Gulzar Khan

The varying topography and environment that resulted from paleoorogeny and climate fluctuations of the Himalaya–Hengduan Mountains (HHM) areas had a considerable impact on the evolution of biota during the Quaternary. To understand the phylogeographic pattern and historical dynamics ofTriosteum himalayanum(Caprifoliaceae), we sequenced three chloroplast DNA fragments (rbcL-accD,rps15-ycf1, andtrnH-psbA) from 238 individuals representing 20 populations. Nineteen haplotypes (H1–H19) were identified based on 23 single-site mutations and eight indels. Most haplotypes were restricted to a single population or neighboring populations. Analysis of molecular variance revealed that variations among populations were much higher than that within populations for the overall gene pool, as well as for the East Himalayan group (EH group) and the North Hengduan group (NHM group), but not for the Hengduan Mountains group (HM group). Ecoregions representing relatively high genetic diversity or high f...

Background and AimsHosting several global biodiversity hotspots, the region of the Qinghai-Tibetan Plateau (QTP) is exceptionally species-rich and harbours a remarkable level of endemism. Yet, despite a growing number of studies, factors fostering divergence, speciation and ultimately diversity remain poorly understood for QTP alpine plants. This is particularly the case for the role of hybridization. Here, we explored the evolutionary history of three closely related Gentiana endemic species, and tested whether our results supported the mountain geo-biodiversity hypothesis (MGH).MethodsWe genotyped 69 populations across the QTP with one chloroplast marker and 12 nuclear microsatellite loci. We performed phylogeographical analysis, Bayesian clustering, approximate Bayesian computation and principal components analysis to explore their genetic relationship and evolutionary history. In addition, we modelled their distribution under different climates.Key ResultsEach species was compos...

Parnassia L., a perennial herbaceous genus in the family Celastraceae, consists of about 60 species and is mainly distributed in the Pan-Himalayan and surrounding mountainous regions. The taxonomic position and phylogenetic relationships of the genus are still controversial. Herein, we reassessed the taxonomic status of Parnassia and its intra- and inter-generic phylogeny within Celastraceae. To that end, we sequenced and assembled the whole plastid genomes and nuclear ribosomal DNA (nrDNA) of 48 species (74 individuals), including 25 species of Parnassia and 23 species from other genera of Celastraceae. We integrated high throughput sequence data with advanced statistical toolkits and performed the analyses. Our results supported the Angiosperm Phylogeny Group IV (APG IV) taxonomy which kept the genus to the family Celastraceae. Although there were topological conflicts between plastid and nrDNA phylogenetic trees, Parnassia was fully supported as a monophyletic group in all cases....

  The aim of the present study was to investigate the phylogeographic patterns of Spiraea alpina (Rosaceae) and clarify its response to past climatic changes in the climate‐sensitive Qinghai‐Tibetan Plateau (QTP). We sequenced a chloroplast DNA fragment (trnL–trnF) from 528 individuals representing 43 populations. We identified 10 haplotypes, which were tentatively divided into three groups. These haplotypes or groups were distributed in the different regions of the QTP. Only half the populations were fixed by a single haplotype, whereas the others contained two or more. In the central and eastern regions, adjacent populations at the local scale shared the same haplotype. Our phylogeographic analyses suggest that this alpine shrub survived in multiple refugia during the Last Glacial Maximum and that earlier glaciations may have trigged deep intraspecific divergences. Post‐glacial expansions occurred only within populations or across multiple populations within a local range. The fin...

Plantago ovata (Plantaginaceae) is an economically and medicinally important species, however, least is known about its genomics and evolution. Here, we report the first complete plastome genome of P. ovata and comparison with previously published genomes of related species from Plantaginaceae. The results revealed that P. ovata plastome size was 162,116 bp and that it had typical quadripartite structure containing a large single copy region of 82,084 bp and small single copy region of 5,272 bp. The genome has a markedly higher inverted repeat (IR) size of 37.4 kb, suggesting large-scale inversion of 13.8 kb within the expanded IR regions. In addition, the P. ovata plastome contains 149 different genes, including 43 tRNA, 8 rRNA, and 98 protein-coding genes. The analysis revealed 139 microsatellites, of which 71 were in the non-coding regions. Approximately 32 forward, 34 tandem, and 17 palindromic repeats were detected. The complete genome sequences, 72 shared genes, matK gene, and...

Triosteum pinnatifidum Maxim., an alpine plant, is traditionally used for several medicinal purposes. Here, both chloroplast DNA sequences and nuclear low copy sequence markers were used to investigate the genetic diversity and population structure of T. pinnatifidum. Materials were collected from thirteen localities in the northeast Qinghai–Tibet Plateau (QTP) and adjacent highlands and advanced analytical toolkits were used to access their origin and range shifts. The results revealed a higher level of population differentiation based on chloroplast DNA (cpDNA) concatenated sequences compared with the nuclear DNA sequences (FST = 0.654 for cpDNA, FST = 0.398 for AT103), indicating that pollen flow was still extensive in T. pinnatifidum. A decline in haplotype variation was observed from the plateau edge and adjoining highlands toward the platform of the QTP. The hypothesis “dispersal into the QTP,” proposing that T. pinnatifidum experienced migration from the plateau edge and adja...

There are about 10% of the world’s land plants in China, of which 11% are threatened species. Here, we used China as a proxy to identify hotspots of threatened species, evaluate the effectiveness of current conservation networks and assess the correlations between distribution patterns of different groups. We built the most complete database of 3,881 species of threatened land plants in China (TLPCs) to date, based on 43,710 occurrence records at county level. A total of 467 counties identified as hotspot by species richness, complementarity, and weighted algorithms, mostly confined to the mountainous areas in southern China, which account for 15.58% of land area, however, hold 95.34% of the total TLPCs. The correlation analysis revealed weak to moderate relationship between the distribution patterns of three groups (bryophytes, ferns, and gymnosperms) and angiosperms of TLPCs. We found 86.34%, 84.05% and 95.77% of TLPCs protected by NNRs, PNRs and NRs [nature reserves, including bo...

PREMISE Classification of taxa depends on the quality of inferred phylogenies. Rhododendron, a highly species-rich genus (>1156 species) of woody plants, has a highly debated infrageneric classification, due to its huge diversity, homoplasy in key characters, and incongruence among data sets. We provide a broad coverage of representative species to resolve Rhododendron infrageneric phylogeny and highlight the areas of incongruence. We further investigate the effect of polyploidy and genome size evolution on diversification of Rhododendron. METHODS We generated two plastid and two nuclear loci for 260 Rhododendron species. We analyzed the loci separately as well as concatenated, utilizing both likelihood and Bayesian methods. We tested incongruence both among the data sets and with previous studies. We estimated genome sizes for 125 species through flow cytometry. RESULTS Our results suggest stronger support for larger subgenera; however, the smaller subgenera pose several problems; for example, R. tomentosum (former genus Ledum) occupies incongruent positions based on different DNA regions. The main shift to higher diversification in the genus occurs in the Himalayan/Southeast Asian clade of R. subg. Hymenanthes. We found that polyploidy occurs in almost all subgenera but most frequently within R. subg. Rhododendron sections Rhododendron and Schistanthe. CONCLUSIONS We endorse the recognition of five major clades at the subgeneric level, but a number of species cannot be confidently assigned to these clades due to incongruency. With regard to genome size evolution, results support previous reports that genome sizes of tropical plants are lower than those of colder and temperate regions and that genome downsizing promotes diversification.

Uebelmannia is a cactus genus represented by three microendemic species with patchy distributions in campo rupestre landscapes in the Espinhaço Range in eastern Brazil. It is one of the ten genera of Cactaceae listed as threatened with extinction due to habitat loss and illegal overcollection. Assessment of the genetic diversity and population structure of this threatened genus is crucial to provide guidelines for both in situ and ex situ conservation and management efforts. Here, we genotyped 12 microsatellite loci from samples covering the entire distribution of this genus (485 individuals from 20 localities) to investigate the genetic diversity, spatial population structure, and demography of Uebelmannia species. The results identified moderate-to-high levels of genetic diversity in Uebelmannia, comparable to the wide-range cacti from Cerrado biome. The results confirmed an extremely high population structure even at small geographic scales, with population clusters exhibiting high inbreeding and genetic signatures of a recent bottleneck. Based on this study, we suggest some conservation strategies, including in situ management for populations at the borders of protected areas and ex situ seed collection, for further management of this genus. Furthermore, the results suggest the use of a precautionary approach for translocation plans and highlight that effective conservation management of Uebelmannia should target genetically clustered populations instead of species or subspecies.

Succulent cacti (Cactaceae) are among the most threatened taxonomic groups assessed to date. Here we evaluated the genetic diversity and population structure of a narrow endemic columnar cactus Pilosocereus aureispinus. This species is only found in a small area of c. 300 km2 of rocky savanna from eastern Brazil and it is currently classified as vulnerable (VU) on the International Union for Conservation of Nature (IUCN) red list. Eight microsatellite loci were genotyped for 91 individuals from four localities of the known P. aureispinus range. In contrast with expectations for narrow endemic species, we found relatively high levels of genetic diversity (e.g., HE = 0.390 to 0.525; HO = 0.394 to 0.572) and very low population structure based on the variation of six loci. All the analyzed individuals were clustered in one unique genetic group in assignment tests. We also generated the sequences of two plastid markers (trnT-trnL and psbD-trnT) and found no variation on a subsample of 3...

Rhodiola alsia, which has been used widely in traditional Chinese medicine for a considerable time, grows on moist habitats at high altitude near the snow line. Microsatellite loci were developed for R. alsia to investigate its population genetics. In total, 17 polymorphic microsatellites were developed based on ESTs from the Illumina HiSeq(TM) 2000 platform. The microsatellite loci were checked for variability using 80 individuals of R. alsia sampled from four locations on the Qinghai-Tibet Plateau. The total number of alleles per locus ranged from 10 to 20, and the observed heterozygosity ranged from 0.000 to 1.000. The null allele frequency ranged from 0.000 to 0.324. These microsatellites are expected to be helpful in future studies of population genetics in R. alsia and related species.

In allopatric systems, where gene flow is highly constrained, the distinction between intraspecific differentiation and
speciation is a challenging task. Pilosocereus jauruensis is a columnar cactus restricted to patchy dry habitats of Pantanal,
Cerrado, and Chaco biomes in south-western Brazil and neighbouring countries. This species was recently reinstated after
having been synonymized with P. machriisi, now including P. paraguayensis, P. saudadensis, and P. densivillosus as its
synonyms. These taxa have been placed within the informal AURISETUS group. The present study aimed to investigate the
genetic structure of P. jauruensis in order to identify possible distinct evolutionary lineages, and to support further
refinement of the taxonomy of this species. For this purpose, 10 microsatellite loci were genotyped for 156 individuals of
P. jauruensis. To provide a proxy for the expected interspecific differentiation level within this allopatric system, two
populations (49 individuals) of P. vilaboensis (a species closely related to P. jauruensis) were also included. Additionally,
two cpDNA markers (trnSGCU-trnGUCC and trnT-trnL) for a subsample of 44 individuals of both species were
sequenced. The results obtained showed that even though P. jauruensis populations are relatively small and isolated, they
still maintain a high level of genetic diversity (e.g., HE D 0.557 to 0.725; HO D 0.253 to 0.409). The study suggests the
existence of two distinct taxa/evolutionary lineages through their entire distribution. Two populations found in the same
geographic region of the now synonymized P. densivillosus showed significant genetic divergence when compared with
other populations of P. jauruensis. In contrast, our results did not support an evolutionary independence hypothesis for
populations that occur in the same geographic region of the synonymous P. saudadensis

Medicago ruthenica (L.) Ledebour, a species well adapted to dry, stony and desert habitats, has more tolerance to drought, cold and saline conditions than other alfalfas. Characterization of the genetic diversity and population genetic structure of M. ruthenica is important for its domestication as a legume forage species and for the development of other cultivated alfalfas with abiotic stress tolerance. However, studies of the genetic diversity and pattern of genetic structure of M. ruthenica distributed on the Qinghai-Tibetan Plateau (QTP) have been limited. In this study, nuclear internal transcribed spacer (ITS) and chloroplast (psbA-trnH) DNA regions were used to evaluate the genetic diversity, structure and population dynamics of 12 wild M. ruthenica populations distributed on the QTP and Inner Mongolia. Although the chloroplast psbA-trnH region was more variable than nuclear ITS, both markers indicated high interpopulation genetic differentiation, with all populations clustered into two groups based on neighbor joining clustering. Mismatch distribution and neutrality tests revealed local or small-scale demographic expansion. As inferred by morphology and genetic structure, M. ruthenica can be divided into two eco-types, a result suggested previously. Our findings imply that the genetic divergence of M. ruthenica may be due to climatic oscillations or earlier uplifts of the QTP.

Distribution of similar taxa between the East Asia (old world) and new worlds fascinated the Botanists and Bio-geographers since the Linnaean time. The current study represents phylogenetic investigation of 39 Spiraea L., species covering their entire distribution in the new world (America) to the old world (Tibet PR China). In this study we used both plastidial marker (trnL-F) and nuclear internal transcribed spacer (nrDNA ITS). Phylogeny among the species implemented in the program PAUP* while divergence time was calibrated in BEAST 1.7.5. The analysis revealed that all 39 species of the genus are monophyletic. The study further suggested that ancestors of Spiraea were in the new world but their center of diversification is in East Asia. The estimated divergence time showed that S. virginiana endemic to North America is the oldest species with divergence time 21.1 MY. The divergence time of Spiraea species with disjunct distribution in the new world, Europe and East Asia e.g., S. hypericifolia, S. chamaedryfolia, S. douglasii, S. salicifolia and S. latifolia ranged from 7.44-1.83 MY with most during Pliocene (within the last 5 MY). The results concluded that isolation of Spiraea species occurred during the severe eco-climatic fluctuations period throughout the late Tertiary and Quaternary.

The genetic structure and phylogeographical history of the alpine shrubs Sibiraea angustata (Rosaceae) and Sibiraea laevigata from the QinghaieTibetan 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 ri-bosomal 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 YushueNangqian 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 1.60e2.58 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.

BioOne (www.bioone.org) is a nonprofit, online aggregation of core research in the biological, ecological, and environmental sciences. BioOne provides a sustainable online platform for over 170 journals and books published by nonprofit societies, associations, museums, institutions, and presses.

Rhodiola alsia, which has been used widely in traditional Chinese medicine for a considerable time, grows on moist habitats at high altitude near the snow line. Microsatellite loci were developed for R. alsia to investigate its population genetics. In total, 17 polymorphic microsatellites were developed based on ESTs from the Illumina HiSeq TM 2000 platform. The microsatellite loci were checked for variability using 80 individuals of R. alsia sampled from four locations on the Qinghai-Tibet Plateau. The total number of alleles per locus ranged from 10 to 20, and the observed heterozygosity ranged from 0.000 to 1.000. The null allele frequency ranged from 0.000 to 0.324. These microsatellites are expected to be helpful in future studies of population genetics in R. alsia and related species.

The Qinghai-Tibetan Plateau (QTP) and adjacent regions comprise an excellent mountainous system to study plant diversification and speciation within East Asia. The uplift and eco-environmental processes of QTP have had an obvious effect on evolution of organisms in this region. The present study intends to test the potential correlation between evolutionary events (such as speciation and diversification) and orogenetic events (such as the intense uplift of QTP). Sequence data from five plastid DNA regions (trnL–trnF, rpl20–rpl12, rps15–ycf1, psbA–trnH, and trnS– trnG) and one nuclear ribosomal internal transcribed spacer of 19 species of the genus Spiraea L. were used in the study. Maximum parsimony and maximum likelihood trees were constructed in PAUP*, while divergence time was estimated with BEAST v1.7.5. Phylogenetic reconstruction revealed that these species form a single clade and can be divided into three sections. Diversification of Spiraea species began in middle Miocene (ca. 13.38 million years ago) during the first stage of uplifting at QTP. Diversification of Spiraea was further triggered and accelerated during the second stage of QTP uplifting in late Pliocene (ca. Last four million years). The estimated divergences time indicate that this rapid diversification was most likely triggered by the uplifting of QTP in early Pliocene, and accelerated during the Quater-nary climatic oscillations.

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 phylo-geographic 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 eITS 4) 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 ¼ 0.741*). The estimated divergence time revealed that the main lineages of S. alpina diversified during the Quaternary 1.2e0.6 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.

BioOne sees sustainable scholarly publishing as an inherently collaborative enterprise connecting authors, nonprofit publishers, academic institutions, research libraries, and research funders in the common goal of maximizing access to critical research. BioOne (www.bioone.org) is a nonprofit, online aggregation of core research in the biological, ecological, and environmental sciences. BioOne provides a sustainable online platform for over 170 journals and books published by nonprofit societies, associations, museums, institutions, and presses.

Transcriptome sequencing is a powerful tool for the assessment of gene expression and the identification and characterization of molecular markers in non-model organisms. Rhodiola algida L. (Crassulaceae), endemic to the Qinghai-Tibetan Plateau, has long been used in traditional Chinese medicine to prevent altitude sickness and eliminate fatigue. Illumina-based high-throughput transcriptome sequencing of aboveground and underground tissues of R. algida respectively yielded 5.40 million and 5.18 million clean reads. A total of 82,664 unigenes averaging 577 bp in length were generated from the aboveground clean reads, with 86,237 unigenes of 502-bp mean length obtained from the underground tissues. Of 55,028 unigenes compared with sequences in UniProt databases, 20,413 unigenes had significant similarities with existing sequences in NR, NT, Swiss-Prot, GO, KEGG, and COG databases. Single nucleotide polymorphism (SNP) analysis identified 237,294 SNPs from 154,636 contigs of aboveground tissues and 197,540 SNPs from 144,963 underground-derived contigs. The information uncovered in this study should serve as a valuable resource for the characterization of important traits related to secondary metabolite formation and for the identification of associated molecular mechanisms.

Armillaria luteo-virens is a type of ectomycorrhiza whose fruit body is widely used as an edible mushroom in the Qinghai-Tibetan Plateau. In total, 404 individuals of A. luteo-virens from 23 geographically separate populations were analyzed using eight pairs of SSR markers. The average number of alleles among nine populations was 28.65 with a range from 20 to 38. The mean observed (H O) and expected (H E) heterozygosity ranged from 0.446 to 0.501 and from 0.499 to 0.554, respectively. An analysis of molecular variance (AMOVA) showed that most genetic variation occurred within populations (83.32%). The mean value of F ST (0.176) suggested low genetic differentiation among populations. The 23 studied populations were divided into two main clusters based on the NJ dendrogram, which was also confirmed by STRUCTURE analysis. This study may aid in not only the protection of this species but also the management of genetic resources for future artificial cultivation.

Distribution of similar taxa between the East Asia (old world) and new worlds fascinated the Botanists and Biogeographers since the Linnaean time. The current study represents phylogenetic investigation of 39 Spiraea L., species covering their entire distribution in the new world (America) to the old world (Tibet PR China). In this study we used both plastidial marker (trnL-F) and nuclear internal transcribed spacer (nrDNA ITS). Phylogeny among the species implemented in the program PAUP* while divergence time was calibrated in BEAST 1.7.5. The analysis revealed that all 39 species of the genus are monophyletic. The study further suggested that ancestors of Spiraea were in the new world but their center of diversification is in East Asia. The estimated divergence time showed that S. virginiana endemic to North America is the oldest species with divergence time 21.1 MY. The divergence time of Spiraea species with disjunct distribution in the new world, Europe and East Asia e.g., S. h...

The aim of the present study was to investigate the phylogeographic patterns of Spiraea alpina (Rosaceae) and clarify its response to past climatic changes in the climate-sensitive Qinghai-Tibetan Plateau (QTP). We se-quenced a chloroplast DNA fragment (trnL–trnF) from 528 individuals representing 43 populations. We identified 10 haplotypes, which were tentatively divided into three groups. These haplotypes or groups were distributed in the different regions of the QTP. Only half the populations were fixed by a single haplotype, whereas the others contained two or more. In the central and eastern regions, adjacent populations at the local scale shared the same haplotype. Our phylogeographic analyses suggest that this alpine shrub survived in multiple refugia during the Last Glacial Maximum and that earlier glaciations may have trigged deep intraspecific divergences. Post-glacial expansions occurred only within populations or across multiple populations within a local range. The findings of the present study together with previous phylogeographic reports suggest that evolutionary histories of plants in the QTP are complex and variable depending on the species investigated.