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Recent radiations provide excellent models to gain more insights into evolution, speciation and adaptation. To this end, a well-resolved phylogenetic tree is needed. However, resolving phylogenetic relationships within recent radiations has been difficult as traditional phylogenetic markers failed to provide enough information. We here use plastome data to test their capacity in resolving phylogenetic relationships among a recent rapidly diverging group, Rhodiola, on the Qinghai-Tibetan Plateau. We reconstructed a robust phylogenetic backbone of Rhodiola using 23 plastomes representing all subgenera and sections in previous taxonomic treatments. Based on the backbone, we inferred the spatio-temporal pattern of diversification of the genus. We also traced evolution of five important morphological characters of Rhodiola, including sexual system, inflorescence type and flowering stem, based on the maximum likelihood and the threshold models. Two well-supported clades were revealed in Rhodiola, and the two clades were distinguished by sexual system: species in clade I are mostly hermaphrodite (except R. stapfii and R. integrifolia), and those in clade II are all dioecious. Biogeographic analysis showed that Rhodiola probably originated in the Qinghai-Tibetan Plateau and the Hengduan Mountains. The two major clades diverged c. 6.34 Mya, corresponding to a period of rapid uplift of the Hengduan Mountains and intensification of the Asian monsoon. Character evolution analysis confirmed parallel evolution of dioecy and other adaptive traits, such as marcescent flowering stems, in the genus. We demonstrate that plastome data could significantly improve phylogenetic resolution in plant groups resulting from recent radiations. Our results not only shed new light on the evolutionary history of Rhodiola, but also indicate that more plastome data should be used in resolving phylogenetic relationship in plant groups that have undergone recent radiations.

Aquilegia ecalcarata Maxim. is the only spurless species within the genus Aquilegia and comprises a monophyletic clade with A. yabeana Kitag., A. kansuensis Bruhl, and A. rockii Munz. Our previous study on the genetic diversity of those four species revealed that the populations of A. ecalcarata can be divided into two groups, indicating possible genetic difference within A. ecalcarata. However, it is not clear whether the genetic difference is related to the morphological variation among species and groups of A. ecalcarata populations. To answer that question, the morphological variation patterns based on 22 floral and 19 vegetative traits from 42 populations, covering the entire distribution of A. ecalcarata and its relatives, were analyzed in the present study. The result showed that: (i) the differences among the four species were reflected in the floral rather than the vegetative traits; (ii) populations of A. yabeana and A. rockii fell into one cluster each, and each of the six clusters occupied its own distribution range; (iii) one of two A. ecalcarata clusters fell into a subgroup and shared common floral traits with A. rockii; (iv) the individuals of A. ecalcarata form. ecalcarata and form. semicalcarata were often mixed in the same population; and (v) the populations of A. kansuensis were split into two clusters, which differed obviously in floral traits. These results will provide an important morphological basis for the redefinition of species and lay a foundation for the further exploration of the “spurless” A. ecalcarata.

Fargesia, a temperate woody bamboo genus, is one of the largest genera and constitutes a taxonomically problematic group due to unusual life cycles and the rarity of flowering. We explored phylogenetic relationships within Fargesia and its allies based on sequence data from three cpDNA regions (matK, psbA-trnH and trnL-trnF) and one nuclear region (nrITS). A representative sample of 49 species, including 36 Fargesia and nine Yushania, were sampled, and maximum parsimony, maximum likelihood and Bayesian inference were used to reconstruct the phylogeny of Fargesia. The results suggest that Fargesia is polyphyletic, with F. crassinoda and F. damuniu in the Thamnocalamus clade, F. ampullaris, F. semiorbiculata, F. gyirongensis and F. collaris in the Drepanostachyum + Himalayacalamus clade, and the rest of species of Fargesia and all sampled species of Yushania in a Fargesia + Yushania clade, which was further divided into weakly supported Fargesia spathe and non-spathe clades. Species in the Fargesia spathe clade have the derived “spathe-like leaf sheath syndrome,” which may have evolved as a result of an adaptive advantage of compressed inflorescences in colder temperatures.

Ormosia hosiei (Fagaceae), a critically endangered plant species, is famous for its excellent wood from which the carving craft and high-grade furniture can be made. In this study, we characterized the complete chloroplast genome of O. hosiei based on next generation sequencing to analyze its phylogenetic position. The circular complete chloroplast genome of O. hosiei was 171,642 bp in length, containing a large single-copy (LSC) region of 72,295 bp and a small single-copy (SSC) region of 18,659 bp. These two regions were separated by a pair of inverted repeat regions (IRa and IRb), each of them 40,344 bp. A total of 144 functional genes were encoded, consisted of 98 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The overall GC content of the chloroplast genome was 38.1%, and the GC contents of the LSC, SSC, and IR regions were 33.5, 29.8, and 39.3%, respectively. The phylogenetic analysis by maximum likelihood showed that the O. hosiei is clustered into one clade with Styphnolobium japonicum by strong support values, and thus is closely related to Styphnolobium.

Dalbergia hainanensis is a vulnerably endangered tree species with high economic and ornamental value. The complete chloroplast (cp) genome of D. hainanensis was determined to provide the underlying information for genetic and conservation studies and explore possible phylogenetic relationship within leguminous family in this study by next generation Illumina pair-end sequencing dataset. The whole genome was 156,073 bp in length and contains a pair of 182,574 bp inverted repeats regions, which were separated by a large single copy region and a small single copy region of 85,831 and 18,838 bp in length, respectively. The cp genome contained 131 genes, including 86 protein-coding genes, 36 tRNAs and 8 rRNAs. The overall GC content of the whole genome was 36.09%. A neighbour-joining phylogenetic analysis suggested a close relationship between D. hainanensis and Arachis hypogaea.

A phosphate-solubilizing bacterium, designated CPCC 100624T, was isolated from a freshwater reservoir in south-west China. The 16S rRNA gene sequence comparison of strain CPCC 100624T with the available sequences in the GenBank database showed that the isolate was closely related to members of the genus Spirosoma . In the phylogenetic tree based on 16S rRNA gene sequences, strain CPCC 100624T formed a stable phylogenetic subclade with Spirosoma soli MIMBbqt12T within the genus Spirosoma , which indicated that strain CPCC 100624T could be identified as a member of the genus Spirosoma . The strain grew at 10–40 °C (optimum 30 °C), at pH 6.5–8.0 (optimum pH 7.0–7.5) and in the presence of 0–5 % (w/v) NaCl (optimum 0–1 %). MK-7 was detected as the main menaquinone, with a minor amount of MK-7(H6) in its menaquinone system. Cells contained summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 1ω5c and iso-C15 : 0 as the major fatty acids. The polar lipids of strain CPCC 100624T contained phosphatidylethanolamine, one unidentified aminolipid, two aminophospholipids and three unidentified lipids. The genomic DNA G+C content was 49.3 mol%. On the basis of the above taxonomic data and differences in physiological characteristics from the closely related type strains, strain CPCC 100624T represents a novel species of the genus Spirosoma , for which the name Spirosoma lacussanchae sp. nov. is proposed. The type strain is CPCC 100624T (=NBRC 111852T=DSM 101771T).

Fargesia is ecologically and economically important in mountainous forests. Many Fargesia species are also important sources of food for some endangered animals such as the giant panda. Recent molecular phylogenetic analyses have revealed Fargesia as a polyphyletic group despite some unclear lineage affinities. In the present study, we reconstructed the phylogeny of Fargesia and its allies, including Thamnocalamus, Arundinaria (incl. Bashania), Yushania, Indocalamus, Ampelocalamus and Phyllostachys, from a plastome sequence matrix that contained 20 Fargesia and five Yushania species as ingroups, 16 species from nine other bamboo genera plus Oryza sativa and Zea mays as outgroups. Fargesia and its allies were broken into eight clades. Several Fargesia species were clustered into the Thamnocalamus clade and the Drepanostachyum + Himalayacalamus clade that rendered the polyphyly of Fargesia. The remaining six clades, including the Fargesia spathe clade, the Phyllostachys clade, Arundinaria fargesii, the Ampelocalamus clade, the Fargesia grossa clade, and the Fargesia macclureana clade, were identified. Molecular phylogenetic analyses supported that Yushania should be included in Fargesia (s.l.) which had synapomorphy of expanded leaf sheaths in varying degree at the basis of inflorescences, and further divided into the Fargesia spathe clade, the Fargesia grossa clade, and the Fargesia macclureana clade. All sampled species of Yushania were nested within the Fargesia grossa clade. The probable model of the origin of the species in the Fargesia spathe clade with spathe-like leaf sheath syndrome was proposed. Moreover, the formation of the spathe-like leaf sheath syndrome may be correlated with cold climatic conditions in Quaternary. Our results provide new sight into the phylogenetic relationship within Fargesia.

PREMISE Collecting and characterizing the genetic diversity of wild relatives of crops can contribute importantly to sustainable crop production and food security. Wild sunflower, Helianthus niveus, occurs in arid regions in western North America and is partially cross-compatible with the cultivated sunflower (H. annuus). We assessed phylogenetic relationships and patterns of genetic divergence among three previously described subspecies (subsp. niveus, subsp. canescens, and subsp. tephrodes) as well as two new morphotypes of H. niveus recently discovered in extreme drought and dune habitats in Baja California, Mexico. METHODS We measured 50 plants growing in a common garden for 27 morphological traits and conducted principal component analysis to assess patterns of phenotypic variation. Genome size of each accession was determined using flow cytometry. Pollen viability of first generation hybrids between taxa was tested to infer the strength of intrinsic postzygotic reproductive barriers. Finally, genotyping-by-sequencing data were used to investigate the genetic structure and phylogenetic relationships among the previously described subspecies and new morphotypes. RESULTS The intraspecific genetic and phenotypic divergence of H. niveus populations closely tracks their geographical distribution. Subspecies niveus is phenotypically, genetically, and reproductively distinct from the other two subspecies and has a larger genome. Therefore, H. niveus as currently circumscribed should be considered to contain two distinct species, H. niveus and H. tephrodes. ABBA-BABA tests revealed substantial introgression between subsp. canescens and its sympatric congener H. petiolaris, which might contribute to their morphological similarities. The two new morphotypes collected in Mexico represent local ecotypes of subsp. niveus that occur in extreme drought and dune environments. Mantel tests showed a strong positive correlation between genetic and geographic distances. CONCLUSIONS We conclude that geographic isolation is primarily responsible for intraspecific genomic divergence within H. niveus, while patterns of phenotypic variation appear to have been shaped by ecological selection and interspecific introgression.

Staphyleaceae traditionally comprises three genera of temperate and tropical trees and shrubs: Euscaphis Siebold & Zucc., Staphylea L., and Tuprinia Vent. These genera are clearly supported by morphology, but a recent classification based on four chloroplast genes and nuclear ITS treats Staphylea, Euscaphis, and New World Turpinia in Staphylea s.l. and Old World Turpinia in Dalrympelea Roxb. In this study, our objectives were to (1) resolve the phylogenetic relationships within Staphyleaceae using two nuclear and six chloroplast markers, (2) explore morphological synapomorphies that support major clades, and (3) discuss the implications of our results on generic delimitation and biogeography. Our phylogenetic results show five major clades in Staphyleaceae: (1) Old World Turpinia, (2) New World Turpinia, (3) a clade of exclusively Old World Staphylea, (4) an Asian-North American clade of Staphylea comprising all New World species and the rest of the Old World ones, and (5) Euscaphis. Within the two clades each of Staphylea and Turpinia, morphological features traditionally used for delimiting the genera may exhibit convergence. Among morphological features examined in this study, we found that pollen is not taxonomically informative, features of leaf teeth and epicuticular waxes show limited support for the traditional genera of Staphylea and Tuprinia, respectively, and petal length (i.e., flower size) is significantly smaller in Old World Turpinia compared to New World Turpinia. With respect to biogeography, our results support a rare disjunction between eastern North America and the Himalayas.

Reticulate evolution resulting from hybridization and introgression has been recognized as a creative source of species and diversification in bamboos. Previous phylogenetic studies revealed that Fargesia (s.l.) (Fargesia and Yushania) was divided into the Fargesia spathe clade and the non-spathe clade. Interestingly, the Fargesia spathe clade may have originated from hybridization among other clades within Fargesia (s.l.). Understanding the hybrid origin of this clade requires a robust phylogenetic framework in which major clades within Fargesia (s.l.) are resolved. Here, we used three nuclear genes to reconstruct the evolutionary history of Fargesia (s.l.) and its allies to identify putative patterns in the origin of the Fargesia spathe clade and to examine the extent to which reticulate evolution has occurred at the interspecific level in bamboos. Bashania species form a clade with Fargesia (s.l.), which is further divided into Group I and Group II. The Fargesia spathe clade, the Alpine Bashania clade, and Fargesia yajiangensis comprise Group I, while the Bashania fargesii clade and the remaining Fargesia (s.l.) species form Group II. Incongruence between the current nuclear-based and previous plastid phylogenies demonstrate several possible hybridization events among Fargesia (s.l.) species and related taxa, which have given rise to the Fargesia spathe clade, the Phyllostachys clade, and the Ampelocalamus clade. We also detected several putative hybrid species of Fargesia (s.l.). Our results show that reticulate evolution has played a prominent role in Fargesia (s.l.) evolution, which could, in part, account for the taxonomic difficulty associated with Fargesia (s.l.) and the alpine bamboos. The study also underscores the importance of hybridization in the evolution of bamboos, at both intergeneric and intrageneric levels.

The amount of plastome sequence data available has soared in the last decade, but the nature of plastome evolution during rapid radiations is largely unknown. Moreover, although there is increasing evidence showing that plastomes may have undergone adaptive evolution in order to allow adaptation to various environments, few studies have systematically investigated the role of the plastome in alpine adaptation. To address these questions, we sequenced and analyzed 12 representative species of Rhodiola, a genus which includes ca. 70 perennial herbs mainly growing in alpine habitats in the Qinghai-Tibet Plateau and the Hengduan Mountains. Rapid radiation in this genus was triggered by the uplift of the Qinghai-Tibet Plateau. We also included nine species of Crassulaceae as the outgroups. All plastomes were conserved with respect to size, structure, and gene content and order, with few variations: each contained 134 genes, including 85 protein-coding genes, 37 tRNAs, 8 rRNAs, and 4 potential pseudogenes. Four types of repeat sequence were detected. Slight contraction and expansion of the inverted repeats were also revealed. Both the genome-wide alignment and sequence polymorphism analyses showed that the inverted repeats and coding regions were more conserved than the single-copy regions and the non-coding regions. Positive selection analyses identified three genes containing sites of positive selection (rpl16, ndhA, ndhH), and one gene with a faster than average rate of evolution (psaA). The products of these genes may be involved in the adaptation of Rhodiola to alpine environments such as low CO2 concentration and high-intensity light.

How geological events and climate oscillations in the Pleistocene glaciation shaped the geographic distribution of genetic variation of species on the Qinghai-Tibetan Plateau (QTP) and its adjacent areas has been extensively studied. However, little studies have investigated whether closely related species in the same genus with similar physiological and life history traits responded similarly to the glacial climatic oscillations. If this is not the case, we would expect that the population histories of studied species were not driven by extrinsic environmental changes alone. Here we conducted a phylogeographic study of a succulent alpine plant Rhodiola fastigiata, using sequences from chloroplast genome and nrITS region, as well as ecological niche modeling. The results of R. fastigiata were compared to other congeneric species that have been studied, especially to R. alsia and R. crenulata. We found that for both markers, two geographic groups could be revealed, corresponding to the QTP plateau and the Hengduan Mountains, respectively, indicating isolated refugia in those two areas. The two groups diverged 1.23 Mya during the Pleistocene. We detected no significant population expansion by mismatch distribution analysis and Bayesian Skyline Plot. We found that even these similar species with similar physiological and life history traits have had different demographic histories in the Quaternary glacial periods. Our comparative phylogeographic study sheds new lights into phylogeographic research that extrinsic environmental changes are not the only factor that can drive population demography, and other factors, such as coevolved interactions between plants and their specialized pathogens, that probably played a role need to be examined with more case studies.

The roots and rhizomes of Rhodiola crenulata and R. rosea have been used worldwide as adaptogens for hundreds of years. However, rapid growth in demand has resulted in merchants using other species of Rhodiola as adulterants. Here, we surveyed 518 individuals representing 47 of the 55 species in the genus, including 253 R. crenulata individuals from 16 populations and 98 R. rosea individuals from 11 populations, to evaluate the utility of the internal transcribed spacer 2 (ITS2) barcode for identification of Rhodiola species. We detected six haplotypes in R. crenulata and only one haplotype in R. rosea. An obvious overlap between intra- and inter-specific distance was detected, and the authentication efficacy of ITS2, which was assessed by BLAST1, a nearest distance method, and a tree test, was much lower than in other groups. However, R. crenulata and R. rosea could be exactly identified. Analysis showed that the secondary structure of ITS2 differs in R. crenulata and its closest relatives. Our results demonstrated that both a mini barcode from ITS2 and the structure of ITS2 are effective markers for the identification of R. crenulata and R. rosea. This study represents the most comprehensive database of ITS2 barcodes in Rhodiola to date and will be useful in Rhodiola species identification.

Background Quaternary climatic oscillations had tremendous effects on the current distribution of species. Here, we aim to elucidate the glacial history of Rhodiola crenulata, a perennial herb almost exclusively restricted to rock crevices on mountain peaks, and to test whether the nunatak or massif de refuge hypotheses could explain its distribution pattern. Results Six haplotypes and six ribotypes were detected in the cpDNA data set and the ITS data set, respectively. The divergence of R. crenulata and its closest relatives was dated have occurred ca. 0.65 Mya, during the Naynayxungla glaciation on the QTP. Mismatch distribution analysis suggested that the species experienced a range expansion around 0.31 Mya. Populations with high genetic and haplotype diversity were found on the QTP platform as well in the Hengduan Mountains. The ecological niche modeling results showed that there were suitable habitats on both the QTP platform and in the Hengduan Mountains during the LGM. Conclusion Our results support a scenario that both nunataks and the massif de refuge hypotheses could explain the distribution of R. crenulata. We also confirmed that Quaternary climatic oscillations could promote plant speciation in some circumstances. This study adds to a growing body of evidence suggesting that the QTP plant lineages exhibited diverse reactions to the Quaternary climatic oscillations. Electronic supplementary material The online version of this article (10.1186/s12862-018-1270-6) contains supplementary material, which is available to authorized users.

Quaternary climatic oscillations have had tremendous effects on current distribution of species. Previous studies unraveled multiple microrefugia on the Qinghai-Tibetan Plateau (QTP) in two woody plants. Still we know little whether herbs growing in forests responded to climatic oscillations similarly. We herein conducted a phylogeographic study on Rhodiola sect. Trifida, an herbaceous group endemic to the QTP, which mainly growing on the forest floors, using plastid and ITS sequences as well as ecological niche modeling. The origin and divergence of major clades of sect. Trifida were in accordance with the last phase of the QTP uplifts. Mismatch distribution analysis indicated a range expansion dated to ca. 135 thousand years ago. A high frequency and an even distribution of private haplotypes in both plastid and ITS data sets throughout the distribution of sect. Trifida were detected. The ecological niche modeling results showed that there were suitable habitats on the QTP platform during the LGM. Our results found that multiple microrefugia existed on the QTP platform, supporting the hypothesis that species with similar geographic distribution and inhabiting the same community had similar responses to the Quaternary climatic oscillations. Furthermore, species delimitations in sect. Trifida need to be tested based on integrative evidence from morphological, ecological and genetic data.

The roots and rhizomes of Rhodiola crenulata and R. rosea have been used worldwide as adaptogens for hundreds of years. However, rapid growth in demand has resulted in merchants using other species of Rhodiola as adulterants. Here, we surveyed 518 individuals representing 47 of the 55 species in the genus, including 253 R. crenulata individuals from 16 populations and 98 R. rosea individuals from 11 populations, to evaluate the utility of the internal transcribed spacer 2 (ITS2) barcode for identification of Rhodiola species. We detected six haplotypes in R. crenulata and only one haplotype in R. rosea. An obvious overlap between intra- and inter-specific distance was detected, and the authentication efficacy of ITS2, which was assessed by BLAST1, a nearest distance method, and a tree test, was much lower than in other groups. However, R. crenulata and R. rosea could be exactly identified. Analysis showed that the secondary structure of ITS2 differs in R. crenulata and its closest relatives. Our results demonstrated that both a mini barcode from ITS2 and the structure of ITS2 are effective markers for the identification of R. crenulata and R. rosea. This study represents the most comprehensive database of ITS2 barcodes in Rhodiola to date and will be useful in Rhodiola species identification.

Rhodiola L. (Crassulaceae) is a mid-sized plant genus consisting of about 70 species, with most species distributed on the Qinghai-Tibetan Plateau (QTP) and the adjacent areas, and several species in north-east Asia, Europe, and North America. This study explored the origin and diversification history of Rhodiola and tested the biogeographic relationships between the QTP and other regions of the Northern Hemisphere. We sequenced the nuclear ribosomal internal transcribed spacers and eight plastid DNA fragments representing 55 species of Rhodiola, and reconstructed phylogenetic relationships with maximum parsimony, maximum likelihood and Bayesian inference. Several instances of incongruence between the nuclear and the plastid data sets were revealed, which can best be explained by reticulate evolution. Species of Rhodiola and Pseudosedum form a well-supported clade sister to Phedimus. Dating analysis suggested that the origin and diversification times of this group are largely correlated with the extensive uplifts of the Qinghai-Tibetan Plateau. Ancestral state reconstruction supports the hypothesis that Rhodiola originated on the QTP, and then dispersed to other regions of the Northern Hemisphere. Our findings highlight the importance of the uplifts of the Qinghai-Tibetan Plateau in promoting species diversification and the possible role of reticulate evolution in the diversification process. Our results also suggest the biogeographic significance of QTP as the source area in alpine plant evolution in the Northern Hemisphere.

Rhodiola (Crassulaceae) comprises about 70 species and shows a high level of morphological diversity. The genus is mainly distributed in alpine areas and cold regions of the Northern Hemisphere with the Qinghai-Tibetan Plateau as its center of diversity. The phylogenetic relationships within Rhodiola remain poorly understood largely because of difficulties in collecting samples and specimens. In the present study, 51 species/varieties from Rhodiola representing all morphological sections were analyzed using sequences of the nuclear ribosomal internal transcribed spacers region and the plastid psbA-trnH and trnL-F markers. Our results suggest that Rhodiola and Pseudosedum form a well-supported clade, but the relationship between these two genera is not resolved. None of the four currently recognized subgenera is monophyletic; yet three of seven sections, R. sects. Trifida, Prainia, and Pseudorhodiola are each supported to be monophyletic. Rhodiola rosea is a popular medicinal plant that has an ada...

Rhodiola rosea L. is used in herbal medicine in many countries for a long time. Here, its complete chloroplast genome was assembled and annotated. The genome is 151,348 bp long and comprises a pair of inverted repeat regions (IRs, 25,790 bp each), a large single-copy region (LSC, 82,716 bp), and a small single-copy region (SSC, 17,052 bp). It contained 113 gene species (79 protein coding, 29 tRNA, 4 rRNA, and 1 pseudogene), with 20 of them occurring in double copies. Introns were detected in 12 PCG and 5 tRNA species. The nucleotide composition is inhomogeneous (30.9% A, 19.2% C, 18.5% G, and 31.4% T) with an overall A + T content of 62.3%. Phylogenetic analysis indicated that Rhodiola rosea is sister to the remaining species of Rhodiola with maximum support in phylogeny.

As an industrial organic solid waste, oil residue, with wide sources and low price, but could not find an effective way to use currently. In addition, with the development of mushroom industry and rising price of traditional raw-materials, it is very necessary to find the substitute raw material to reduce production cost of mushroom cultivation. This study attempts to produce the strains of Flammulina velutipes by taking use of oil residue to replace part of the traditional raw material, there are two groups in the experiment: the test group is adding 5%, 10%, 15%, 20%, 40% of the oil residue to replace the culture medium of cottonseed hull and wheat bran; the control group is the traditional culture medium, then comparatively observed the growth of the mycelium. The results showed that it can promote the growth of the mycelium and shorten the cycle of seed production to add the oil residue in the test. But the growth rate of mycelium will be hindered when the concentration exceeds a certain range.The optimal culture medium to add the oil residue is as follows: 15% of the oil residue, 64% cottonseed hull, 20% coarse wood chips, 0% wheat bran , 1% lime. Oil residue contains a lot of the nutritional components to benefit the growth of edible fungi, and without the heavy metal pollution, can replace the culture medium of cottonseed hull and wheat bran and other traditional materials, reduce cost of production the strains, a fair-sized economic efficiency can be received, the environment can be protected.

DNA barcoding, the identification of species using one or a few short standardized DNA sequences, is an important complement to traditional taxonomy. However, there are particular challenges for barcoding plants, especially for species with complex evolutionary histories. We herein evaluated the utility of five candidate sequences - rbcL, matK, trnH-psbA, trnL-F and the internal transcribed spacer (ITS) - for barcoding Rhodiola species, a group of high-altitude plants frequently used as adaptogens, hemostatics and tonics in traditional Tibetan medicine. Rhodiola was suggested to have diversified rapidly recently. The genus is thus a good model for testing DNA barcoding strategies for recently diversified medicinal plants. This study analyzed 189 accessions, representing 47 of the 55 recognized Rhodiola species in the Flora of China treatment. Based on intraspecific and interspecific divergence and degree of monophyly statistics, ITS was the best single-locus barcode, resolving 66% of the Rhodiola species. The core combination rbcL+matK resolved only 40.4% of them. Unsurprisingly, the combined use of all five loci provided the highest discrimination power, resolving 80.9% of the species. However, this is weaker than the discrimination power generally reported in barcoding studies of other plant taxa. The observed complications may be due to the recent diversification, incomplete lineage sorting and reticulate evolution of the genus. These processes are common features of numerous plant groups in the high-altitude regions of the Qinghai-Tibetan Plateau.

The evolution and current distribution of the Sino-Tibetan flora have been greatly affected by historical geological events, such as the uplift of the Qinghai-Tibetan Plateau (QTP), and Quaternary climatic oscillations. Rhodiola kirilowii, a perennial herb with its distribution ranging from the southeastern QTP and the Hengduan Mountains (HM) to adjacent northern China and central Asia, provides an excellent model to examine and disentangle the effect of both geological orogeny and climatic oscillation on the evolutionary history of species with such distribution patterns. We here conducted a phylogeographic study using sequences of two chloroplast fragments (trnL-F and trnS-G) and internal transcribed spacers in 29 populations of R. kirilowii. A total of 25 plastid haplotypes and 12 ITS ribotypes were found. Molecular clock estimation revealed deep divergence between the central Asian populations and other populations from the HM and northern China; this split occurred ca. 2.84 million year ago. The majority of populations from the mountains of northern China were dominated by a single haplotype or ribotype, while populations of the HM harbored both high genetic diversity and high haplotype diversity. This distribution pattern indicates that HM was either a diversification center or a refugium for R. kirilowii during the Quaternary climatic oscillations. The present distribution of this species on mountains in northern China may have resulted from a rapid glacial population expansion from the HM. This expansion was confirmed by the mismatch distribution analysis and negative Tajima's D and Fu's F S values, and was dated to ca. 168 thousand years ago. High genetic diversity and population differentiation in both plastid and ITS sequences were revealed; these imply restricted gene flow between populations. A distinct isolation-by-distance pattern was suggested by the Mantel test. Our results show that in old lineages, populations may harbour divergent genetic forms that are sufficient to maintain or even increase overall genetic diversity despite fragmentation and low within-population variation.

SummaryBackgroundThe pathogenesis of idiopathic pulmonary arterial hypertension (IPAH) is unknown, and the syndrome of IPAH remains a diagnostic and therapeutic challenge. The present study investigated the disease-specific proteins that aid in the diagnosis of IPAH and thus to study their role in the disease process.MethodsA comparative proteomic analysis was used for clinical screening of serum proteins in 10 patients with IPAH and compared with 10 normal subjects. Furthermore, enzyme linked immunosorbent assay (ELISA) was performed for comparison with serum proteins between individual IPAH patients and controls.ResultsNine proteins and their isoforms, including leucine-rich α-2-glycoprotein (LRG), haptoglobin precursor, albumin isoform 2, transferrin variant, C3 complement, hydroxypyruvate reductase isoform 1, RAF1, fibrinogen isoformγ-A and fibrinogen isoformγ-B showed significant changes in serum of IPAH patients compared with controls by proteomic analysis. And significant higher serum levels of LRG in IPAH patients compared with controls were found by ELISA. Correlation analysis disclosed a significant association between serum LRG concentrations and New York Heart Association (NYHA) functional class (r=0.71, P