groupings of pygmy whitefish associated with known glacial refugia. Coalescent simulations of the mitochondrial DNA (mtDNA) data were used to test hypotheses of population structure. Results This species is composed of two monophyletic mitochondrial clades across its North American range. The two mtDNA clades differed by an average 3.3% nucleotide sequence divergence. These clades were also distinguished by ITS‐2, but the relationships among lineages were not resolved by the ITS‐1 analysis. Coalescent analyses rejected the null hypothesis of the current disjunct distributions being a result of fragmentation of a single widespread ancestral lineage across a variety of effective population sizes and divergence times. Main conclusions The current range disjunctions of pygmy whitefish in North America probably resulted from isolation, genetic divergence, and selective dispersal from at least two major Pleistocene glacial refugia: Beringia and Cascadia. More recent isolation and dispersal from an upper Mississippi refugium is suggested by relationships within one of the clades and by distributional evidence from co‐distributed species. The Beringian and Cascadian refugia have played major roles in the zoogeography of Nearctic temperate aquatics, but the roles of smaller refugia appear more variable among other species.     

Responses of plants to changes in Qinghai–Tibetan Plateau and glaciations: Evidence from phylogeography of a Sibiraea (Rosaceae) complex

The genetic structure and phylogeographical history of the alpine shrubs Sibiraea angustata (Rosaceae) and Sibiraea laevigata from the Qinghai–Tibetan Plateau (QTP) were investigated to identify alpine plant responses to changes in the QTP and glaciations. Fifty-five populations were analyzed using four chloroplast DNA (cpDNA) regions and (nuclear ribosomal internal transcribed spacer) nrITS sequence data. In all, 21 cpDNA haplotypes and 13 nrITS sequence types were detected. Analyses of the genetic diversity and phylogenetic relationships detected two rarely reported glacial refugia. One was the Yushu–Nangqian area, and the other consisted of the area from the Songpan Plateau to the southeastern margin of the QTP. Sibiraea species populations experienced divergent evolution and founder effects when they recolonized the QTP platform and adjacent high-altitude regions following glaciations. The divergence times of the main lineages and haplotypes were in the range of 1.60–2.58 Ma. The population size of Sibiraea species in the QTP decreased approximately 23-fold during the last 0.12 Ma, indicating that Sibiraea species were significantly affected by environmental changes in the QTP. Therefore, the rapid uplift of the QTP and subsequent glaciations likely played an important role in driving genetic divergence and population size changes of Sibiraea species in the QTP.     

Phylogeographical structure of the boreal‐montane orchid Malaxis monophyllos as a result of multi‐directional gene flow

We investigated the phylogeographical structure of the boreal‐montane orchid Malaxis monophyllos in its Eurasian geographical range. We analysed four sequences of plastid DNA (trnL, trnL–trnF, rps16 and accD‐psaI), resulting in 19 haplotypes and revealing a high level of intraspecific diversity (H_D = 0.702 and π = 0.196 × 10⁻²), but showing a lack of phylogeographical structure. This pattern might be caused by multiple phenomena and processes, e.g. broad‐fronted recolonization with accompanying multi‐directional gene flow between populations and expansion from at least two refugial areas. Despite the lack of phylogeographical structure, three centres of haplotype diversity were indicated in the European part of the range of M. monophyllos. According to these data, alpine and lowland glacial refugia located between the ice sheets in the European Alps and the Scandinavian glaciers seem most likely to be in Europe. Moreover, models of climatically suitable areas during the Last Glacial Maximum (LGM) confirmed the Alps as a possible refuge, and indicated an opportunity for the persistence of M. monophyllos populations in Beringia and parts of Siberia. Using two models [Model for Interdisciplinary Research on Climate (MIROC) and Community Climate System Model (CCSM)], we predicted a significant reduction in climatically suitable areas for M. monophyllos in the future (2080). Our study also demonstrated that the biological features of M. monophyllos, including breeding system and dispersal mode, seem to be crucial in understanding its phylogeographical pattern. Our results also highlighted the importance of anthropogenic habitats as reservoirs of genetic diversity and alternative habitats for this species in the context of declining natural populations. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 178 , 138–154.     

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.     

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

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

Rhytidium rugosum (Bryophyta) colonized Scandinavia from at least two glacial refugial source populations

The Scandinavian post‐glacial history of the moss Rhytidium rugosum is traced on the basis of information from the nuclear markers ITS and gpd for 229 Scandinavian and 81 other specimens. Some haplotypes, groups or lineages identified in a NeighborNet split network are predominantly northern Scandinavian, whereas others are southern. With the distributions of individual haplotypes and the timing of the deglaciation in different parts of Scandinavia, this implies colonization from the south and from the north or north‐east. High haplotype and nucleotide diversity and the occurrence of certain private haplotypes in the north suggest that the species may have survived the Last Glacial Maximum in local refugia. Slightly higher numbers of private haplotypes in Scandinavia than in central or north‐eastern Europe also favour an explanation with at least some local glacial survival. Low diversity in the southernmost contiguous region of the Scandinavian mountain range is probably a result of recent land uplift and late colonization. The Scandinavian lowland regional populations probably represent remains of an earlier widespread population that became increasingly restricted to small and isolated areas when the vegetation closed during the post‐glacial period. Some of the lowland populations require extensive management to survive. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 635–657.     

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

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

Phylogeography of Liquidambar styraciflua (Altingiaceae) in Mesoamerica: survivors of a Neogene widespread temperate forest (or cloud forest) in North America?

We investigate the genetic variation between populations of the American sweetgum (Liquidambar styraciflua), a tree species with a disjunct distribution between northeastern Texas and Mexico, by analyzing sequences of two chloroplast DNA plastid regions in Mesoamerica. Our results revealed phylogeographical structure, with private haplotypes distributed in unique environmental space at either side of the Trans‐Mexican Volcanic Belt, and a split in the absence of gene flow dating back ca. 4.2–1.4 million years ago (MYA). Species distribution modeling results fit a model of refugia along the Gulf and Atlantic coasts but the present ranges of US and Mesoamerican populations persisted disjunct during glacial/interglacial cycles. Divergence between the US and Mesoamerican (ca. 8.4–2.8 MYA) populations of L. styraciflua and asymmetrical gene flow patterns support the hypothesis of a long‐distance dispersal during the Pliocene, with fragmentation since the most recent glacial advance (120,000 years BP) according to coalescent simulations and high effective migration rates from Mesoamerica to the USA and close to zero in the opposite direction. Our findings implicate the Trans‐Mexican Volcanic Belt as a porous barrier driving genetic divergence of L. styraciflua, corresponding with environmental niche differences, during the Pliocene to Quaternary volcanic arc episode 3.6 MYA, and a Mesoamerican origin of populations in the USA.     

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.     

River islands,refugia and genetic structuring in the endemic brown frog Rana kukunoris (Anura,Ranidae) of the Qinghai‐Tibetan Plateau

Frequently, Pleistocene climatic cycling has been found to be the diver of genetic structuring in populations, even in areas that did not have continental ice sheets, such as on the Qinghai‐Tibetan Plateau (QTP). Typically, species distributed on the plateau have been hypothesized to re‐treat to south‐eastern refugia, especially during the Last Glacial Maximum (LGM). We evaluated sequence variation in the mitochondrial DNA gene Cytb and the nuclear DNA gene RAG‐1 in Rana kukunoris, a species endemic to the QTP. Two major lineages, N and S, were identified, and lineage N was further subdivided into N1 and N2. The geographical distribution and genealogical divergences supported the hypothesis of multiple refugia. However, major lineages and sublineages diverged prior to the LGM. Demographical expansion was detected only in lineage S and sublineage N2. Sublineage N1 might have survived several glacial cycles in situ and did not expand after the LGM because of the absence of suitable habitat; it survived in river islands. Genetic analysis and environment modelling suggested that the north‐eastern edge of QTP contained a major refugium for R. kukunoris. From here, lineage S dispersed southwards after the LGM. Two microrefugia in northern Qilian Mountains greatly contributed to current level of intraspecific genetic diversity. These results were found to have important implications for the habitat conservation in Northwest China.     

Phylogeography of a subalpine tall‐herb Ranunculus platanifolius (Ranunculaceae) reveals two main genetic lineages in the European mountains

A phylogeographical analysis of Ranunculus platanifolius, a typical European subalpine tall‐herb species, indicates the existence of two main genetic lineages based on amplified fragment length polymorphism (AFLP) markers. One group comprises populations from the Balkan Peninsula and the south‐eastern Carpathians and the other includes the remaining part of the range of the species, encompassing the western Carpathians, Sudetes, Alps, Pyrenees and Scandinavia. The main phylogeographical break observed in this species runs across the Carpathians and separates the main parts of this range (western and south‐eastern Carpathians), supporting a distinct glacial history of populations in these areas. The high genetic similarity of the Balkan Peninsula and south‐eastern Carpathian populations could indicate a common glacial refugium for these contemporarily isolated areas of species distribution. The western and northern part of the species range displays an additional weak differentiation into regional phylogeographical groups, which could have been shaped by isolation in glacial refugia or even by a postglacial isolation. The observed weak phylogeographical structure could also be linked with ecological requirements, allowing survival along streams in relatively low, forested mountain ranges. © 2013 The Linnean Society of London     

Phylogeographical patterns of two closely related desert shrubs,Nitraria roborowskii and N. sphaerocarpa (Nitrariaceae), from arid north‐western China

To investigate the influence of climate aridification and oscillations on the genetic diversity and evolutionary processes of organisms in the Quaternary in north‐western China, we selected Nitraria roborowskii and N. sphaerocarpa and examined the geographical apportionment of genetic variation in their vast range. In the study, 21 plastid haplotypes were identified in N. roborowskii based on two plastid DNA regions. We found significant genetic differentiation between populations in both N. roborowskii and N. sphaerocarpa. We also found similar phylogeographical patterns of allopatric divergence and regional range expansion in both species, but the degree of allopatric divergence in N. roborowskii was lower. Finally, areas to the south of the Alxa Desert, the Hexi Corridor and Ningxia Province were identified as possible refugia for N. roborowskii.     

Genetic drift drives evolution in the bird‐pollinated,terrestrial island endemic Grevillea georgeana (Proteaceae)

Plant species distributed across terrestrial islands can show significant genetic divergence among populations if seed and pollen dispersal are restricted. We assessed the genetic connectivity between populations of Grevillea georgeana, restricted to seven disjunct inselbergs in semi‐arid Western Australia. The phylogeographical pattern and population genetics of populations were determined using sequence data from two plastid DNA intergenic spacers and ten nuclear microsatellite loci. The plastid DNA markers indicated high genetic differentiation among the majority of populations. Haplotypes were restricted to individual inselbergs, with the exception of two that were shared among three isolated populations that formed part of an elongated greenstone belt and that may be connected via inaccessible populations of G. georgeana. There was also strong differentiation within some of the populations, suggesting long‐term isolation and persistence of G. georgeana on these terrestrial islands. Overall, the genetic patterns suggest limited seed dispersal, with differentiation in the plastid DNA genome being driven by genetic drift. In contrast, pollen movement, although generally restricted, may occur between neighbouring populations, resulting in a pattern of isolation by distance in the nuclear markers. This potential for limited or no seed dispersal, but connectivity via pollen flow, should be considered, given that many of the inselbergs are under consideration for resource development. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 178 , 155–168.     

Phylogeography of Podocarpus matudae (Podocarpaceae): pre‐Quaternary relicts in northern Mesoamerican cloud forests

Aim Cloud forests of northern Mesoamerica represent the northern and southern limit of the contact zone between species otherwise characteristic of North or South America. Several phylogeographic studies featuring temperate conifer species have improved our understanding of species responses to environmental changes. In contrast, conifer species that presumably colonized northern Mesoamerica from South America are far less studied. A phylogeographic study of Podocarpus matudae (Podocarpaceae) was conducted to identify any major evolutionary divergences or disjunctions across its range and to determine if its current distribution is associated with pre‐Quaternary climatic and/or long‐distance dispersal events. Location Northern Mesoamerica (Mexico and Guatemala). Methods Sixteen populations (157 individuals) of P. matudae were screened for variation at two plastid DNA markers. The intra‐specific phylogenetic relationships among haplotypes were reconstructed using Bayesian inference. Population genetic analyses were undertaken to gain insight into the evolutionary history of these populations. To test whether genetic divergence among populations occurred at different time‐scales plastid DNA sequence data and fossil‐ and coalescent‐based calibrations were integrated. Results The combination of plastid markers yielded 11 haplotypes. Differentiation among populations based on DNA variation (G_ST) (0.707, SE 0.0807) indicated a clear population structure in P. matudae. Differentiation for ordered alleles (N_ST) (0.811, SE 0.0732) was higher than that for G_ST, indicating phylogeographical structure in P. matudae. Most of the total variation (81.3%, P < 0.0001) was explained by differences among populations. The estimated divergence time between the unique haplotypes from a Guatemalan population and the two most common haplotypes from the Sierra Madre Oriental in Mexico was between 10 and 20 Ma, and further haplotype divergence in the poorly resolved clade of the Sierra Madre Oriental occurred between 3 and 0.5 Ma. Main conclusions Divergence estimations support the hypothesis that extant Podocarpus matudae populations are pre‐Quaternary relicts. This finding is consistent with fossil and pollen data that support a Miocene age for temperate floristic elements in Mesoamerican cloud forests, whereas further haplotype divergence within the Sierra Madre Oriental, Chiapas and Guatemala occurred more recently, coinciding with Pleistocene cloud forest refugia.