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Mandragora L. (Solanaceae) is the only genus of the tribe Mandragoreae, one of the two tribes of the cosmopolitan nightshade family, which occur exclusively in Eurasia and northern Africa. The genus occurs discontinuously in the Mediterranean region, Turanian region, and on the Tibetan Plateau, representing a classical disjunction pattern in the biogeography of the Old World flora. In this study, we reconstructed the genus phylogeny using AFLP, eight plastid DNA regions and one nuclear (ITS) gene, and evaluated the taxonomic value of quantitative traits time to flowering, fruit and seed size. We also analyzed the evolutionary history of the genus based on a phylogenetic framework and dating inferred from a combined data set of seven plastid regions with one fossil calibration point. Our data suggest that Mandragora originated in the Eocene, apparently along the Tethyan coast in broadleaf deciduous mesophytic forests that covered most of the Mediterranean region at that time. The Mediterranean-Turanian clade diverged from the Tibetan Plateau clade about 20.5 million years ago (Ma) as a result of the plateau uplift which probably was enhanced by aridification in the interior of Eurasia. A second split within the genus occurred about 11.1 Ma and resulted in Western Mediterranean and Near East-Turanian clades. Mandragora turcomanica was found to have very closely related evolutionary history with plants from the Near East indicating a possible ancient human assisted migration from Israel to Persia in historic times. In the Tibetan Plateau area, the morphologically distinctive M. chinghaiensis is nested within the M. caulescens clade indicating a very recent diversification within this lineage., (Copyright © 2018 Elsevier Inc. All rights reserved.)

Cyananthus (Campanulaceae) is a small genus consisting of ca. 20 species endemic to the Sino-Himalayan region. Based on phylogenetic analysis using nuclear ribosomal ITS and four plastid markers (matK, rbcL, psbA-trnH and trnG-S), our results strongly support the monophyly of Cyananthus and its close relationship with the Codonopsis clade of the platycodonoids. Three major clades are supported, corresponding to the three sections of the genus, with sect. Cyananthus, which mainly occurs in the Himalayas, being a sister to the clade comprising the other two sections (sect. Stenolobi and sect. Annui) distributed primarily in the Hengduan Mountain region. We also observed that Cyananthus exhibits variation in its sexual system, possessing both hermaphroditic and gynodioecious species. Character evolution analyses using Mesquite suggest that gynodioecy evolved from hermaphroditism only once in sect. Stenolobi, but that there is a reversal in C. formosus. Molecular dating and biogeographic analysis with LAGRANGE support dispersal from the Himalayas to the Hengduan Mountains during the early evolution of Cyananthus. The extensive uplift of the Qinghai-Tibetan Plateau and the Hengduan Mountains played an important role in the subsequent diversification of the genus., (Copyright © 2013 Elsevier Inc. All rights reserved.)

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., (© 2013 John Wiley & Sons Ltd.)

Premise of the Study: Southwestern China is an area of active tectonism and erosion, yielding a dynamic, deeply eroded landscape that is hypothesized to have influenced the genetic structure of the resident populations of plants and animals. However, few studies have been conducted to examine the influence of changing river channels, particularly in the Yarlung Tsangpo area, on genetic distributions in plants. We here examine the population structure of Buddleja crispa, a dominant element of the dry, warm/hot river-valley communities, seeking to delimit the current population genetic structure and its relation to past changes in the courses of the major rivers in this area. •, Methods: Two chloroplast DNA fragments were used to estimate the genetic variation and phylogeographic structure of the populations, and to infer nested clades, of the species. •, Key Results: We detected low intrapopulational haplotype diversity and higher overall population haplotype diversity (h(S) = 0.085, h(T) = 0.781). Molecular variance was mainly observed between groups (81.42%). Robust population genetic structure were detected by AMOVA (F(ST) = 0.967), coinciding with three nested clades (identified by NCPA) and five phylo-groups linked with paleo-drainage systems (identified by SAMOVA). No support for extensive spatial or demographical expansion was obtained. •, Conclusions: A general pattern of genetic isolation by vicariance was inferred, and detected disjunct patterns strongly indicate that currently discontinuous drainage systems were historically linked. Most importantly, population subdivisions and genetic variation perfectly reflect the putative Paleo-Red-River drainage pattern, and Yarlung Tsangpo populations are closely related to Central Yunnan Plateau populations, indicating that they were previously connected by ancient river courses. Divergence times between these river systems estimated by molecular dating (in the Pleistocene) agree with previous findings.

Background: The Ampelopsis clade (Ampelopsis and its close allies) of the grape family Vitaceae contains ca. 43 species disjunctly distributed in Asia, Europe, North America, South America, Africa, and Australia, and is a rare example to study both the Northern and the Southern Hemisphere intercontinental disjunctions. We reconstruct the temporal and spatial diversification of the Ampelopsis clade to explore the evolutionary processes that have resulted in their intercontinental disjunctions in six continents., Results: The Bayesian molecular clock dating and the likelihood ancestral area analyses suggest that the Ampelopsis clade most likely originated in North America with its crown group dated at 41.2 Ma (95% HPD 23.4-61.0 Ma) in the middle Eocene. Two independent Laurasian migrations into Eurasia are inferred to have occurred in the early Miocene via the North Atlantic land bridges. The ancestor of the Southern Hemisphere lineage migrated from North America to South America in the early Oligocene. The Gondwanan-like pattern of intercontinental disjunction is best explained by two long-distance dispersals: once from South America to Africa estimated at 30.5 Ma (95% HPD 16.9-45.9 Ma), and the other from South America to Australia dated to 19.2 Ma (95% HPD 6.7-22.3 Ma)., Conclusions: The global disjunctions in the Ampelopsis clade are best explained by a diversification model of North American origin, two Laurasian migrations, one migration into South America, and two post-Gondwanan long-distance dispersals. These findings highlight the importance of both vicariance and long distance dispersal in shaping intercontinental disjunctions of flowering plants.

Following the rapid uplift of the Qinghai-Tibetan Plateau, the reorganization of the major river drainages in southwest China was primarily caused by river capture events. However, the impact of these past changes in drainage patterns on the current distribution and genetic structure of the endemic flora of this region remains largely unknown. Here we report a survey of amplified fragment length polymorphism (AFLP) in Terminalia franchetii, an endemic shrub or small tree of the deep and dry-hot river valleys of this region. We surveyed AFLP variation within and among 21 populations (251 individuals) of T. franchetii, distributed disjunctively between northern and southern drainage systems. Using STRUCTURE, principal coordinates analysis, and genetic distance methods, we identified two main population genetic groups (I and II) and four subgroups within the species, as follows: (I) the Upper Jinshajiang Valley (subgroup I((north))) and the Honghe drainage area (subgroup I((south))); (II) the Middle and Lower Jinshajiang and Yalongjiang Valleys (subgroup II((north))) and the Nanpanjiang drainage area (subgroup II((south))). Genetic diversity was lower in group I than in group II. According to the genetic diversity and genetic structure results, we suggest that the modern disjunctive distribution and associated patterns of genetic structure of T. franchetii result from vicariance caused by several historical drainage capture events, involving the separation of the Upper Jinshajiang, Yalongjiang and Daduhe from the Honghe or Nanpanjiang in southwest China.

Historic events such as the uplift of Qinghai-Tibet Plateau (Q-T Plateau) and climatic oscillations in the Quaternary period greatly affected the evolution and modern distribution of Sino-Tibetan flora. Stellera chamaejasme, a perennial herb with flower color polymorphism that is distributed from the mountainous southeastern Q-T Plateau (Hengduan Mountains, H-D Mountains) to the vast platform of the Q-T Plateau and the adjacent plain of northern China, provides an excellent model to explore the effects of historic events on the origination and variation of species. In this study, we conducted a phylogenetic and phylogeographical study using three chloroplast sequences (trnT-L, trnL-F and rpL16) in 26 populations of S. chamaejasme and 12 outgroups from the Thymeleaceae. Phylogenetic analysis and molecular clock estimation revealed that the monophyletic origin of S. chamaejasme occurred ca. 6.5892 Ma, which is consistent with the radical environment changes caused by the rapid uplift of the Q-T Plateau ca. 7 Ma. Intra-specific differentiation of S. chamaejasme is estimated to have occurred after ca. 2.1 Ma. Twelve haplotypes were revealed from combined trnL-F and rpL16 sequences. High genetic diversity (h(T)=0.834) and population differentiation (N(ST)=0.997 and G(ST)=0.982) imply restricted gene flow among populations and significant geographical or environmental isolation. All populations from the vast plain of northern China were dominated by one haplotype (H1), and the same haplotype was fixed in most populations from the high elevation platform of the western and northern Q-T Plateau. In contrast, the majority of the haplotypes were found in the relatively narrow area of the H-D Mountains, in the southeastern distribution of S. chamaejasme. The contrasting haplotype distribution patterns suggested that the H-D Mountains were either a refugium for S. chamaejasme during the Quaternary climatic oscillations or a diversification center of this species. The present wide distribution of this species on the Q-T Plateau platform and in northern China is likely to have resulted from a rapid post-glacial population expansion from the southeastern refugium involving founder effects, facilitated by the adjacent geographic range with a similar grassland habitat., (Copyright © 2010 Elsevier Inc. All rights reserved.)

The mountains of Southwest China comprise a significant large mountain range and biodiversity hotspot imperiled by global climate change. The high species diversity in this mountain system has long been attributed to a complex set of factors, and recent large‐scale macroevolutionary investigations have placed a broad timeline on plant diversification that stretches from 10 million years ago (Mya) to the present. Despite our increasing understanding of the temporal mode of speciation, finer‐scale population‐level investigations are lacking to better refine these temporal trends and illuminate the abiotic and biotic influences of cryptic speciation. This is largely due to the dearth of organismal sampling among closely related species and populations, spanning the incredible size and topological heterogeneity of this region. Our study dives into these evolutionary dynamics of speciation using genomic and eco‐morphological data of Stellera chamaejasme L. We identified four previously unrecognized cryptic species having indistinct morphological traits and large metapopulation of evolving lineages, suggesting a more recent diversification (~2.67–0.90 Mya), largely influenced by Pleistocene glaciation and biotic factors. These factors likely influenced allopatric speciation and advocated cyclical warming–cooling episodes along elevational gradients during the Pleistocene. The study refines the evolutionary timeline to be much younger than previously implicated and raises the concern that projected future warming may influence the alpine species diversity, necessitating increased conservation efforts. [ABSTRACT FROM AUTHOR]

Background: How geographical isolation and ecological divergence act together to promote plant diversity in mountainous regions remains largely unknown. In this study, we chose two genera comprising a small number of species distributed in the Sino-Himalayan region, Megacodon (Gentianaceae) and Beesia (Ranunculaceae), which both exhibit a fragmented distribution pattern and are found across a wide range of elevations. By summarizing their common patterns of speciation and/or divergence processes, we aim to understand how environmental changes accelerated lineage diversification in the Sino-Himalayan region through ancient allopatry and ecological divergence. Results: Using ddRAD-seq, chloroplast genome sequences, and specific molecular markers, we studied the phylogenetic relationships, population structure, and historical biogeography of Beesia and Megacodon. Both genera began to diverge from the late Miocene onwards, with ancient allopatry at lower elevations formed narrow-range species or relict populations. Mantel tests between genetic distance and climatic, elevational, or geographic distance revealed an isolation-by-distance pattern in Beesia and Megacodon stylophorus. Megacodon showed two clades occupying entirely different altitudinal ranges, whereas Beesia calthifolia exhibited a genetic divergence pattern along an elevation gradient. Furthermore, we conducted morphological measurements on Beesia calthifolia and found that different elevational groups had distinct leaf shapes. Conclusions: The regional disjunctions of plant groups in the Sino-Himalayan region are drastic and closely related to several biogeographic boundaries. As a consequence of major geological and climate change, ecological divergence when different elevations are colonized often happens simultaneously within plant groups. Although habitat fragmentation and parapatric ecological divergence each spur speciation to different extents, a combined effect of these two factors is a common phenomenon in the Sino-Himalayan region. [ABSTRACT FROM AUTHOR]

Aim: East Asia exhibits complex geomorphological and climatic characteristics. The aim of this study was to test whether the so‐called three‐step landforms of China, together with the East China Sea (ECS), have acted to shape specific phylogeographical patterns and affected the biogeographical history of the species belonging to the East Asian Flora. Location: China and Japan. Taxon: Kerria japonica (L.) DC. Methods: Three chloroplast DNA regions and 15 nuclear microsatellite (nSSR) loci were sequenced and genotyped in 576/450 individuals of K. japonica. Phylogeographical analyses were performed to assess the genetic structure, historical gene flow and demographical history of these individuals, and climatic factors were examined to determine their effects on phylogeographical breaks. Furthermore, time‐calibrated phylogenetic trees and ancestral range reconstruction were used to infer the biogeographical history of K. japonica. Potential habitats at present and during the last glacial maximum (LGM) were identified using ecological niche modelling. Results: Distinct phylogeographical breaks were found across the ECS and along the boundary of the three‐step landforms of China. Low historical gene flow and significant climatic differences were detected in each pair of adjacent regions. The results of molecular dating and ancestral range reconstruction indicated that K. japonica originated in North America during the mid‐Miocene (14.76 Ma), and intra‐specific diversification began in the late Miocene (7.78 Ma). Compared to the relatively stable distribution range of Chinese populations, Japanese populations experienced range expansion after the LGM in response to Quaternary climate change. Main conclusions: Kerria japonica has a complex biogeographical history, with a mid‐Miocene origin in North America and subsequent migration into East Asia via the Bering land bridge. The onset of intra‐specific diversification was probably associated with Asian monsoon intensifications, while exposure to the ECS floor facilitated the formation of the Japanese lineage in the late Miocene. The spatiotemporal population differentiation on the Chinese mainland demonstrates the significant role of biogeographical divides delineated by the three‐step landforms of China and provides clues to understand the floristic regionalization and evolutionary history of plant diversity in East Asia, especially with respect to the Hengduan Mountains, Central China and East China. [ABSTRACT FROM AUTHOR]

Geoclimatic factors related to the uplift of the Himalaya and the Quaternary climatic oscillations influence the population genetic connectivity in the Himalaya–Hengduan Mountains (HHM) biodiversity hotspot. Therefore, to explore the relative roles played by these two factors, we examined the population dynamics and dispersal corridors of Incarvillea arguta (Royle) Royle incorporating ensemble species distribution modelling (SDM). Thirty‐seven populations were genotyped using plastid chloroplast DNA and low copy nuclear gene (ncpGS) sequences. Phylogeographic analysis was carried out to reveal the genetic structure and lineage differentiation. Ensemble SDMs were carried out for distributional change in the last glacial maximum, present, and future. Finally, the least cost path method was used to trace out possible dispersal corridors. The haplotypes were divided into four clades with strong geographical structure. The late Miocene origin of I. arguta in the western Himalaya ca. 7.92 Ma indicates lineage diversification related to the uplift of the HHM. The variability in habitat connectivity revealed by SDM is due to change in suitability since the Pleistocene. A putative dispersal corridor was detected along the drainage systems and river valleys, with strong support in the eastern Hengduan Mountains group. Our results support the signature of geoclimatic influence on population genetic connectivity of I. arguta in the HHM. We proposed that the major drainage systems might have assisted the rapid dispersal of isolated riverine plant species I. arguta in the HHM. The population genetic connectivity, using the fine‐tuned ensemble SDMs, enables scientists and policymakers to develop conservation strategies for the species gene pool in the HHM biodiversity hotspots. [ABSTRACT FROM AUTHOR]

It has been hypothesized that geological and climatic changes in the Sino–Himalayan region played a significant role in evolutionary history. In this study, we tested this hypothesis by investigating the phylogeography of Excoecaria acerifolia (Euphorbiaceae), a riparian plant species that is widely distributed in the hot/warm-dry river valleys of the Sino–Himalayan region. Spatial analysis of molecular variance, a median-joining network and a Bayesian phylogenetic tree based on plastid DNA, all suggested three major lineages corresponding to the Jialing-Min-Dadu (JMD lineage), Jinsha-Yalong-Salween (JY lineage) and Yarlung Tsangpo-Mekong-Red-Nanpan (YMRN lineage) drainage basins. This was also generally supported by the results based on nuclear DNA. The divergence times of these three major lineages based on both datasets fell in the early Pleistocene, coinciding with the period of drainage reorganization events in the Sino–Himalayan region. The diversification times in the lineages were, however, dated back to the mid Pleistocene, corresponding to the Naynayxungla glaciation (0.72–0.50 Mya) and the penultimate glaciation (0.30–0.13 Mya), which were the most and second most severe glaciations in this region, respectively. Furthermore, mismatch analyses, neutrality test and ecological niche modelling suggest long-term demographic stability of the JY and JMD populations, with expansion only in the YMRN populations during the period(s) from the late penultimate glaciation (138.12 Kya) to the Last Interglacial (95.79 Kya), probably because of less extensive glaciations since the late Pleistocene and the gradually warming interglacial stage. Our study provides one of the few pieces of evidence indicating that combined historical drainage reorganization and climatic change since the Pleistocene might also have acted as important factors in the evolutionary history of riparian plants in the region. [ABSTRACT FROM AUTHOR]

The genetic architecture within a species in the Himalaya-Hengduan Mountains (HHM) region was considered as the consolidated consequence of historical orogenesis and climatic oscillations. The visualization of dispersal corridors as the function of population genetic connectivity became crucial to elucidate the spatiotemporal dynamics of organisms. However, geodiversity and physical barriers created by paleo geo-climatic events acted vigorously to impact notable alterations in the phylogeographic pattern and dispersal corridors. Therefore, to achieve detailed phylogeography, locate dispersal corridors and estimate genetic connectivity, we integrated phylogeography with species distribution modelling and least cost path of Mirabilis himalaica (Edgew.) Heimerl in the HHM. We amplified four cpDNA regions (pet L- psb E, rps 16- trn K, rps 16 intron, trn S- trn G), and a low copy nuclear gene (G3pdh) from 241 individuals of 29 populations. SAMOVA, genealogical relationships, and phylogenetic analysis revealed four spatially structured phylogroups for M. himalaica with the onset of diversification in late Pliocene (c. 3.64 Ma). No recent demographic growth was supported by results of neutrality tests, mismatch distribution analysis and Bayesian skyline plot. Paleo-distribution modelling revealed the range dynamics of M. himalaica to be highly sensitive to geo-climatic change with limited long-distance dispersal ability and potential evolutionary adaptation. Furthermore, river drainage systems, valleys and mountain gorges were identified as the corridors for population genetic connectivity among the populations. It is concluded that recent intense mountain uplift and subsequent climatic alterations including monsoonal changes since Pliocene or early Pleistocene formulated fragmented habitats and diverse ecology that governed the habitat connectivity, evolutionary and demographic history of M. himalaica. The integrative genetic and geospatial method would bring new implications for the evolutionary process and conservation priority of HHM endemic species. [ABSTRACT FROM AUTHOR]

The phylogeographical analysis and ecological niche modeling (ENM) of the widely distributed Northern Hemisphere Sibbaldia procumbens s.l. can help evaluate how tectonic motion and climate change helped shape the current distribution patterns of this species. Three chloroplast regions (the atpI-atpH and trnL-trnF intergenic spacers and the trnL intron) were obtained from 332 (156 from present study and 176 from the previous study) individuals of S. procumbens s.l. An unrooted haplotype network was constructed using the software NETWORK, while BEAST was used to estimate the divergence times among haplotypes. ENM was performed by MAXENT to explore the historical dynamic distribution of S. procumbens s.l. The haplotype distribution demonstrates significant phylogeographical structure (N ST > G ST; P < 0.01). The best partitioning of genetic diversity by SAMOVA produced three groups, while the time to the most recent common ancestor of all haplotypes was estimated to originate during the Miocene, with most of the haplotype diversity having occurred during the Quaternary. The MAXENT analysis showed S. procumbens s.l. had a wider distribution range during the last glacial maximum and a narrower distribution range during the last interglacial, with predictions into the future showing the distribution range of S. procumbens s.l. shrinking. [ABSTRACT FROM AUTHOR]

Prinsepia Royle (Rosaceae) is a genus native to China and the Himalayan region. In order to explain its current fragmented distribution pattern and to compare the impact of relatively recent climate changes on the genetic structure of Prinsepia species in different regions of China, a total of 66 populations and 617 individuals of four species of Prinsepia were genotyped, using three cpDNA markers. Meanwhile, phylogenetic reconstructions and divergence dating were conducted using the cpDNA haplotypes dataset and the nuclear ribosomal internal transcribed spacer (ITS) dataset, respectively. Ecological niche modeling (ENM) was performed to predict the potential distribution of each species of Prinsepia at present and during the Last Glacial Maximum. Both ITS and cpDNA gene trees support a north-south divergence of Prinsepia species in China. The divergence time of the northern and southern Clades occurred around the late Oligocene epoch. Combining the present distribution of Prinsepia species and their habitats, we inferred that the transition to a monsoon climate system in East Asia during the late Oligocene epoch, created a humid forest vegetation zone from central to East China, which potentially gave rise to the north-south divergence of Prinsepia species. Both regional climates and allopatric divergence may have played an important role in the speciation of P. sinensis and P. uniflora. P. sinensis had the lowest genetic diversity and a putative northward post-glacial colonization. The distribution range of P. uniflora was also extremely sensitive to interglacial-glacial cycles. P. utilis from southwestern China preserved more haplotypes than P. sinensis and P. uniflora due to its multiple and isolated refugia. [ABSTRACT FROM AUTHOR]

Previous phylogeographical studies of the Sino-Himalaya (SH) regions have mainly focused on seed plants from forest or alpine grassland habitats, whereas the flora of the subnival summits, especially the ferns, has largely been ignored. Here, we report on phylogeographical studies on Polystichum glaciale, a rare fern endemic to the subnival belt of the SH region. Based on cpDNA/nDNA sequences, strikingly rich genetic diversity was detected in P. glaciale. Combined with the lack of ‘isolation by distance’ and the major genetic differentiation among populations revealed by AMOVA, they collectively suggested that P. glaciale exhibited island-like population genetic structure. Phylogeographical structure with two genetic groups (N vs. S) was further identified in P. glaciale by the SAMOVA based on cpDNA data, of which the geographical pattern was mainly associated with the biogeographical boundary between the northern and southern Hengduan Mountains at 29°N latitude. We concluded that extremely complex topography of SH region and highly fragmented subnival habitat have played a critical role in shaping phylogeographical structure and genetic differentiation of P. glaciale. Mismatch distribution analyses and ecological niche modelling suggested P. glaciale has undergone north-westward retreat after the LGM. Predictions of its future distribution indicated the possibility of compression within suitable subnival habitats. We suggest in situ conservation should be urgently implemented to preserve this rare fern. Our results represent a first framework for a comprehensive understanding of the biogeographical history of fern species associated with the subnival belt of the SH region and the effects of historical events on its genetic architecture. [ABSTRACT FROM AUTHOR]

Clarifying the relationship between distribution patterns of organisms and geological events is critical to understanding the impact of environmental changes on organismal evolution. Quercus sect. Heterobalanus is now distributed across the Himalaya-Hengduan Mountains ( HHM) and warm lowland in East China, yet how the distribution patterns of this group changed in response to the HHM uplift remains largely unknown. This study examines the effect of tectonic events in the HHM region on the oaks, providing a biological perspective on the geological history of this region. Fifty-six populations of Quercus sect. Heterobalanus were genotyped using four chloroplast DNA regions and nine nuclear simple sequence repeat loci to assess population structure and diversity, supplemented by molecular dating and ancestral area reconstructions. The underlying demographic dynamics were compared using ecological niche models of the species distributions during the last glacial maximum and the present. These analyses illustrate that Quercus sect. Heterobalanus diversified as the HHM uplifted and climatic cooling during the mid-Miocene, colonizing the cold habitats from warm broadleaf mixed forests. Lineages in cold highlands and warm lowlands have diverged as a consequence of local adaptation to diverging climates since the late Miocene. Our results suggest that continuous uplift of the HHM in the late Miocene to early Pliocene accompanied by simultaneous cooling triggered the differentiation of oaks. The biogeography of Quercus sect. Heterobalanus illuminates the geological events responsible for the modern-day HHM. [ABSTRACT FROM AUTHOR]

Eastern Asia (EA) is a key region for the diversification of flowering plants in the Northern Hemisphere, but few studies have focused on the biogeographic history within EA in the context of the other northern continents. Polygonatum is an important medicinal genus widely distributed in the Northern Hemisphere with its highest species richness in EA, and it represents an excellent model for studying the evolution of biogeographic patterns in this region. Divergence time estimation was used to examine the biogeographic history of Polygonatum based on nuclear ITS and four plastid sequences (rbcL, matK, psbA–trnH and trnC–petN) from 30 Polygonatum species and 35 outgroup taxa. The ancestral area of Polygonatum and subsequent dispersal routes were inferred using Bayes-Lagrange. Polygonatum was estimated to have originated in southern EA during the middle Miocene (14.34–13.57 Ma) with subsequent south-to-north expansion in the late Miocene. Multiple intercontinental dispersal events were inferred between EA and Europe or North America, and all of them have occurred recently in the late Miocene to Pliocene. The separation of Polygonatum into the south and north lineages and their subsequent diversifications in the late Miocene supports the existence of a biogeographic divide between the northern and southern parts of EA that also coincides with the retreat and redevelopment of the arid zone in EA in the Neogene. Our results demonstrate the complexity of biogeographic history of Polygonatum in the Northern Hemisphere including early vicariance followed by frequent and recent dispersals in the Neogene. [ABSTRACT FROM AUTHOR]

Aim: We investigated the historical biogeography and diversification of Gentiana L. (Gentianaceae). Our study depicts the origin and dispersal routes of this alpine genus, and the role of the uplift of the Qinghai-Tibet Plateau (QTP) and past climate changes as triggers for its diversification. Location: Tibeto-Himalayan region and world-wide mountain habitats. Methods: Our sampling represents more than 50% of the extant Gentiana species, including all sections across their entire geographical ranges. We investigated the evolutionary history of Gentiana using phylogenetic reconstructions (maximum likelihood and Bayesian inference) of ITS, atpB-rbcL and trnL-trnF sequences, as well as molecular dating with beast. We tested two approaches of ancestral area reconstructions (DEC, DIVA) in BioGeoBEARS and investigated diversification rates using BAMM. Results: The common ancestor of Gentiana and subtribe Gentianinae lived in the QTP region at around 34 (25-45) million years ago (Ma), and 40 (29-52) Ma respectively. From the surroundings of the QTP, Gentiana lineages dispersed to eastern China, Taiwan, Europe, North and South America, Australia and New Guinea, from mid-Miocene onward (c. 15 Ma-present), with only one older dispersal event to Europe (c. 37-21 Ma). Diversification rates gradually increased over time, and two switches of diversification rates were identified in Gentianinae (c. 7 Ma, simultaneously in the Pneumonanthe/Cruciata lineage and in Tripterospermum). Main conclusions: Gentiana existed in the QTP region throughout most of its uplift history following the India-Asia collision. This region acted as the primary source area for dispersals to many areas of the world. Because steady increase in diversification rates coincides with the extension of the QTP, we argue that the museum theory rather than the explosive radiation theory prevails for gentians in this region, although rare shifts of diversification rates are associated with niche shifts across the alpine/subalpine ecotone. [ABSTRACT FROM AUTHOR]

Tibetia and Gueldenstaedtia are two morphologically similar and small genera in Fabaceae, with distributions largely corresponding to the Sino-Himalayan and Sino-Japanese subkingdoms in eastern Asia, respectively. These two genera have confusing relationships based on morphology; therefore, we aimed to provide a clear understanding of their phylogenetic and biogeographic evolution within eastern Asia. In our investigations we included 88 samples representing five Gueldenstaedtia species, five Tibetia species, and outgroup species were sequenced using five markers (nuclear: ITS; chloroplast: matK, trnL-F, psbA-trnH and rbcL). Our phylogenetic results support (1) the monophyly of Tibetia and of Gueldenstaedtia, respectively; and (2) that Tibetia and Gueldenstaedtia are sister genera. Additionally, our data identified that Tibetia species had much higher sequence variation than Gueldenstaedtia species. Our results suggest that the two genera were separated from each other about 17.23 million years ago, which is congruent with the Himalayan orogeny and the uplift of the Tibetan Plateau in the mid Miocene. The divergence of Tibetia and Gueldenstaedtia is strongly supported by the separation of the Sino-Himalayan and Sino-Japanese region within eastern Asia. In addition, the habitat heterogeneity may accelerate the molecular divergence of Tibetia in the Sino-Himalayan region. [ABSTRACT FROM AUTHOR]

The Hengduan Mountains are the core of the Sino-Himalayan Floristic Region. Rosa soulieana Crép. is an important wild rose species that is widely distributed in the Hengduan Mountains. To provide better future utilization of this wild rose, and also to add some possible proof of the effect of geomorphological and ecological characteristics of the Hengduan Mountains on the current spatial distribution and genetic diversity of local species, the genetic diversity and genetic structure of 556 individuals from 37 populations of R. soulieana were studied using fluorescent amplified fragment length polymorphisms (AFLPs). R. soulieana showed a moderately high level of genetic diversity and a high level of genetic differentiation at the species level. The total percentage of polymorphic loci, total heterozygosity (Ht), Shannon index (I), and heterozygosity value within populations (Hs) were 97.8%, 0.253, 0.339, and 0.139, respectively. More than half of the total genetic variation (54.0%) occurred within populations, and the overall gene differentiation coefficient (Gst) was 0.451. The genetic differentiation among populations was positively and significantly correlated with geographic distance. The neighbor-joining cluster and the Bayesian analysis divided all the populations and individuals into 3 groups, and did not support the morphology based intraspecific varieties. The results confirmed that the ancient R. soulieana of the third group survived in northwestern Yunnan and Yalongjiang valley and then moved upnorth along the valley. The spatial distribution of the other two groups was the result of allopatric divergence due to long period of adaptation to the different climatic conditions of its distribution at either side of the Yalongjiang River. [ABSTRACT FROM AUTHOR]

Aim The Himalaya-Hengduan Mountain (HHM) biodiversity hotspot including the 'sky islands' of Southwest China harbour exceptional plant diversity and endemicity at subnival summits (most of them exceeding 4300 m a.s.l.). This study is the first using a comparative phylogeographical framework to gain insights into the temporal origin of this highly fragmented subnival flora, and the historical factors shaping its genetic architecture as exemplified by four perennial herbs. Location Himalaya-Hengduan Mountains, China. Methods Based on nuclear and/or chloroplast (cp) DNA sequences for each of the four studied species, we performed AMOVA and mismatch distributional analyses to assess molecular structure, diversity and demographic history in relation to current and last glacial distributions using ecological niche modelling (ENM). Time-calibrated phylogenetic reconstructions of cpDNA data were used to infer species-specific stem and crown ages. Results Our time estimates suggest that these species originated during the Late Pliocene or early-to-mid Pleistocene, whereas their onset of diversification generally falls into the mid-Pleistocene. All four species exhibited island-like population genetic structures, with all of them showing signatures of recent population growth and/or spatial expansion based on cpDNA. By contrast, ENM indicated that species broad-scale distributions remained fairly stable over the last glacial/post-glacial cycle. Main conclusions The temporal origin of the four subnival HHM species is likely associated with tectonic changes in the region, while their near-simultaneous onset of diversification during the 'Naynayxungla Glaciation' (0.72-0.50 Ma) could reflect initial population divergence through climate-induced habitat fragmentation. Despite a rather stable distributional history, geographical population isolation and localized range expansion/contractions likely resulted in significant genetic structure and differentiation over the last glacial/ post-glacial cycle. Overall, the present results are strongly indicative of shared evolutionary histories and phylogeographical structures among subnival plants from the 'sky island system' of the HHM region. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

In reconstructing taxon evolution, historical biogeography is concerned with two kinds of speciation events, both resulting in a fragmented taxon distribution – vicariance and dispersal. We used PCR-RFLP of plastid DNA and a ribosomal internal transcribed spacer, sequencing of therps16-trnKchloroplast region, flow cytometry (florescence-activated cell sorter; FACS), and ecological niche modeling to understand the role of these two processes in a disjunct distribution of genusMandragora. The observed phylogeographic structure only partly coincided with currently recognized species. Commonly used recognition of a single species in the whole Mediterranean is not supported, given that a single haplotype observed from Morocco and Spain to Turkey is strikingly different from the haplotypes found in Israel. In the Sino-Himalayan area, the previously recognizedM. chinghaiensisis nested within theM. caulescensclade indicating a very recent diversification within this lineage. And, most importantly, the obtained minimum spanning tree, observed haplotype distribution, and results of FACS call into question the existence ofM. turkomanicaas a species, and even as a lower taxonomic unit. Rather, the mandrake from Central Asia is nested within those from Israel, suggesting their closely related evolutionary history and ancient human assisted migration from Israel to Persia in historic times. Our study suggests that human assisted migration can explain the cases of disjunct species distribution for which vicariance was previously considered as the only plausible explanation. [ABSTRACT FROM AUTHOR]

Climate oscillations and landscape heterogeneity make the historical population processes of organisms of the Qinghai-Tibet Plateau quite complex. We used chloroplast DNA sequences and amplified fragment length polymorphism (AFLPs) to study the phylogeography and genetic variation of the Qinghai-Tibet Plateau endemic Spenceria ramalana Trimen. The parsimony network contains two star-like evolutionary units, nested into two nested clades, coinciding with geographic population groups indicated by SAMOVA software. The central group shows genetic homogeneity, indicating a bottleneck or founder effect of population dynamics. Margin groups contribute more haplotype diversity ( CT), indicating potential refugia. Several expansion events during several interglacial periods were detected. The latest expansion of the eastern population contributed to the modern population structure of the central area. Four AFLP clusters were detected. Higher CT, a relict pattern of haplotype distribution and DW values of marginal populations, confirmed the location of potential montane refugia. Relict distribution pattern, nested clade phylogeographic analysis conclusions, and restricted gene flow detected by AFLPs indicated an isolation pattern of the populations of montane areas. Heterogeneity of landscape of the western and southern montane areas could be the main barrier for gene flow. Moisture conditions and ecotype transformation might help to build the phylogeographic pattern of this species. Neither chloroplast DNA markers nor AFLP was able to differentiate the two varieties of this species. [ABSTRACT FROM AUTHOR]

Phylogeographic studies on alpine plants endemic to the Hengduan Mountains of the southeastern Qinghai-Tibet Plateau are still limited in number. In this study, we used sequence variation of one nuclear gene ( ncpGS, which encodes the chloroplastic glutamine synthetase) and in two chloroplast DNA segments to investigate the phylogeographic structure and population demographic history of Cyananthus delavayi, a narrow-range species endemic to this region. We identified eight chlorotypes and 16 nuclear genotypes in a survey of 10 populations sampled throughout the range of the species. The results of both phylogenetic and network analyses suggested that the genealogical relationships of both chlorotypes and nuclear genotypes showed a clear geographical correlation. High total genetic diversity, low levels of within-population diversity, and strong population differentiation (chloroplast DNA: hT= 0.827, hS= 0.087, NST= 0.899, GST= 0.895; nuclear DNA: hT= 0.910, hS= 0.348, NST= 0719, GST= 0.618) were identified. Based on the mismatch distribution analyses, no evidence of recent demographic population expansion was found for this species. Nested clade analyses of both chlorotypes and nuclear genotypes indicated that restricted gene flow resulting from isolation by distance and allopatric fragmentation were likely to have been the major processes that shaped their present-day spatial distribution. Our dating of the genetic divergences between three major geographic lineages suggested that the largest glaciation of the early Quaternary developed in the Qinghai-Tibet Plateau and mountainous isolation may have together led to deep intraspecific vicariance within this species. [ABSTRACT FROM AUTHOR]

Abstract: The reorganization of major river drainages in the Sino-Himalayan region of Southwest China was caused primarily by river separation and capture events following the most recent uplift of the Tibetan Plateau (⩽3.4Ma). Terminalia franchetii is a shrub or small tree species endemic to the river valleys of this region. Based on a range-wide sampling comprising 28 populations and 258 individuals, we investigated the relationship between the modern phylogeographic structure of T. franchetii and geological changes in drainage patterns, using chloroplast DNA sequences (trnL–F, petL–psbE). T. franchetii was found to harbor high haplotype diversity (h T =0.784) but low average within-population diversity (h S =0.124). Mismatch distribution and neutrality tests provided no evidence of recent demographic population growth. Two (out of five) population groups identified exhibited a disjunctive distribution of dominant haplotypes between northern and southern valleys, corresponding to the geography of past drainage systems. We conclude that the modern disjunctive distribution of T. franchetii, and associated patterns of cpDNA haplotype variation, result from vicariance caused by several historical river separation and capture events. Overall, our inferred timings of these events (mostly mid-to-late Pleistocene) agree with previous time estimates of drainage re-arrangements in the Sino-Himalayan region. [Copyright &y& Elsevier]

[Display omitted] • The "ampliative" Spiraea japonica complex was put forward. • Phylogeographical pattern is related to the regionalization of East Asian flora. • Genetic and diterpenoid alkaloids data support a transition belt in central China. • Diversification and demographic dynamics were shaped by the geological events. • Polyploidization contributed to the population expansion in east China. Each subkingdom of East Asian flora (EAF) has a unique evolutionary history, but which has rarely been described based on phylogeographic studies of EAF species. The Spiraea japonica L. complex, which is widespread in East Asia (EA), has received considerable attention because of the presence of diterpenoid alkaloids (DAs). It provides a proxy for understanding the genetic diversity and DA distribution patterns of species under various environmental conditions associated with the geological background in EA. In the present study, the plastome and chloroplast/nuclear DNA of 71 populations belonging to the S. japonica complex and its congeners were sequenced, combined with DA identification, environmental analyses, and ecological niche modelling, to investigate their phylogenetic relationships, genetic and DAs distribution patterns, biogeography, and demographic dynamics. An "ampliative" S. japonica complex was put forward, comprising all species of Sect. Calospira Ser. Japonicae , of which three evolutionary units carrying their respective unique types of DAs were identified and associated with the regionalization of EAF (referring to the Hengduan Mountains, central China, and east China). Moreover, a transition belt in central China with its biogeographic significance was revealed by genetic and DA distribution patterns from the perspective of ecological adaptation. The origin and onset differentiation of the "ampliative" S. japonica complex was estimated in the early Miocene (22.01/19.44 Ma). The formation of Japanese populations (6.75 Ma) was facilitated by the land bridge, which subsequently had a fairly stable demographic history. The populations in east China have undergone a founder effect after the Last Glacial Maximum, which may have been promoted by the expansion potential of polyploidization. Overall, the in-situ origin and diversification of the "ampliative" S. japonica complex since the early Miocene is a vertical section of the formation and development of modern EAF and was shaped by the geological history of each subkingdom. [ABSTRACT FROM AUTHOR]