BackgroundPanax L. is a medicinally important genus within family Araliaceae, where almost all species are of cultural significance for traditional Chinese medicine. Previous studies suggested two independent origins of the East Asia and North America disjunct distribution of this genus and multiple rounds of whole genome duplications (WGDs) might have occurred during the evolutionary process.ResultsWe employed multiple chloroplast and nuclear markers to investigate the evolution and diversification of Panax. Our phylogenetic analyses confirmed previous observations of the independent origins of disjunct distribution and both ancient and recent WGDs have occurred within Panax. The estimations of divergence time implied that the ancient WGD might have occurred before the establishment of Panax. Thereafter, at least two independent recent WGD events have occurred within Panax, one of which has led to the formation of three geographically isolated tetraploid species P. ginseng, P. japonicus and P. quinquefolius. Population genetic analyses showed that the diploid species P. notoginseng harbored significantly lower nucleotide diversity than those of the two tetraploid species P. ginseng and P. quinquefolius and the three species showed distinct nucleotide variation patterns at exon regions.ConclusionOur findings based on the phylogenetic and population genetic analyses, coupled with the species distribution patterns of Panax, suggested that the two rounds of WGD along with the geographic and ecological isolations might have together contributed to the evolution and diversification of this genus.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0669-0) contains supplementary material, which is available to authorized users.

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Genera Lamiophlomis and Paraphlomis were originally separated from genus Phlomis s.l. on the basis of particular morphological characteristics. However, their relationship was highly contentious, as evidenced by the literature. In the present paper, the systematic positions of Lamiophlomis, Paraphlomis, and their related genera were assessed based on nuclear internal transcribed spacer (ITS) and chloroplast rpl16 and trnL-F sequence data using maximum parsimony (MP) and Bayesian methods. In total, 24 species representing six genera of the ingroup and outgroup were sampled. Analyses of both separate and combined sequence data were conducted to resolve the systematic relationships of these genera. The results reveal that Lamiophlomis is nested within Phlomis sect. Phlomoides and its generic status is not supported. With the inclusion of Lamiophlomis rotata in sect. Phlomoides, sections Phlomis and Phlomoides of Phlomis were resolved as monophyletic. Paraphlomis was supported as an independent genus. However, the resolution of its monophyly conflicted between MP and Bayesian analyses, suggesting the need for expended sampling and further evidence.

In this research, we aimed to study the genetic variation and phylogeographic pattern of Ligularia tongolensis, a perennial herb endemic to the Hengduan Mountains region of China. We sequenced two chloroplast DNA (cpDNA) intergenic spacers (trnQ‐5′rps16, trnL‐rpl32) in 140 individuals from 14 populations of three groups (Jinshajiang vs. Yalongjiang vs. Wumeng) within this species range. High levels of haplotype diversity (Hd = 0.814) and total genetic diversity (Ht = 0.862) were detected at the species level, based on a total of 12 haplotypes identified. Low levels of intrapopulation diversity (Hs = 0.349), high levels of genetic divergence (Gst = 0.595, Nst = 0.614, Fst = 0.597), and the absence of isolation by distance tests were also found in L. tongolensis. Furthermore, H2 and H5, the dominant haplotypes that located at internal nodes and deviated from extinct ancestral haplotype in the network, were found to be shared between Jinshajiang and Yalongjiang groups. These results indicate that past fragmentation may be the important factor responsible for the present phylogeographical pattern of L. tongolensis. Meanwhile, the locations occupied by each group might have served as independent refugia for L. tongolensis during the Quaternary glaciation. Unimodal mismatch distribution and star‐like genealogies indicated this species underwent past demographic expansion events, with expansion ages of 274 ka BP.

Panax notoginseng, a traditional Chinese medicinal plant, has been cultivated and domesticated for approximately 400 years, mainly in Yunnan and Guangxi, two provinces in southwest China. This species was named according to cultivated rather than wild individuals, and no wild populations had been found until now. The genetic resources available on farms are important for both breeding practices and resource conservation. In the present study, the recently developed technology RADseq, which is based on next-generation sequencing, was used to analyze the genetic variation and differentiation of P. notoginseng. The nucleotide diversity and heterozygosity results indicated that P. notoginseng had low genetic diversity at both the species and population levels. Almost no genetic differentiation has been detected, and all populations were genetically similar due to strong gene flow and insufficient splitting time. Although the genetic diversity of P. notoginseng was low at both species and population levels, several traditional plantations had relatively high genetic diversity, as revealed by the He and π values and by the private allele numbers. These valuable genetic resources should be protected as soon as possible to facilitate future breeding projects. The possible geographical origin of Sanqi domestication was discussed based on the results of the genetic diversity analysis.

The key process in speciation concerns the formation and maintenance of reproductive isolating barriers between diverging lineages. Although species boundaries are frequently investigated between two species across many taxa, reproductive isolating barriers among multiple species (>2) that would represent the most common phenomenon in nature, remain to be clarified. Here, we use double digest restriction-site associated DNA (ddRAD) sequencing to examine patterns of hybridization at a sympatric site where three Ligularia species grow together and verify whether those patterns contribute to the maintenance of boundaries among species. The results based on the RAD SNP datasets indicated hybridization Ligularia cyathiceps × L. duciformis and L. duciformis × L. yunnanensis were both restricted to F s plus a few first-generation backcrosses and no gene introgression were identified, giving rise to strong reproductive isolation among hybridizing species. Moreover, hybrid swarm simulation, using HYBRIDLAB, indicated the RAD SNP datasets had sufficient discriminatory power for accurate hybrid detection. We conclude that parental species show strong reproductive isolation and they still maintain species boundaries, which may be the key mechanism to maintain species diversity of Ligularia in the eastern Qinghai-Tibetan Plateau and adjacent areas. Moreover, this study highlights the effectiveness of RAD sequencing in hybridization studies.

Natural hybridization occurred frequently in the sunflower family. To date, however, no study on natural hybridization involving in Ligularia and Cremanthodium has been reported. Here, we presented the molecular evidence for natural hybridization between Ligularia nelumbifolia (Bureau & Franch.) Hand.-Mazz. and Cremanthodium stenoglossum Ling & S.W.Liu. Four nuclear DNA regions were sequenced to test the natural hybridization hypothesis, and three chloroplast DNA regions were sequenced to determine the direction of hybridization. Analyses of the investigated DNA data suggested that all of the putative hybrid individuals were derived from hybridization between L. nelumbifolia and C. stenoglossum and that bidirectional hybridization occurred. Moreover, sympatric Ligularia tsangchanensis (Franch.) Hand.-Mazz. and Ligularia virgaurea (Maxim.) Mattf. ex Rehder & Kobuski were not apparently involved in the hybridization. Although NewHybrids analysis showed that all the putative hybrid individuals were F1 class, a low frequency of backcrossing to C. stenoglossum might exist in the hybrid swarm. In such a case, hybrids might serve as a bridge facilitating gene flow between L. nelumbifolia and C. stenoglossum, and hybrid speciation is unlikely to happen for these hybrid individuals without asexual reproduction. Given the poorly resolved phylogenetic relationship between Ligularia and Cremanthodium, the occurrence of natural hybridization between L. nelumbifolia and C. stenoglossum might provide new insights into the recircumscription and redelimitation of these two genera.

-Salvia is a genus with surprisingly diverse chromosome numbers. In this paper six species were cytologically studied from Hengduanshan Mountains region, where is one of two diversification centers of the genus. S. przewalskii var. przewalskii is a tetraploid with the chromosome number of 2n=4x=32, other five species are the diploids with chromosome numbers of 2n=2x=16. The basic chromosome number x=8 was inferred for all species studied, which was different from x=7, 11 and 16 reported for species of the genus distributed in other regions. Several recent cytological studies on different groups from Hengduanshan Mountains region showed that only few polyploids infers that variation of karyotype structure at the diploid level seems to play a leading role and sympatric speciation via hybridization and polyploidization has played a minor role in speciation of some groups in Hengduanshan Mountains region.