Parallel evolution provides an excellent framework to infer the genetic bases of adaptive traits and understand the importance of natural selection in shaping current biodiversity. The upper leaves of the “glasshouse plants” transform into translucent bracts that show numerous adaptions in alpine habitats. It remains unknown whether similar molecular changes occur under the parallel bract evolution of different “glasshouse” species. In this study, we compared the results on phenotypic and physiological differences and presented the results of cDNA-AFLP analyses of transcriptional changes between translucent bracts and normal leaves in Rheum alexandrae. We also examined the homologous candidate genes with the same expression changes between this species and another “glasshouse” species, R. nobile. We found that bracts of R. alexandrae are similar to those of R. nobile in anatomical features: chloroplasts have degenerated and chlorophyll contents are greatly reduced, which suggests that foliar photosynthetic functions in bracts of both species have been reduced or totally altered. Among the 6000 transcript-derived fragments (TDFs) in bracts and leaves of R. alexandrae, 420 (7%) were differentially expressed (up- or downregulated) between bracts and normal leaves. There were a total of 13 homologous TDFs with the same expression changes between R. alexandrae and the previously studied R. nobile. Except for the two that were not functionally annotated, eight of the homologous TDFs were found to be involved in stress and defense responses whereas the other three were related to photosynthesis. The up- or downregulation of these candidate genes was highly congruent with anatomical characteristics and adaptive functions of the bracts found for “glasshouse” plants. These findings suggested that the “glasshouse” phenotypes may have common molecular bases underlying their parallel evolution of similar adaptive functions and highlighted the importance of the natural selection in producing such phenotypes.

Three nuclear regions nuclear ribosomal internal transcribed spacer (nrITS) and intron regions of two nuclear low-copy genes—gapCp, and pgiC, in combination with one chloroplast genome region were employed to explore patterns of reticulate evolution in the fern genus Asplenium. This is the one of the first studies using DNA sequences of multiple nuclear markers in ferns. All three nuclear markers amplified well with PCR and several copies were recovered by cloning PCR products. All three nuclear regions showed congruent results by recovering the neo-allotetraploid Asplenium adulterinum as the hybrid of diploid A. trichomanes and diploid A. viride. Conflicting results were obtained for several nodes. First, gapCp did not discriminate between A. aethiopicum and A. praegracile whereas the other markers recovered these two taxa as distinct. Conflicts among gene-trees were found in respect to A. monanthes, chloroplast and pgiC suggested a sister relationship of A. monanthes and A. trichomanes but gapCp and nrITS nested A. monanthes within A. normale. Our results confirm: (i) the usefulness of several nuclear regions, in particular gapCp and pgiC, to unravel reticulate evolution in ferns and species differentiation and (ii) highlights the need to employ more than one nuclear region to obtain reliable hypotheses on reticulate events versus incomplete lineage sorting. Especially, if one assumes that the reticulation event might have occurred in the more distant past. Considering the expected high frequency of reticulate evolution in ferns, the establishment of robust and informative nuclear genomic markers is critical to achieve further progress in our efforts to elucidate fern evolution.

The phylogenetic position of the monotypic genus Kontumia (Polypodiaceae) is contentious. It has been suggested that Kontumia is related to Gymnogrammitis dareiformis (Drynarioideae) based on spore ornamentation and blade dissection, or it has been assigned as a member of microsoroid ferns (Microsoroideae) based on the shape of rhizome scales. In the present study, we determined the phylogenetic position of K. heterophylla using four chloroplast DNA regions (rbcL, atpB, rps4 + rps4-trnS intergenic spacer [IGS], and trnL-F IGS). A parsimony consensus tree indicated that K. heterophylla is not related to G. dareiformis, but is nested within the Leptochilus lineage of Microsoroideae. This relationship is also supported by sharing of clathrate scales on the rhizome, which is not found in G. dareiformis. Although marked morphological disparities are found between K. heterophylla and the Leptochilus lineage in terms of leaf dissection, fertile-sterile leaf differentiation, and sori arrangement, our results indicate that these characters have evolved independently several times in Polypodiaceae.

Maddenia (Rosaceae) was long recognized as a distinct genus closely related to Prunus and was recently merged with the latter. The Maddenia clade of Prunus has been revised taxonomically with four species from eastern Asia recognized. Recent molecular studies have provided evidence that this group is nested within Prunus, having a close relationship with the Padus–Laurocerasus complex. To further test the phylogenetic position of Maddenia, this study investigates pollen morphology of all former Maddenia species and 28 other Prunus species, using scanning electron microscopy and light microscopy. The Prunus species sampled here represent major subgenera: Amygdalus, Cerasus, Laurocerasus, Padus, and Prunus s.s. We found that pollen grains of these groups are all monad and tricolporate with striate or rugulate sculpturing. The pollen evidence supports a close relationship between Maddenia and species of Padus and Laurocerasus subgroups (excluding the Pygeum group), all of which have elongated, thicker, and less directional muri. Pollen of the subgenera of Cerasus, Amygdalus, and Prunus has generally thinner, highly directional, and predominantly parallel muri. The pollen grains of the Pygeum subgroup are quite distinct from the other groups of Prunus. Pygeum pollen has rugulate exines with much shorter and rod-shaped muri.

With 84 native species, China is a center of distribution of the genus Salvia (Lamiaceae). These species are mainly distributed in Yunnan and Sichuan provinces (southwestern China), notably the Hengduan Mountain region. Traditionally, the Chinese Salvia has been classified into four subgenera, Salvia, Sclarea, Jungia, and Allagospadonopsis. We tested this classification using molecular phylogenetic analysis of 43 species of Salvia from China, six from Japan, and four introduced species. The nuclear ribosomal internal transcribed spacer region and three chloroplast regions (rbcL, matK, and trnH-psbA) were analyzed by maximum parsimony, maximum likelihood, and Bayesian methods. Our results showed that the Chinese (except Salvia deserta) and Japanese Salvia species formed a well-supported clade; S. deserta from Xinjiang grouped with Salvia officinalis of Europe. In addition, all introduced Salvia species in China were relatively distantly related to the native Chinese Salvia. Our results differed from the subgeneric and section classifications in Flora Reipublicae Popularis Sinicae. We suggested that sections Eusphace and Pleiphace should be united in a new subgenus and that sect. Notiosphace should be removed from subg. Sclarea and form a new subgenus. Our data could not distinguish a boundary between subg. Allagospadonopsis and sect. Drymosphace (subg. Sclarea); the latter should be reduced into the former. Further clarification of the phylogenetic relationships within Salvia and between Salvia and related genera will require broader taxonomic sampling and more molecular markers.

A detailed knowledge of the geographical distribution of cytotypes within and between species comprising a polyploid complex is critical to our understanding of the history and evolution of such complexes. In the present study we examined the geographical distributions of cytotypes within six tentatively delimited species comprising the Chrysanthemum indicum complex in China. We determined the ploidy of 188 individuals sampled from 47 populations, based on DNA content using flow cytometry. In addition, chromosome counts were made on samples of each taxon. We confirmed that all samples of C. rhombifolium and C. lavandulifolium were diploid (2n = 18), those of C. hypargyrum and C. potentilloides were tetraploid (2n = 36), and those of C. vestitum were hexaploid (2n = 54). In contrast, we confirmed that C. indicum contained both diploid and tetraploid cytotypes. We found that in addition to marked differences in genome size between ploidy levels, there was a variation in genome size between species of the same ploidy level. Although the diploid, tetraploid, and hexaploid taxa of the complex, as well as the diploid form of C. indicum, occurred only in central and northern China, the tetraploid form of C. indicum was widespread both north and south of the Yangtze River. We suggest that the tetraploid form of C. indicum may have expanded its range southward during recent Quaternary glacial periods when forests retreated in south China as conditions became drier.

Polymorphism at the single copy RPB2 locus was investigated to define the relationship between wild and domesticated grapevines. Two different forms still coexist in Eurasia, the cultivated (Vitis vinifera L. ssp. vinifera) and the wild (Vitis vinifera L. ssp. sylvestris (Gmelin) Hegi), referred to as separate subspecies. Using the observed number of mutations at the RPB2 locus, as well as archaeological data, to define an approximate age of domestication, we have estimated a high nucleotide substitution rate (4.25 × 10⁻⁷) in the domesticated group. Moreover, the dynamics of population size in the RPB2 gene were estimated using Bayesian coalescent inference. The Bayesian skyline plot offered interesting information on the past dynamics of RPB2 for both wild and domesticated groups. The signal of exponential growth observed in grapevine accessions can be viewed as a consequence of human breeding activity during the domestication of the species. However, a recent and drastic decline of population size has been observed in the Mediterranean wild lineages. This event mirrors the demographic decline of wild grape, probably explained by anthropogenic pressure on its natural habitats and by the introduction of pathogens from North America in recent centuries.

Two freshwater cryptomonads, Cryptomonas obovata Skuja and Cryptomonas curvata Ehrenberg, are reported for the first time in China. Identification was based on light microscopy and scanning electron microscopy. Cryptomonas obovata was characterized by its obovoid cell shape, lobed cell subapex, and a large number of starch grains. Cryptomonas curvata was characterized by its sigmoid cell shape, rostrate cell apex, and numerous pyrenoids. Nuclear and nucleomorph small subunit rDNA phylogenetic analyses revealed Cryptomonas curvata collected from China was very similar to C. curvata strains cultivated in Germany, and the closest relative of C. obovata was found to be C. pyrenoidifera Geitler. Controversially, some quite morphologically different members of the genus Cryptomonas Ehrenberg were clustered into the same group in phylogeny analyses, which emphasized the complexity of the genus Cryptomonas.