Peng-Cheng Fu

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.

Isolation of 16 Microsatellite Markers for Spiraea alpina and S. mongolica (Rosaceae) of the Qinghai–Tibet Plateau

Premise of the study: A set of microsatellite markers were developed to characterize the level of genetic diversity and gene flow in two plant species endemic to the Qinghai–Tibet Plateau, Spiraea alpina and S. mongolica. Methods and Results: Using the Fast Isolation by AFLP of Sequences Containing repeats (FIASCO) method, 16 microsatellite loci showed polymorphisms in both species. In two populations of each species, the number of alleles per locus ranged from three to 18 in S. alpina and from four to 30 in S. mongolica. Conclusions: These microsatellite markers provide an efficient tool for population genetic studies and will be used to assess the genetic diversity and spatial genetic structure of S. alpina and S. mongolica.

The Complete Plastome Sequences of Seven Species in Gentiana sect. Kudoa (Gentianaceae): Insights Into Plastid Gene Loss and Molecular Evolution

The chloroplast (cp) genome is useful in the study of phylogenomics, molecular dating, and molecular evolution. Gentiana sect. Kudoa is a predominantly alpine flowering plant that is valued for its contributions to medicine, ecology, and horticulture. Previous evolutionary studies showed that the plastid gene loss pattern and intra-sectional phylogenetics in sect. Kudoa are still unclear. In this study, we compared 11 Gentiana plastomes, including 7 newly sequenced plastomes from sect. Kudoa, to represent its three serious: ser. Ornatae, ser. Verticillatae, and ser. Monanthae. The cp genome sizes of the seven species ranged from 137,278 to 147,156 bp. The plastome size variation mainly occurred in the small single-copy and long single-copy regions rather than the inverted repeat regions. Compared with sect. Cruciata, the plastomes in ser. Ornatae and ser. Verticillatae had lost approximately 11 kb of sequences containing 11 ndh genes. Conversely, far fewer losses were observed in ser. Monanthae. The phylogenetic tree revealed that sect. Kudoa was not monophyletic and that ser. Monanthae was more closely related to other sections rather than sect. Kudoa. The molecular dating analysis indicated that ser. Monanthae and sect. Kudoa diverged around 8.23 Ma. In ser. Ornatae and ser. Verticillatae, the divergence occurred at around 0.07–1.78 Ma. The nucleotide diversity analysis indicated that the intergenic regions trnH-psbA, trnK-trnQ, ycf3-trnS and rpl32-trnL constituted divergence hotspots in both sect. Kudoa and Gentiana, and would be useful for future phylogenetic and population genetic studies.

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.

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.