Phylogeographic analysis of the endemic species Sibiraea angustata reveals a marginal refugium in the Qinghai–Tibet Plateau

The phylogeography of Sibiraea angustata, an endemic shrub species, was studied in the Qinghai–Tibet plateau (QTP). We investigated 466 individuals of S. angustata from 39 populations basically covering its total distribution area. Eight haplotypes (A–H) were detected by sequencing the intergenic chloroplast spacer trnS–trnG (600 bp), and one ancestral haplotype (A) was found to be widely distributed. The level of differentiation among populations was very high (G_ST=0.768; N_ST=0.850) and a significant phylogeographical structure was revealed (N_ST>G_ST). Analysis of molecular variance (AMOVA) similarily revealed a high level of differentiation among populations (84%, F_ST=0.842), indicating that little gene flow has occurred among populations mutually isolated by high mountains and rivers in the QTP. On the QTP platform there was only one widespread haplotype (A) in most populations, while populations along the eastern and southeastern edges had high diversity and unique haplotypes. Our results suggest that a glacial refugium may have been located on the eastern or southeastern edges of QTP during the last glaciation, and that interglacial and postglacial range expansion occurred from that refugium. Nested clade analysis (NCA) also suggests this scenario, which indicates that the current spatial distribution of cpDNA haplotypes and populations mainly resulted from long distance colonization, possibly coupled with subsequent or past fragmentation followed by range expansion and allopatric fragmentation.     

Long-Distance Dispersal after the Last Glacial Maximum (LGM) Led to the Disjunctive Distribution of Pedicularis kansuensis (Orobanchaceae) between the Qinghai-Tibetan Plateau and Tianshan Region

Quaternary climate fluctuations have profoundly affected the current distribution patterns and genetic structures of many plant and animal species in the Qinghai-Tibetan Plateau (QTP) and adjacent mountain ranges, e.g. Tianshan (TSR), Altay, etc. In this greater area disjunct distributions are prominent but have nevertheless received little attention with respect to the historical processes involved. Here, we focus on Pedicularis kansuensis to test whether the current QTP and TSR disjunction is the result of a recent Holocene range expansion involving dispersal across arid land bridge(s) or a Pleistocene range fragmentation involving persistence in refugia. Two chloroplast DNA spacers were sequenced for 319 individuals from 34 populations covering the entire distribution range of this species in China. We found a total of 17 haplotypes of which all occurred in the QTP, and only five in the TSR. Overall genetic diversity was high (H_T = 0.882, H_S = 0.559) and higher in the QTP than in the TSR. Genetic differentiation among regions and populations was relatively low (G_ST = 0.366) and little evidence for a phylogeographic pattern emerged. The divergence times for the four main lineages could be dated to the early Pleistocene. Surprisingly, the two ubiquitous haplotypes diverged just before or around the Last Glacial Maximum (LGM) and were found in different phylogenetic lineages. The Species Distribution Model suggested a disappearance of P. kansuensis from the TSR during the LGM in contrast to a relatively constant potential distribution in the QTP. We conclude that P. kansuensis colonized the TSR after the LGM. The improbable long-distance dispersal by wind or water across arid land seed flow may well have had birds or men as vector.     

Allopatric divergence and phylogeographic structure of the plateau zokor (Eospalax baileyi), a fossorial rodent endemic to the Qinghai–Tibetan Plateau

Aim Most species of temperate regions are believed to have shifted to lower latitudes or elevations during the glacial periods of the Quaternary. In this study we test whether this phylogeographic assumption is also true for the plateau zokor (Eospalax baileyi), a fossorial rodent endemic to the climate-sensitive Qinghai–Tibetan Plateau (QTP), which ranges in elevation from 2600 to 4600 m. Location The QTP of western China. Methods Phylogeographic analyses were conducted based on the mitochondrial cytochrome b gene sequences of 193 individuals from 20 populations over the entire range of the species. Results A total of 54 haplotypes identified in the present study clustered into four geographically correlated clades located in the interior of the QTP (clade A) and at the plateau edge (B, C and D). Molecular calibrations suggest that the interior plateau (A) and plateau-edge (B–D) clades diverged at 1.2 Ma and that the three plateau-edge clades diverged between 0.85 and 0.80 Ma. These estimates are concordant with diastrophism and glaciation events in the QTP. Coalescent tests rejected both the hypothesis that all current populations originated from a single refugium at a low elevation during the Last Glacial Maximum (LGM) and the hypothesis that the two lineages diverged during the LGM. The tests instead supported the hypothesis that there were four refugia during the LGM, and that the four clades diverged prior to the late Pleistocene. Main conclusions Our results suggest that Quaternary diastrophisms and glaciations repeatedly promoted allopatric divergence of the plateau zokor into geographical clades, and that these regional clades subsequently persisted at high elevations, rather than migrating to the low-elevation plateau edge during subsequent glacial ages.     

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.     

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.     

Intraspecific divergences of Rhodiola alsia (Crassulaceae) based on plastid DNA and internal transcribed spacer fragments

In the present study, we used two maternally inherited plastid DNA intergenic spacers, rpl20‐rps12 and trnS‐trnG, and the biparentally inherited nuclear ribosomal internal transcribed spacer (ITS) region to explore genetic variation and phylogeographical history of Rhodiola alsia, a herb endemic to the Qinghai‐Tibetan Plateau (QTP). Based on range‐wide sampling (18 populations and 227 individuals), we detected 45 plastid DNA haplotypes and 19 ITS sequence types. Only three plastid DNA haplotypes were widespread; most haplotypes were restricted to single sites or to neighbouring populations. Analysis of molecular variance revealed that most of the genetic variance was found within populations (51.24%) but that populations were also distinct (F_ST = 0.48759). We found three areas with relatively high plastid DNA diversity and these could further be recognized as potentially isolated divergence centres based on the ITS sequence type distribution. These represent three potentially isolated glacial refugia for R. alsia: one of them has long been recognized as an important refugium on the south‐eastern edge of the QTP, whereas the others are new and located in the north and south of the Tanggula Mountains on the plateau platform. Divergence time estimates based on ITS suggest that the main lineages of R. alsia diverged from each other 0.35–0.87 Mya, indicating that climatic oscillations during the Pleistocene may have been an important driver of intraspecific divergence in R. alsia. Rhodiola alsia probably experienced a phylogeographical history of retreat to isolated glacial refugia during Quaternary glaciations that led to different degrees of allopatric intraspecific divergence. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 168 , 204–215.     

Extensive population expansion of Pedicularis longiflora (Orobanchaceae) on the Qinghai‐Tibetan Plateau and its correlation with the Quaternary climate change

The Qinghai‐Tibetan Plateau (QTP) is thought to be more strongly affected by the Quaternary glaciations than most other regions of the same latitude. It would be of great interest to investigate the population genetic structure of organisms distributed on the platform and its correlation with the Quaternary climatic oscillations. Here we used the chloroplast (cp)DNA trnT‐trnF sequence to study genetic variation and phylogeography of Pedicularis longiflora, an alpine herb with extensive distribution on the QTP. Based on a range‐wide sampling comprising 41 populations and 910 individuals, we detected 30 cpDNA haplotypes that were divided into five clades by phylogenetic and network analyses and a strong phylogeographical structure. All haplotypes but one in the three basal clades occur exclusively in the southeast QTP, whereas haplotypes in the young clade V occupy almost the whole species range. In particular, the young haplotype H18 occurs in 420 individuals, even at a frequency of 100% in some QTP platform populations and the Altai population. The haplotype distribution pattern, together with molecular clock estimation and mismatch distribution analysis, suggests that the southeast QTP was either a refuge for P. longiflora during the Quaternary climatic change or is the place of origin of the species. The present wide distribution of the species on the QTP platform has resulted from recent population expansions which could be dated back to 120 000–17 000 years ago, a period mostly before the last glacial maximum. The possible relationships among geographic genetic structure, climatic change and species diversification in Pedicularis are also discussed.     

Migration patterns of Gentiana crassicaulis,an alpine gentian endemic to the Himalaya–Hengduan Mountains

The Himalaya–Hengduan Mountain region is one of the hotspots of biodiversity research. The uplift of the Qinghai–Tibetan Plateau (QTP) and the Quaternary glaciation caused great environmental changes in this region, and the responses of many species in the QTP to the Quaternary climate are still largely unknown. The genetic structure and phylogeographical history of Gentiana crassicaulis Duthie ex Burk, an endemic Chinese alpine species in this area, were investigated based on four chloroplast fragments and internal transcribed spacer region of the nuclear ribosomal DNA (nrITS) sequences of 11 populations. The populations with highly diverse chloroplast haplotypes were mainly found at the edge of the QTP. There were two main haplotypes of nrITS clones, one shared by the Yunnan and Guizhou populations, and the other by the remaining populations. The population with the highest diversity was the Gansu population, located at the edge of the plateau. Based on molecular dating, the diversification of G. crassicaulis at the edge of the plateau occurred before the Last Glacial Maximum (LGM), and the species may have completed its expansion from the edge to the platform. Ecological niche models were conducted to predict the distributional ranges of G. crassicaulis at present, during the LGM, and during the last interglacial (LIG) period. The results demonstrated that G. crassicaulis survived on the QTP platform and at the edge during the LGM but afterward retreated from the platform to the southern edge, followed by expansion to the platform.     

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.     

Microrefugia and Shifts of Hippophae tibetana (Elaeagnaceae) on the North Side of Mt. Qomolangma (Mt. Everest) during the Last 25000 Years

Microrefugia at high altitudes or high latitudes are thought to play an important role in the post-glacial colonization of species. However, how populations in such microrefugia have responded to climate changes in alternating cold glacial and warm interglacial stages remain unclear. Here we present evidence to indicate the Rongbuk Valley of the Mt. Qomolangma (Mt. Everest) area, the highest region on earth, had microrefugia for Hippophae tibetana and discuss how this low shrub was adapted to the extreme climate fluctuations of the last 25,000 years by shifts. By integrating geological, glaciological, meteorological, and genetic information, we found that the Rongbuk Valley was not only a glacial microrefugium but also an interglacial microrefugium for H. tibetana: the former was located on the riverbank below 4800 m above sea level (asl) or lower area and the latter at ∼5000 m asl. Our results show that after the Last Glacial Maximum (LGM), H. tibetana in the valley has undergone upward and downward migrations around ∼5000 m driven by climate fluctuations and the population in the glacial microrefugium has suffered extinction or extreme contraction. Moreover, with the rise of temperature in the last four decades, the upper limit of H. tibetana has shifted at least 30 m upward. Combining population history and recent range shift of this species is important in predicting the fate of this endemic species to future climate changes.     

Molecular phylogeography and intraspecific divergence of Spiraea alpina (Rosaceae) distributed in the Qinghai-Tibetan Plateau and adjacent regions inferred from nrDNA

The Qinghai-Tibetan plateau (QTP) uplift had a decisive effect on climatic and eco-environmental evolution in East Asia during the Quaternary. In the current study phylogeographic structure and diversification history of Spiraea alpina across the QTP were investigated for the first time based on nuclear internal transcribed spacer. The nuclear internal transcribed spacers (ITS_1a–ITS₄) were generated for a total of 284 individuals distributed within 31 natural populations. A clear phylogeographic structure was found for S. alpina. The results showed that this species colonized in three different glacial refugia during the Quaternary extensive glaciation and expanded during the Interglacial period. Analysis of molecular variance (AMOVA) showed 74.13% genetic diversity among populations and 25.87% genetic variation within populations with distinct phylogeographic structure (F_ST = 0.741*). The estimated divergence time revealed that the main lineages of S. alpina diversified during the Quaternary 1.2–0.6 million years ago. The study concluded that severe climatic oscillations during Quaternary and the uplift of QTP had a profound effect on intraspecific divergence of S. alpina.     

Phylogeographic analyses suggest that a deciduous species (Ostryopsis davidiana Decne., Betulaceae) survived in northern China during the Last Glacial Maximum

Aim Palaeontologial data suggest that all temperate forest species in northern China migrated southwards during the Last Glacial Maximum (LGM) and recolonized post‐glacially within the Holocene. We tested this assumption using phylogeographical studies of a temperate deciduous shrub species (Ostryopsis davidiana Decne., Betulaceae), which has a wide distribution in northern China. Location Northern China. Methods We sequenced two chloroplast DNA (cpDNA) fragments (trnL–trnF and psbA–trnH, together about 1300 bp in length) of 294 plants from 21 populations across the total distribution range of this species. We used maximum parsimony and haplotype network methods to construct phylogenetic relationships among haplotypes. Results The analysis of cpDNA variation identified eight haplotypes. A single haplotype was fixed in all populations except for one population that was polymorphic, having two haplotypes. The population subdivisions were extremely high (G_ST = 0.972 and N_ST = 0.974), suggesting very low gene flow between populations. Haplotypes clustered into two tentative clades, both of which occur in the southern region of the species’ range but only one of which occurs in the northern region. Across the sampled populations, the haplotype distributions were differentiated geographically. Main conclusions Our analyses suggest that multiple refugia were maintained across the range of O. davidiana in both northern (north of the Qing Mountains) and southern (south of the Qing Mountains) regions during the LGM rather than that the species survived only in the south and subsequently colonized northwards. The extremely low within‐population diversity of this species suggests strong bottleneck or founder effects within each fragmented region during the Quaternary climatic oscillations. These findings provide important clues for understanding range shifts and changes in within‐ and/or between‐population genetic diversity of temperate forests in response to past climatic oscillations in northern China.     

Chloroplast phylogeographic patterns of Calligonum sect. Pterococcus (Polygonaceae) in arid Northwest China

To understand the impacts of past climatic change and geological events on the evolutionary history of Calligonum sect. Pterococcus, including C. aphyllum, C. rubicundum and C. leucocladum, a total of 128 individuals from 14 populations, mainly from arid Northwest China, were sampled. Two cpDNA intergenic spacer regions (rpl32‐trnL and ycf6‐psbM) were sequenced and 11 haplotypes were identified. Levels of genetic differentiation between populations was low in C. rubicundum (F_ST = 0.54317, p < 0.001) and C. aphyllum (F_ST = 0.55795), while much higher in C. leucocladum (F_ST = 0.95800, p < 0.001), possibly as an effct of differences in geographic distributions and habitats. Analysis of molecular variance (AMOVA) revealed that most of the total genetic variations occurred among species (72.97%). Among eleven identified haplotypes, only H1 and H2 were shared between C. aphyllum and C. rubicundum, while nine were private for one of the three species. The eleven identified haplotypes were divided into two major clades, but they did not yield three species‐specific lineages. Calligonum sect. Pterococcus therefore not appeared reciprocally monophyletic, more likely due to incomplete lineage sorting than hybridization. Mismatch distribution analysis suggested that only C. aphyllum has experienced recent demographic expansion. Divergence time among the 11 haplotypes was estimated at between 2.84 Ma and 0.06 Ma. Within the two clades, haplotype divergence began in early Pleistocene and mainly occurred during the middle to late Pleistocene and was most likely triggered by Quaternary climatic oscillations and increasing aridity of the region.     

Macaronesia: a source of hidden genetic diversity for post‐glacial recolonization of western Europe in the leafy liverwort Radula lindenbergiana

Aim Bryophytes exhibit apparently low rates of endemism in Macaronesia and differ from angiosperms in their diversity patterns by the widespread occurrence of endemics within and among archipelagos. This paper investigates the phylogeography of the leafy liverwort Radula lindenbergiana to determine: (1) whether or not morphologically cryptic diversification has occurred in Macaronesia, and (2) the relationships between Macaronesian and continental populations. Location Macaronesia, Europe, Africa. Methods Eighty‐four samples were collected across the species’ distribution range and sequenced at four chloroplast DNA (cpDNA) loci (atpB–rbcL, trnG, trnL and rps4). Phylogenetic reconstructions and Bayesian ancestral area reconstructions were used in combination with population genetics statistics (H, N_ST, F_ST) to describe the pattern of present genetic diversity in R. lindenbergiana and infer its biogeographic history. Results Patterns of genetic diversity in R. lindenbergiana exhibit a striking westwards gradient, wherein haplotype (0.90) and nucleotide (0.0038 ± 0.0019) diversity peak in Macaronesia, with a substantial endemic component. We found 20.9% of the genetic variance between biogeographic regions, and most pairwise F_ST comparisons between regions are significantly different from zero. The global N_ST (0.78) is significantly higher than the global F_ST (0.20), providing evidence for the presence of phylogeographic signal in the data. Ancestral area reconstructions suggest that the haplotypes currently found in western Europe share a Macaronesian common ancestor. Main conclusions The haplotype diversification exhibited by R. lindenbergiana in Macaronesia is comparable to that reported for many angiosperm groups at the species level. The apparent lack of radiation among Macaronesian bryophytes may thus reflect the reduced morphology of bryophytes in comparison with angiosperms. The high diversity found among Macaronesian haplotypes, especially in Madeira and the Canary Islands, and the significant N_ST/F_ST ratio between Macaronesia and all the other biogeographic regions (an indication that mutation rate exceeds dispersal rates) suggest that Macaronesian archipelagos could have served as a refugium during the Quaternary glaciations. Many haplotypes currently found in Europe share a Macaronesian common ancestor, and this further suggests that Macaronesia might have played a key role in the back‐colonization of the continent.     

Bumblebees take the high road: climatically integrative biogeography shows that escape from Tibet,not Tibetan uplift,is associated with divergences of present‐day Mendacibombus

Many claims that uplift of the Qinghai‐Tibetan plateau (QTP) drove the divergences of extant high‐elevation biota have recently been challenged. For Mendacibombus bumblebees, high‐elevation specialists with distributions centred on the QTP, we examine broader explanations. We extend integrative biogeography to cover multiple contributing factors by using a framework of sequential filters: 1) molecular evidence from four genes is used to estimate phylogenetic relationships, with time calibration from a published estimate; 2) spatial evidence from current distributions is combined with the phylogeny and constrained by a model of short‐distance dispersal along mountain corridors to estimate ancestral distributions by both S‐DIVA and S‐DEC analysis; 3) geological evidence from the literature is used to constrain when high mountain ranges were uplifted to become potential corridors; and 4) climatological evidence from Mendacibombus niche‐evolution reconstructions and from palaeoclimate simulations is used to constrain when habitat was suitable in key gaps within corridors. Explanations for Mendacibombus distributions can be identified that require only short‐distance dispersal along mountain corridors, commensurate with the limited dispersal ability observed for bumblebees. These explanations depend on the timing of uplift of mountain ranges, regional climate change, and climate‐niche evolution. The uplift of the QTP may have contributed to the initial Oligocene divergence of the common ancestor of Mendacibombus from other bumblebees, but for the first two thirds of the history of Mendacibombus, only a single lineage has present‐day descendants. Divergence of multiple extant Mendacibombus lineages coincided with the Late Miocene–Pliocene uplift of externally connecting mountains, combined with regional climate cooling. These changes provided greater connectivity of suitable habitat, allowing these bumblebees to disperse out of the western QTP via new high bridges, escaping along the mountain corridors of the Tian Shan and Hindu Kush ranges, reaching eventually far to the west (Iberian Peninsula) and to the north‐east (Kamchatka).     

Chloroplast DNA Phylogeography Reveals Repeated Range Expansion in a Widespread Aquatic Herb Hippuris vulgaris in the Qinghai-Tibetan Plateau and Adjacent Areas

Background

The Qinghai-Tibetan Plateau (QTP) is one of the most extensive habitats for alpine plants in the world. Climatic oscillations during the Quaternary ice age had a dramatic effect on species ranges on the QTP and the adjacent areas. However, how the distribution ranges of aquatic plant species shifted on the QTP in response to Quaternary climatic changes remains almost unknown.

Methodology and Principal Findings

We studied the phylogeography and demographic history of the widespread aquatic herb Hippuris vulgaris from the QTP and adjacent areas. Our sampling included 385 individuals from 47 natural populations of H. vulgaris. Using sequences from four chloroplast DNA (cpDNA) non-coding regions, we distinguished eight different cpDNA haplotypes. From the cpDNA variation in H. vulgaris, we found a very high level of population differentiation (G _ST = 0.819) but the phylogeographical structure remained obscure (N _ST = 0.853>G _ST = 0.819, P>0.05). Phylogenetic analyses revealed two main cpDNA haplotype lineages. The split between these two haplotype groups can be dated back to the mid-to-late Pleistocene (ca. 0.480 Myr). Mismatch distribution analyses showed that each of these had experienced a recent range expansion. These two expansions (ca. 0.12 and 0.17 Myr) might have begun from the different refugees before the Last Glacial Maximum (LGM).

Conclusions/Significance

This study initiates a research on the phylogeography of aquatic herbs in the QTP and for the first time sheds light on the response of an alpine aquatic seed plant species in the QTP to Quaternary climate oscillations.     

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.     

Allozymic differentiation in the land snail Arianta arbustorum (Stylommatophora, Helicidae): historical inferences

The intraspecific genetic differentiation depends to a large part on historical factors. The mode of dispersal is an important determinant of the genetic diversity especially of newly founded populations. Fast long-distance colonization of formerly unsuitable habitats results in reduced genetic diversity and lineages originating from different glacial refugia form well-defined hybrid zones, where they meet. Slow dispersers, on the other hand, preserve their refugial genetic diversity. Paleontological findings and a previous analysis of mtDNA suggest that the land snail Arianta arbustorum, which today is widely spread across Europe, has survived the Pleistocene glaciations within the boundaries of permafrost. In the present paper, we asked, whether the differentiation of nuclear markers, i.e. allozymes, supports these results. We investigated the allozymic differentiation at 15 polymorphic loci in 14 Alpine and one English populations of the land snail A. arbustorum. Various tests of genetic population differentiation yielded ambiguous results. Allele frequencies differed significantly across populations and all but five pairwise F_ST values were significant. Genetic distances between populations were comparatively high. On the other hand, an exact test of population differentiation found no differences and the assignment of individuals to their populations of origin was poor. This indicates that allozymic differentiation is constrained. Whether these constraints are of natural or methodological nature remains open. Matrices of genetic and geographical distances were correlated only after removal of the English population from the analysis. Similarly, with one exception F_ST values increased as the number of regions included in the calculations increased. Thus, on a regional scale, we largely observed a pattern of isolation by distance, which does no longer hold on a larger scale. This is well in accordance with the previous findings based on mtDNA. Mitochondrial lineages were widely distributed across Europe and overlapped extensively. Considering the low potential for dispersal of a land snail, the patchy distribution of lineages, and the high genetic diversity also found in the present study suggests that A. arbustorum has survived the Pleistocene within the boundaries of permafrost.     

Quaternary climate change and habitat preference shaped the genetic differentiation and phylogeography of Rhodiola sect. Prainia in the southern Qinghai–Tibetan Plateau

There are two long‐standing biogeographic hypotheses regarding the glacial survival of plant species in the Qinghai–Tibetan Plateau (QTP): the in situ survival hypothesis and the tabula rasa hypothesis. We tested these two hypotheses in a phylogeographic study of Rhodiola sect. Prainia, a monophyletic section with ecologically divergent lineages. Molecular data from the nuclear internal transcribed spacer, six plastid markers and 13 nuclear microsatellite loci were analyzed for 240 individuals from 19 populations of this section. Environmental data were used to analyze the niches of major phylogenetic lineages within this section and to model changes in their distributions since the Last Glacial Maximum (LGM). We found that Rhodiola sect. Prainia consists of three evolutionary lineages: all populations of R. stapfii, R. prainii populations at the southern edge of the QTP, and R. prainii populations in the interior part of the QTP. During the LGM, the survival of R. prainii in the interior part of the QTP corresponded with the in situ survival hypothesis, while R. stapfii most probably survived the LGM in a manner corresponding with the tabula rasa hypothesis. The evolutionary history of different lineages of this section was shaped by topography, climate change, and lineage‐specific habitat preferences.     

Phylogeography of Sophora davidii (Leguminosae) across the ‘Tanaka‐Kaiyong Line’, an important phytogeographic boundary in Southwest China

The ‘Tanaka‐Kaiyong Line’ (TKL) is a major phytogeographic boundary in Southwest China, separating East Asia's Sino‐Himalayan and Sino‐Japanese Floras. However, little is known about the importance of this boundary in promoting intraspecific phylogeographic subdivision and divergence. Using chloroplast (cpDNA) and nuclear‐intron (nDNA) sequence data, we reconstructed the population history of Sophora davidii, a drought‐tolerant riparian shrub widely distributed on either side of the TKL. Specifically, we aimed at testing two long‐standing explanations for possible vicariant events across the TKL: (i) Late Pliocene (c. 3 Ma) geological uplift of the eastern Qinghai‐Tibetan Plateau (QTP) or (ii) a sharp environmental gradient associated with the establishment of different monsoon regimes on either side of the TKL during the (Late) Pleistocene. Our genealogical analyses detected a major west–east split in cpDNA, geographically largely consistent with the TKL, and dated to c. 1.28 Ma (95% HPD: 0.21–2.96 Ma), hence postdating the latest phase of eastern QTP uplift. Furthermore, integrating cpDNA phylogeographic patterns with mismatch analyses, we found multiple refugial isolation and long‐term demographic stability of populations in the west (Hengduan Mountain Range) compared with extensive range expansions in the east, possibly during the last glacial period(s) and followed by differentiation into regional sublineages (southeast: Yunnan‐Guizhou Plateau vs. northeast: Qinling Mts./Loess Plateau). Although nuclear differentiation was less marked, the geographical pattern of nDNA haplotypes provided some further indication of the species' eastward expansion, possibly from source populations located just east of the TKL (lower Jinshajiang region). Overall, the present data reject the geological (tectonic) explanation for the TKL and, instead, provide supportive evidence for its role as a climatically driven barrier to present‐day plant dispersal. In addition, our study highlights changing temperatures and vegetation types during the last glacial period(s), along with aspects of regional topography, to be important determinants of the glacial eastward expansion of S. davidii. In consequence, our study lends support to a ‘glacial out‐of‐Hengduan Mts’. hypothesis for the xerophytic‐riparian flora of Southwest China, which in turn is inconsistent with the traditional view of the TKL as a ‘classical’ vicariant‐biogeographic boundary.