Jiu-Li Wang

Phylogeny and speciation in Saxifraga sect. Ciliatae (Saxifragaceae): Evidence from psbA-trnH, trnL-F and ITS sequences

Nearly half of the species in the large genus Saxifraga belong to Saxifraga sect. Ciliatae, a largely Sino-Himalayan taxon. We report here that evidence from chloroplast DNA sequences (psbA-trnH, trnL-F) and from nuclear sequences (ITS) indicates that this section is monophyletic and composed of at least three main lineages, corresponding to (1) a clade made up of species from S. subsect. Gemmiparae, subsect. Cinerascentes, subsect. Flagellares and subsect. Hemisphaericae, in which the last three subsections are nested in the first; (2) a clade of species belonging to S. subsect. Rosulares (including S. subsect. Serpyllifoliae); and (3) a clade of species belonging to S. subsect. Hirculoideae. Species relationships in S. subsect. Rosulares and subsect. Hirculoideae are not well resolved. A molecular clock analysis indicates that the diversification of S. sect. Ciliatae into its three lineages dates from ca. 9.48 Ma, coinciding with orogenic events associated with one of the most important phases of uplift of the Qinghai-Tibet Plateau. Extensive diversifications within S. subsect. Rosulares and subsect. Hirculoideae have been more recent (ca. 4.51 Ma and 2.12 Ma, respectively), again correlated with Qinghai-Tibet Plateau uplift events and, in the case of S. subsect. Hirculoideae, have occurred at a rate comparable to that seen in the radiation of Hawaiian fruit flies.

Phylogenetic analyses of Spiraea (Rosaceae) distributed in the Qinghai-Tibetan Plateau and adjacent regions: insights from molecular data

Abstract 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 Quaternary climatic oscillations.

Population genetic differentiation and taxonomy of three closely related species of saxifraga (Saxifragaceae) from southern tibet and the Hengduan mountains

The effects of rapid, recent uplift of the Hengduan Mountains on evolution and diversification of young floristic lineages still remain unclear. Here, we investigate diversification of three closely related Saxifraga species with a distribution restricted to the Hengduan Mountains (HM) and southern Tibet, and comment on their taxonomy based on molecular evidence. Three chloroplast DNA fragments (rbcL, trnL-F, trnS-G) and the nuclear ribosomal DNA internal transcribed spacer (ITS) were employed to study genetic structure across 104 individuals from 12 populations of Saxifraga umbellulata, S. pasumensis, and S. banmaensis. Chloroplast DNA (cpDNA) phylogenies revealed two well supported clades, corresponding to S. umbellulata and S. pasumensis plus S. banmaensis. Topology of the ITS phylogeny was largely congruent with that generated from cpDNA haplotypes, but with minor conflicts which might be caused by incomplete lineage sorting. Analyses of molecular variance of both cpDNA and ITS datasets revealed that most variation was held between S. pasumensis s.l. (with S. banmaensis) and S. umbellulata (92.31% for cpDNA; 69.78% for ITS), suggesting a high degree of genetic divergence between them. Molecular clock analysis based on ITS dataset suggested that the divergence between S. pasumensis s.l. and S. umbellulata can be dated to 8.50 Ma, probably a result of vicariant allopatric diversification associated with the uplift events of the HM. Vicariance associated with HM uplifts may also have been responsible for infraspecific differentiation in S. pasumensis. In contrast, infraspecific differentiation in S. umbellulata was most likely triggered by Quaternary glaciations. The much lower levels of gene diversity within populations of S. pasumensis compared with S. umbellulata could have resulted from both range contractions and human collection on account of its putative medicinal properties. Combining evidence from morphology, geographical distributions and molecular phylogenetic data, we recommend that S. banmaensis should be treated as a synonym of S. pasumensis which in turn, and based on the same sources of evidence, should be treated as a separate species rather than as a variety of S. umbellulata.

The Complete Chloroplast Genomes of Two Lancea Species with Comparative Analysis

The genus Lancea is native to the Qinghai-Tibetan Plateau and consists of two species, Lancea tibetica Hook. f. et Thoms. and Lancea hirsuta Bonati. Here, we report the complete sequences of the chloroplast genomes of L. tibetica and L. hirsuta, which were 153,665 and 154,045 bp in length, respectively, and each included a pair of inverted repeated regions (25,624 and 25,838 bp in length, respectively) that were separated by a large single copy region (84,401 and 84,588 bp in length, respectively) and a smaller single copy region (18,016 and 17,781 bp in length, respectively). A total of 106 genes in L. tibetica and 105 in L. hirsuta comprised 79 protein-coding genes, and 4 ribosomal RNA (rRNA) genes, as well as 23 and 22 transfer RNA (tRNA) genes in L. tibetica and L. hirsuta, respectively. The gene order, content, and orientation of the two Lancea chloroplast genomes exhibited high similarity. A large number of informative repetitive sequences, including SSRs, were observed in both genomes. Comparisons of the genomes with those of three other Lamiales species revealed 12 highly divergent regions in the intergenic spacers and in the matK, rpoA, rps19, ndhF, ccsA, ndhD, and ycf1 coding regions. A phylogenomic analysis suggested that Lancea forms a monophyletic group that is closely related to the clade composed of the families Phrymaceae, Paulowniaceae, and Rehmanniaceae.

Genetic variation and phylogenetic relationships of the ectomycorrhizal Floccularia luteovirens on the Qinghai-Tibet Plateau

Floccularia luteovirens, as an ectomycorrhizal fungus, is widely distributed in the Qinghai-Tibet Plateau. As an edible fungus, it is famous for its unique flavor. Former studies mainly focus on the chemical composition and genetic structure of this species. However, the phylogenetic relationship between genotypes remains unknown. In this study, the genetic variation and phylogenetic relationship between the genotypes of F. luteovirens in Qinghai-Tibet Plateau was estimated through the analysis on two protein-coding genes (rpb1 and ef-1α) from 398 individuals collected from 24 wild populations. The sample covered the entire range of this species during all the growth seasons from 2011 to 2015. 13 genotypes were detected and moderate genetic diversity was revealed. Based on the results of network analysis, the maximum likelihood (ML), maximum parsimony (MP), and Bayesian inference (BI) analyses, the genotypes H-1, H-4, H-6, H-8, H-10, and H-11 were grouped into one clade. Additionally, a relatively higher genotype diversity (average h value is 0.722) and unique genotypes in the northeast edge of Qinghai- Tibet plateau have been found, combined with the results of mismatch analysis and neutrality tests indicated that Southeast Qinghai-Tibet plateau was a refuge for F. luteovirens during the historical geological or climatic events (uplifting of the Qinghai-Tibet Plateau or Last Glacial Maximum). Furthermore, the present distribution of the species on the Qinghai-Tibet plateau has resulted from the recent population expansion. Our findings provide a foundation for the future study of the evolutionary history and the speciation of this species.

Microbial communities inhabiting the fairy ring of Floccularia luteovirens and isolation of potential mycorrhiza helper bacteria

Floccularia luteovirens, an important edible mushroom widely distributed in the Qinghai–Tibet plateau, is ecologically important as an ectomycorrhizal fungus and can form the fairy ring. To explore the influence of F. luteovirens fairy ring on soil microbial communities, we compared the soil microbial communities in three different fairy ring zones (inside the fairy ring (IN); beneath the fairy ring (ON); and outside the fairy ring (OUT)). A total of 1.77 million bacterial reads and 1.59 million fungal reads were obtained. Moreover, sequence clustering yielded 519,613 (57,735 per sample) bacterial OTUs, and 513,204 (57,023 per sample) fungal OTUs representing. Microbial diversity was lower in samples from the ON zone compared with the other two zones. Mycorrhiza helper bacteria (MHB) such as Bradyrhizobium and Paenibacillus were more common in the ON zone, and we isolated four potential MHB from rhizosphere soil. Canonical correspondence analysis showed that the soil nutritional condition and physical changes caused by F. luteovirens shaped the microbial communities in the ON zone. This is the first report on the study of soil microbial diversity influenced by fairy ring F. luteovirens, and further studies need to be conducted to study the ecological function influenced by this species.

Gene Flow Results in High Genetic Similarity between Sibiraea (Rosaceae) Species in the Qinghai-Tibetan Plateau

Studying closely related species and divergent populations provides insight into the process of speciation. Previous studies showed that the Sibiraea complexs evolutionary history on the Qinghai-Tibetan Plateau (QTP) was confusing and could not be distinguishable on the molecular level. In this study, the genetic structure and gene flow of Sibiraea laevigata and Sibiraea angustata on the QTP was examined across 45 populations using 8 microsatellite loci. Microsatellites revealed high genetic diversity in Sibiraea populations. Most of the variance was detected within populations (87.45%) rather than between species (4.39%). We found no significant correlations between genetic and geographical distances among populations. Bayesian cluster analysis grouped all individuals in the sympatric area of Sibiraea into one cluster and other individuals of S. angustata into another. Divergence history analysis based on the approximate Bayesian computation method indicated that the populations of S. angustata at the sympatric area derived from the admixture of the 2 species. The assignment test assigned all individuals to populations of their own species rather than its congeneric species. Consistently, intraspecies were detected rather than interspecies first-generation migrants. The bidirectional gene flow in long-term patterns between the 2 species was asymmetric, with more from S. angustata to S. laevigata. In conclusion, the Sibiraea complex was distinguishable on the molecular level using microsatellite loci. We found that the high genetic similarity of the complex resulted from huge bidirectional gene flow, especially on the sympatric area where population admixtures occurred. This study sheds light on speciation with gene flow in the QTP.