In this review, we present a detailed account of Alternanthera philoxeroides (alligatorweed), including A. philoxeroides description, intraspecific variation from native to introduced regions, its life history strategies, invasion mechanisms, and management strategies. Alternanthera philoxeroides is a herbaceous amphibious weed of Amaranthaceae, native to South America, distributed from Buenos Aires Province (39° S) to south Brazil. It was first described by Martius in 1826, and consists of several taxa in both its native and non-native ranges. Current knowledge indicates that two forms of alligator weed exist in Argentina: A. philoxeroides f. philoxeroides in the southern range and A. philoxeroides f. angustifolia in the northern range. In Argentina, both forms set fruits and produce viable seeds. Alternanthera philoxeroides is now found as a serious weed from tropical to warm temperate regions, including the USA, China, India, South-East Asia, Australia and New Zealand. It is thought to have been brought to China during the 1930s, and later widely cultivated and spread in southern China as fodder during 1950s. The invasions of alligatorweed in China have caused considerable concerns, and now it is one of the 12 most harmful alien invasive species in China. Alligatorweed is found on stationary and slow moving water bodies, creeks, channels, riverbanks and associated areas that are occasionally flooded. It can also be found in terrestrial habitats as a pasture weed within urban environments. Alligatorweed does not produce viable seed in China and reproduces vegetatively from vegetative fragments (stems, rhizome or root tubes), which can be transported by water movement, boats, machinery and vehicles, and in hay. Movement between river catchments is common because of the human activities. Alligatorweed forms a floating mass which spreads out over the water. Its growth disrupts the ecology of banks and shallows and crowds out other plant species, restricts water flow, increases sedimentation, aggravates flooding, limits access and use by man and provides a favorable breeding area for disease vectors. We need better understanding of the biology and ecology of alligatorweed to assess the efficiency of control methods in any theoretical framework. According to the knowledge of the life history strategy of alligatorweed, we suggest that metapopulation theory is a good tool to improve management efficiency from watershed and regional perspectives.

We review the fossil history of seed plant genera that are now endemic to eastern Asia. Although the majority of eastern Asian endemic genera have no known fossil record at all, 54 genera, or about 9%, are reliably known from the fossil record. Most of these are woody (with two exceptions), and most are today either broadly East Asian, or more specifically confined to Sino-Japanese subcategory rather than being endemic to the Sino-Himalayan area. Of the "eastern Asian endemic" genera so far known from the fossil record, the majority formerly occurred in Europe and/or North America, indicating that eastern Asia served as a late Tertiary or Quaternary refugium for taxa. Hence, many of these genera may have originated in other parts of the Northern Hemisphere and expanded their ranges across continents and former sea barriers when tectonic and climatic conditions allowed, leading to their arrival in eastern Asia. Although clear evidence for paleoendemism is provided by the gymnosperms Amentotaxus, Cathaya, Cephalotaxus, Cunninghamia, Cryptomeria, Glyptostrobus, Ginkgo, Keteleeria, Metasequoia, Nothotsuga, Pseudolarix, Sciadopitys, and Taiwania, and the angiosperms Cercidiphyllum, Choerospondias, Corylopsis, Craigia, Cyclocarya, Davidia, Dipelta, Decaisnea, Diplopanax, Dipteronia, Emmenopterys, Eucommia, Euscaphis, Hemiptelea, Hovenia, Koelreuteria, Paulownia, Phellodendron, Platycarya, Pteroceltis, Rehderodendron, Sargentodoxa, Schizophragma, Sinomenium, Tapiscia, Tetracentron, Toricellia, Trapella, and Trochodendron, we cannot rule out the possibility that neoendemism plays an important role especially for herbaceous taxa in the present-day flora of Asia, particularly in the Sino-Himalayan region. In addition to reviewing paleobotanical occurrences from the literature, we document newly recognized fossil occurrences that expand the geographic and stratigraphic ranges previously known for Dipelta, Pteroceltis, and Toricellia.

Our understanding of eukaryote biology is dominated by the study of land plants, animals and fungi. However, these are only three isolated fragments of the full diversity of extant eukaryotes. The majority of eukaryotes, in terms of major taxa and probably also sheer numbers of cells, consists of exclusively or predominantly unicellular lineages. A surprising number of these lineages are poorly characterized. Nonetheless, they are fundamental to our understanding of eukaryote biology and the underlying forces that shaped it. This article consists of an overview of the current state of our understanding of the eukaryote tree. This includes the identity of the major groups of eukaryotes, some of their important, defining or simply interesting features and the proposed relationships of these groups to each other.

With more and more sequence data available, it has been a widespread practice to apply multiple genes to reconstruct phylogenies at different hierarchical levels. The phenomenon of conflicting gene trees has accordingly become a remarkable and difficult problem. It is increasingly understood that the difference between gene tree and species tree and the causes behind should be fully appreciated in molecular phylogenetic studies. In this paper, we have explored the major causes resulting in conflicting gene trees, including stochastic errors, systematic errors and biological factors. We also introduced a newly developed discipline, phylogenomics, and demonstrated its power and great potential in resolving difficult phylogenetic problems using our recent phyloge-nomic study of Oryza as an example. Furthermore, we discussed some strategies and approaches in elucidating conflicting gene trees and provided some suggestions and recommendations for molecular phylogenetic studies using multiple genes.

Y chromosome haplogroup O3-M122 is the most prevalent haplogroup in East Asia, and provides an ideal tool for dissecting primary dispersals of the East Asians. Most of the sub-haplogroups of O3-M122 have been sufficiently investigated except for O3a1c-002611, despite its great prevalence and huge population, especially in Han Chinese. In this study, we identified 508 individuals with haplogroup O3a1c-002611 out of 7801 males from 117 East and Southeast Asian populations, typed at two newly discovered downstream Y-SNP markers and ten commonly used Y-STRs. Defined by SNPs IMS-JST002611 (in short, 002611), F11, and F238, three lineages internal to haplogroup O3a1c-002611 have distinct geographical distributions. Furthermore, Y-STR diversity shows a general south-to-north decline, which is consistent with the prehistorically northward migration of the other O3-M122 lineages. The northward migration of haplogroup O3a1c-002611 started about 13 thousand years ago (KYA). The expansions of subclades F11 and F238 in ancient Han Chinese began about 5 and 7 KYA immediately after the separation between the ancestors of the Han Chinese and Tibeto-Burman.

The origin and dispersal of Y-Chromosomal haplogroup O2a1-M95, distributed across the Austro Asiatic speaking belt of East and South Asia, are yet to be fully understood. Various studies have suggested either an East Indian or Southeast Asian origin of O2a1-M95. We addressed the issue of antiquity and dispersal of O2a1-M95 by sampling 8748 men from India, Laos, and China and compared them to 3307 samples from other intervening regions taken from the literature. Analyses of haplogroup frequency and Y-STR data on a total 2413 O2a1-M95 chromosomes revealed that the Laos samples possessed the highest frequencies of O2a1-M95 (74% with >0.5) and its ancestral haplogroups (O2*-P31, O*-M175) as well as a higher proportion of samples with 14STR-median haplotype (17 samples in 14 populations), deep coalescence time (5.7 ± 0.3 Kya) and consorted O2a1-M95 expansion evidenced from STR evolution. All these suggested Laos to carry a deep antiquity of O2a1-M95 among the study regions. A serial decrease in expansion time from east to west: 5.7 ± 0.3 Kya in Laos, 5.2 ± 0.6 in Northeast India, and 4.3 ± 0.2 in East India, suggested a late Neolithic east to west spread of the lineage O2a1-M95 from Laos.

Success of flowering plants is greatly dependent on effective seed dispersal. Specific fruit types aid different mechanisms of seed dispersal. However, little is known about what evolutionary forces have driven the diversification of fruit types and whether there were phylogenetic constraints on fruit evolution among angio-sperm lineages. To address these questions, we first surveyed the orders and families of angiosperms for fruit types and found no clear association between fruit types and major angiosperm lineages, suggesting there was little phylogenetic constraint on fruit evolution at this level. We then surveyed fruit types found in two contrasting habitats: an open habitat including the Indian desert and North American plains and prairies, and a closed forest habitat of Australian tropical forest. The majority of genera in the survey of tropical forests in Australia were fleshy fruit trees, whereas the majority of genera in the survey of prairies and plains in central North America were herbs with capsules and achenes. Both capsules and achenes are frequently dispersed by wind in the open, arid habitat, whereas fleshy fruits are generally dispersed by animals. Since desert and plains tend to provide continuous wind to aid dispersal and there are more abundant mammal and bird dispersers in the closed forest, this survey suggests that fruit evolution was driven at least in part by dispersal agents abundant in particular habitats.

The apple is one of the most important fruit species in the world. Turkey has a diverse and ancient apple germplasm that have played a major role in the domestication of the Malus genus. However, so far locally grown Anatolian apple germplasm has largely been uncharacterized. In this study, 171 local apple (M. domestica Borkh.) accessions originated from eco-geographically diverse regions of Anatolia were studied using 16 SSR (simple sequence repeat) loci, which generated 254 alleles. Of the SSR markers used, the CH04g10 locus showed the highest allele diversity. Relatively high genetic similarities were found between some accessions. The factorial correspondence analysis did not clearly separate different all apple accession groups, suggesting that Anatolian apple accessions are highly intermixed. However, most apple accessions were grouped according to their collection sites in structure analyses. In addition, reflecting the richness of the Anatolian apple germplasm, low numbers of synonymous, and identical accessions were identified among the germplasm. Finally, using the publically available SSR data generated in other studies, we investigated genetic relationships between Anatolian accession groups and European apple accession groups. Our results reported here provide a useful base for future studies aimed at investigating the genetic diversity of wild and cultivated apples from Anatolia and the surrounding regions.

Invasive species pose a serious threat to native ecosystems and their biodiversity, and cause considerable economic loss to the regions they invade. In the case of Canada goldenrod (Solidago canadensis L.) (Compositae), a long-lived perennial plant native to North America, it was initially introduced as an ornamental plant to Shanghai in 1935, it then escaped into the wild and it is now spreading rapidly in China, especially in eastern China. We here describe briefly this species in relation to invasion biology. S. canadensis is actually a Canada-goldenrod complex that consists of at least six subspecies and varieties. S. canadensis has great reproductive capacity (through both seed production and clonal growth) and high genetic variation, both of which contribute to its great invasiveness. S. canadensis may outcompete or allelopathically exclude native plant species, resulting in monospecific stands with concomitant loss of plant and insect diversity, and ultimately alteration in ecosystem functioning. Lack of natural enemies in the invaded ecosystems makes this species highly invasive. Abiotic factors such as niche opportunities created by habitat disturbance and human activities, and nitrogen deposition, can promote S. canadensis’ establishment and spread through seed dispersal and vegetative structures. In addition, the species’ capacity for early season emergence and growth, rapid clonal growth, wide physiological tolerance, and high architectural plasticity make the species highly aggressive under a wide range of ecological conditions. Although commonly used control methods of weeds may also be suitable for S. canadensis, minimising its seed production seems to be critical to its effective control, which requires that all the control measures be taken during its vegetative growth.

An angiosperm phylogeny was reconstructed in a maximum likelihood analysis of sequences of four mitochondrial genes, atp1, matR, nad5, and rps3, from 380 species that represent 376 genera and 296 families of seed plants. It is largely congruent with the phylogeny of angiosperms reconstructed from chloroplast genes atpB, matK, and rbcL, and nuclear 18S rDNA. The basalmost lineage consists of Amborella and Nymphaeales (including Hydatellaceae). Austrobaileyales follow this clade and are sister to the mesangiosperms, which include Chloranthaceae, Ceratophyllum, magnoliids, monocots, and eudicots. With the exception of Chloranthaceae being sister to Ceratophyllum, relationships among these five lineages are not well supported. In eudicots, Ranunculales, Sabiales, Proteales, Trochodendrales, Buxales, Gunnerales, Saxifragales, Vitales, Berberidopsidales, and Dilleniales form a basal grade of lines that diverged before the diversification of rosids and asterids. Within rosids, the COM (Celastrales–Oxalidales–Malpighiales) clade is sister to malvids (or rosid II), instead of to the nitrogen-fixing clade as found in all previous large-scale molecular analyses of angiosperms. Santalales and Caryophyllales are members of an expanded asterid clade. This study shows that the mitochondrial genes are informative markers for resolving relationships among genera, families, or higher rank taxa across angiosperms. The low substitution rates and low homoplasy levels of the mitochondrial genes relative to the chloroplast genes, as found in this study, make them particularly useful for reconstructing ancient phylogenetic relationships. A mitochondrial gene-based angiosperm phylogeny provides an independent and essential reference for comparison with hypotheses of angiosperm phylogeny based on chloroplast genes, nuclear genes, and non-molecular data to reconstruct the underlying organismal phylogeny.

A recent model by Currat et al. indicates that when one species colonizes an area already occupied by a closely related species, massive introgression of neutral genes should take place primarily in the direction from the local to the invasive species. Here, I show that this model relies on an assumption that might not capture the true dynamics of how species exchange migrants during admixture. As an alternative, I formulate a new model, based on a different and perhaps more biologically realistic assumption of interbreeding, that demonstrates symmetric introgression as compared to the large and asymmetric introgression predicted by the original model. The new model indicates that asymmetry is not a default property of introgressions, thus necessitating alternative explanations for the common observation of massive asymmetric introgression including sex-biased dispersal.

The microsoroid ferns make up a large group in the family Polypodiaceae, easily characterized by the combination of at least partly clathrate rhizome scales and anastomosing reticulate venation. The diversification of this clade is poorly known, both because of unresolved generic delimitations and the lack of fossil records. In this work, we describe the first microsoroid macrofossil: Palaeosorum ellipticum sp. nov. F. M. B. Jacques & Z. K. Zhou. The fossil specimen, represented by part and counterpart, was found in the middle Miocene sediment of the Dajie Formation in Ailsohan, central Yunnan, southwest China. Epiphytic ferns belonging to Drynariaare found in different locations in Yunnan during the Pliocene. The fossil described in this study deepens the occurrence of epiphytic ferns in Yunnan back to the middle Miocene. It demonstrates that forests with complex ecological relationships have existed in southwest China for more than 10 million years.

Chloranthaceae is one of the earliest diverging angiosperm families and is comprised of approximately 75 species in four genera (Chloranthus, Sarcandra, Ascarina, and Hedyosmum). This family has received considerable attention because of its seemingly primitive morphology, disjunct tropical distribution in Asia and America, and extensive fossil record from the Early Cretaceous. In the present study, we reconstructed the phylogeny of Chloranthaceae based on a combined dataset of three plastid DNA regions and 56 species. We then estimated divergence times in the family using two relaxed molecular clock methods (BEAST and penalized likelihood). We focused on testing the influence of fossil taxa in calibrating the molecular phylogeny, and on assessing the current taxonomy of the family in light of the phylogenetic results. Our results indicate that most intrageneric divisions within Ascarina and Hedyosmum are not monophyletic. The results from the dating analysis suggest that the Hedyosmum-like fossil Asteropollis represents a stem lineage of Hedyosmum, as has been suggested previously from morphological analyses. In contrast, our results indicate that the Chloranthus-like fossil Chloranthistemon, previously suggested on morphological grounds to be a stem relative of Chloranthus, may, instead, belong to the branch leading to the clade Chloranthus+Sarcandra. The median crown ages of Chloranthus, Sarcandra, Ascarina, and Hedyosmum estimated in the BEAST analysis were 26.3, 9.5, 31.0 and 45.8 million years ago (Ma), respectively, whereas the divergence between Chloranthus and Sarcandra, the splitting of Ascarina with the former two genera, and Hedyosmum separating from the three genera were estimated to 63.8, 95.7 and 111.1 Ma. The present study sheds further light on the temporal evolution of Chloranthaceae and exemplifies how molecular dating analyses may be used to explore alternative phylogenetic placements of fossil taxa.

The chloroplast maturase K gene (matK) is one of the most variable coding genes of angiosperms and has been suggested to be a “barcode” for land plants. However, matK exhibits low amplification and sequencing rates due to low universality of currently available primers and mononucleotide repeats. To resolve these technical problems, we evaluated the entire matK region to find a region of 600–800 bp that is highly variable, represents the best of all matK regions with priming sites conservative enough to design universal primers, and avoids the mononucleotide repeats. After careful evaluation, a region in the middle was chosen and a pair of primers named matK472F and matK1248R was designed to amplify and sequence the matK fragment of approximately 776 bp. This region encompasses the most variable sites, represents the entire matK region best, and also exhibits high amplification rates and quality of sequences. The universality of this primer pair was tested using 58 species from 47 families of angiosperm plants. The primers showed a strong amplification (93.1%) and sequencing (92.6%) successes in the species tested. We propose that the new primers will solve, in part, the problems encountered when using matK and promote the adoption of matK as a DNA barcode for angiosperms.

Appropriate and extensive taxon sampling is one of the most important determinants of accurate phylogenetic estimation. In addition, accuracy of inferences about evolutionary processes obtained from phylogenetic analyses is improved significantly by thorough taxon sampling efforts. Many recent efforts to improve phylogenetic estimates have focused instead on increasing sequence length or the number of overall characters in the analysis, and this often does have a beneficial effect on the accuracy of phylogenetic analyses. However, phylogenetic analyses of few taxa (but each represented by many characters) can be subject to strong systematic biases, which in turn produce high measures of repeatability (such as bootstrap proportions) in support of incorrect or misleading phylogenetic results. Thus, it is important for phylogeneticists to consider both the sampling of taxa, as well as the sampling of characters, in designing phylogenetic studies. Taxon sampling also improves estimates of evolutionary parameters derived from phylogenetic trees, and is thus important for improved applications of phylogenetic analyses. Analysis of sensitivity to taxon inclusion, the possible effects of long-branch attraction, and sensitivity of parameter estimation for model-based methods should be a part of any careful and thorough phylogenetic analysis. Furthermore, recent improvements in phylogenetic algorithms and in computational power have removed many constraints on analyzing large, thoroughly sampled data sets. Thorough taxon sampling is thus one of the most practical ways to improve the accuracy of phylogenetic estimates, as well as the accuracy of biological inferences that are based on these phylogenetic trees.

Ten common species of Microcystis, based on the examination of water samples from the Dianchi Lake, Yunnan, China, were morphologically described, and their taxonomy was also discussed. They are Microcystis aeruginosa, M. botrys, M. firma, M. flos-aquae, M. ichthyoblabe, M. novacekii, M. pseudofilamentosa, M. smithii, M. viridis and M. wesenbergii. Taxonomic status of other Microcystis species reported in China was also evaluated.
Key words Cyanophyta, Microcystis, morphology, taxonomy, China.

Genetic relationships between 27 Orthotrichum species of the subgenera Orthotrichum and Pulchella were reconstructed using the internal transcribed spacer regions 1 and 2, the chloroplast trnH-psbA region, and intron–exon splice junction (ISJ) and inter-simple sequence repeats (ISSR) markers. A phylogenetic analysis did not reflect the current division of the subgenus Pulchella into the sections Diaphana, Pulchella, and Rivularia. Species of the section Rivularia did not form a monophyletic group, and the only markers that indicated the distinctness of the section Pulchella were ISJ and ISSR. The most genetically diverse section was Diaphana, whose species were divided into several clades. The only proper phylogenetic unit was the subgenus Orthotrichum. The applied markers revealed the process of cryptic speciation in species of both subgenera.

Rosaceae. consisting of about 126 genera and 3200 species, is widely distributed in warm temperate and subtropical regions of the Northern Hemisphere, while more than half of the genera are Asiatic and more then 80% of the total number of Asiatic occur in China (Table 1). In this paper, the origin and evolution of Chinese genera is discussed mainly. The principal tendency of the whole family is also described from the point of view of evolution. First of all, the systematic position of Rosaceae in Angiospermae is reviewed. According to the records of paleobotany, rosaceous plants occurred first in the Tertiary, from the early period of Eocene (genera such as Spiraea and Prunus) to the late period of Miocene (e.g. Crataegus, Malus amd Rosa). They have quite a long history in geological data. Where has this big and old family originated and what steps does it stand in the long course of evolution of flowering plants? There are several opinions and explanations by different authors. In this paper, a general survey of the six prevailing classical systems (Table 2) is made to give a brief idea of the position of this family in the Angiospermae and of the relationships between the subfamilies and also the relationships between different genera in each subfamily. At the end of this paper, an attempt is made to analyse and sum up the major evolutionary tendency of the whole family. As generally condidered, Rosaceae originated from Magnoliales, and woody plants of the family still hold a dominant position. For instance, subfamily Spiraeoideae consists of only one herbaceous genus (i.e., Aruncus) and subfamily Rosoideae only a few herbaceous genera. All of these herbaceous genera are derived from the closely related woody genera of the same subfamily. In the course of evolution of Angiospermae, Rosaceae stands at the initial to the middle stages of development. All parts of plant body in this family are at the chang ing and developing stages, with carpels, fruits and inflorescences being the most active. The primitive types in this family, such as the members of subfamily Spiraeoideae, usually have 5 and free carpels, the number of which are either reduced to 2-1 or increased to 10-numerous. They have different levels of union and are either completely free from each other or coherent at base. The carpels usually occur on the upper part of the receptacle, because the shapes of receptacle are variable, sometimes disk-shaped, cupshaped, tube-shaped or even bottle-shaped. In the last case carpels grow inside the receptacle. Thus the position of carpels has changed from superior to inferior through halfsuperior. In accordance with the development of the carpels, various kinds of fruits are produced. The primitive types of fruit are follicles, with dry, dehiscent carpels opened along different sutures. The next step, the carpels have developed into an indehiscent, I-celled and l-seeded fruit, the so-caned achene. In different genera, the achenes have different coat types and appendages to facilitate dispersing the seeds. Some of the achenes grow upon the fleshy receptacle (like strawberry) and some of them inside the fleshy receptacle (like rose). Sometimes a few carpels are united with the receptacle and develop into a pome (like apple and pear). Another direction of the fruit development is the single carpel with fleshy exocarp and mesocarp, and a bony endocarp, then becoming a drupe (like peach and plum). In addition to fleshy receptacle of thickened fruit coats, they usually have showy colour, fragrant smell and also plenty of sugars, acids, vitamins, etc. which are edible and attract animals and human beings to assist the dispersion of seeds. In this family, there are various types of flower arrangements, both indefinite inflorescences including raceme, umbel, corymb and panicle, and the definite inflorescence, such as solitary flower, cyme and compound cyme. In the evolution course, they tend to change mostly from multiflowered compound inflorescence towards few-flowered simple inflorescence, and finally becoming a solitary flower: simultaneously with the decreasing of number of flowers on the inflorescence, the increasing of size of petals, which become very showy for attraction of insects so as to guarantee pollination and fertilization of the plants concerned. Another tendency, if the bisexual flowers change to unisexual, either monoecious- or dioecious-polygamous, then they form a dense spike which is beneficial to cross pollination. The abundance, diversity, and wide range of distribution of the species and genera of Rosaceae are considered mainly resulted from their highly developed reproductive organs.

Herbal medicinal materials have been used worldwide for centuries to maintain health and to treat disease. However, adulteration of herbal medicines remains a major concern of users and industry for reasons of safety and efficacy. Identification of herbal medicinal materials by DNA technology has been widely applied, started from the mid-1990s. In recent years, DNA barcoding of global plant species using four standard barcodes (rbcL, matK, trnH–psbA and ITS) has been a major focus in the fields of biodiversity and conservation. These DNA barcodes can also be used as reliable tools to facilitate the identification of herbal medicinal materials for the safe use of herbs, quality control, and forensic investigation. Many studies have applied these DNA barcodes for the identification of herbal medicinal species and their adulterants. The present article reviews efforts in the identification of herbal medicinal materials using the standard DNA barcodes and other DNA sequence-based markers.

The morphological characters, distribution and type locality of Cycas taiwaniana are discussed in this paper. Cycas taiwaniana is only found in central-southern Fujian Province in China, with only one wild plant growing in Pinghe County. The type plant of the species still grows in front of CHEN Yuan-Guang Temple in Zhangzhou City.

The new discovery of angiosperm remains in the Jehol Biota of northeastern China contributes to our understanding of the origin and early evolution of flowering plants. The earliest eudicot genus with reproductive organs, Leefructus, was recently documented from the Lower Cretaceous Yixian Formation at 125.8–123.0 Ma, and was reconsidered to be close to the extant family Ranunculaceae based on gross morphology. However, this hypothesis has not been tested using a cladistic approach. To determine the possible allies of Leefructus within extant eudicots, we constructed a 66 morphological data matrix. Molecular and morphological analyses of extant Ranunculales combined with the fossil suggest that it has an affinity with the Ranunculaceae. The earliest fossil record of the eudicots is 127–125 Ma based on tricolpate pollen grains. Thus, we suggest a hypothesis that the basal eudicots might have experienced an accelerated evolution and diversification during the latest Barremian and earliest Aptian, leading to the stem groups of at least six extant families or lineages, 10–15 Myr earlier than currently documented. Angiosperms have undergone multiple uneven pulses of radiation since their origin. Many key character innovations occurred in different stages that could have triggered those radiations in concert with various biotic and abiotic factors.

The confusion of Huma (胡麻) in Chinese history was discussed after an introduction of Chih Wu Ming Shi T’u K’ao of the Qing Dynasty and its author—Wu Qijun’s contribution to Chinese botany. The morphological characters and distribution of Huma and Jusheng (巨胜) documented in ancient Chinese literature were comparatively studied. Simultaneously, other questions about the Chinese medicament and medicine were inspected in the backgrounds of historical development and social stratum differentiation. We concluded that the earliest recorded Huma in Chinese literature should be Linum usitatissimum. The Chinese name for this plant has been used by the folks until well into modern times. Jusheng (巨胜) should be Sesamum indicum. The reason for the confusion of these two names was also explored. It was further inferred that the confusion of names for traditional Chinese medicine (TCM) originated in the similarity of their property and function while the difference of their morphology and distribution was not taken seriously. We also concluded that Shên Nung Pên Ts’ao Ching was forged by TAO Hongjing (陶弘景) in his Collected Commentaries on Pên Ts’ao Ching but attributed to an ancient author, Shennong (神农). In this book TCM was classified by their property and function, which became the root cause of the confusion of Chinese names for TCM from then on. Some suggestions were also given for the development of Chinese materia medica in the future.

The most recent edition of the International Code of Botanical Nomenclature (Vienna Code) has superseded all previous editions. One of the notable changes in the Vienna Code is that it contains a glossary of nomenclatural terms defined and used in the Code. It has been made clear that the glossary of these terms is an integral part of the Code. This paper presents a Chinese translation of the definitions of the nomenclatural terms in the Code.

Terminology of inflorescence diversity has often been used in a confusing way in the literature, partly because it was based on uncritical and outdated definitions. Especially the terms cyme, thyrse, and panicle have been misused. Although a more critical classification worked out by several authors is available, it is unfortunately not in general use because most of the relevant publications are written in German. In addition, some terms have not been used in the same way by morphologists and developmental geneticists. The present review attempts to remedy the situation with a simple outline of a classification based on (1) different branching patterns, (2) differential elongation of axes of different orders, and (3) repetition of basic ramification patterns in different ways. Racemose and cymose branching are two extreme patterns, the former with limitation of axial orders to two, the second with limitation of lateral axes of each order to two. In a branching system a sequence of racemose → cymose, and, within the cyme, of dichasial → monochasial, is common, but the reverse sequence is not known to occur. Systematic and evolutionary aspects of inflorescences are briefly discussed. Branching patterns are often stable in larger clades. Inflorescences of mutants studied in developmental genetic studies are mainly altered in flower or branch numbers or relative branch length but not in branching patterns. This is also a contribution toward the goal of a unified terminology for the different fields of biology dealing with inflorescences.

DNA barcoding is a molecular tool that uses a standardized DNA region to identify species. Our preliminary study reported here is the first attempt to specifically focus on universality and attributes of candidate barcodes across a wide systematic range of mosses. We tested eight previously proposed plant barcoding regions (atpF-atpH, ITS2, matK, psbK-psbI, rbcL, rpoB, rpoC1, trnH-psbA) and two popular phylogenetic markers (rps4 and trnL-trnF of cpDNA) in 49 moss species and 9 liverwort species, representing half of the orders in moss lineages. The ITS2, rbcL, rpoC1, rps4, trnH-psbA and trnL-trnF regions showed good universality, and therefore the efficacy of these loci as DNA barcodes was further evaluated in 36 mosses and 2 liverworts, each of which included two to three individuals per taxa. The five loci, viz. rbcL, rpoC1, rps4, trnH-psbA and trnL-trnF, were easy to amplify and sequence and showed significant interspecific genetic variability, making them potentially useful DNA barcodes for mosses. The best performing single loci were the rbcL and rpoC1 coding regions. Several loci showed equivalent performance and combinations of them did not greatly increase their discrimination capacity. In addition, phylogenies generated from each of the separate regions and multi-locus combinations by using best-fit and Kimura 2-parameter models were compared, but no significant difference was found.

Asian cultivated rice (Oryza sativa L.), an important cereal crop worldwide, was domesticated from its wild ancestor 8000 years ago. During its long-term cultivation and evolution under diverse agroecological conditions, Asian cultivated rice has differentiated into indica and japonica subspecies. An effective method is required to identify rice germplasm for its indica and japonica features, which is essential in rice genetic improvements. We developed a protocol that combined DNA extraction from a single rice seed and the insertion/deletion (InDel) molecular fingerprint to determine the indica and japonica features of rice germplasm. We analyzed a set of rice germplasm, including 166 Asian rice varieties, two African rice varieties, 30 accessions of wild rice species, and 42 weedy rice accessions, using the single-seeded InDel fingerprints (SSIF). The results show that the SSIF method can efficiently determine the indica and japonica features of the rice germplasm. Further analyses revealed significant indica and japonica differentiation in most Asian rice varieties and weedy rice accessions. In contrast, African rice varieties and nearly all the wild rice accessions did not exhibit such differentiation. The pattern of cultivated and wild rice samples illustrated by the SSIF supports our previous hypothesis that indica and japonica differentiation occurred after rice domestication under different agroecological conditions. In addition, the divergent pattern of rice cultivars and weedy rice accessions suggests the possibility of an endoferal origin (from crop) of the weedy rice included in the present study.

The monotypic genus Platycarya (Juglandaceae) is one of the most widespread temperate tree species in East Asia. In this research, we implemented a phylogeographical study using chloroplast DNA (cpDNA) (psbA-trnH and atpB-rbcL intergenic spacer) sequences on Platycarya strobilacea, in order to identify the locations of the species’ main refugia and migration routes. A total of 180 individuals of P. stobilacea from 27 populations from China and Jeju Island (Korea) were collected. The results revealed that P. strobilacea had 35 haplotypes for the two intergenic spacers and high genetic diversity (h_T= 0.926). This surprisingly high diversity of haplotypes indicates its long evolutionary history, which is in agreement with previous phylogenetic analyses and fossil records. Significant cpDNA population subdivision was detected (G_ST= 0.720; N_ST= 0.862), suggesting low levels of recurrent gene flow through seeds among populations and significant phylogeographical structure (N_ST > G_ST, P < 0.05). The construction of phylogenetic relationships of the 35 chlorotypes detected four major cpDNA clades. Divergence dating analyses using BEAST suggest that the divergence of the major cpDNA clades occurred before the Miocene. Demographic analysis indicated that the Eastern clade underwent localized demographic expansions. The molecular phylogenetic data, together with the geographic distribution of the haplotypes, suggest the existence of multiple glacial refugia in most of its current range in China through Quaternary climatic oscillations.

The formation and development of botanical scientific illustration have a long and tortuous history, which is closely related to the study and development of plant sciences. Botanical scientific illustration saliently differs from other artistic painting in its use and illustrating method. Therefore, an understanding of the historical formation and development of botanical scientific illustration largely depends on the study of illustrating method and use. The main illustrators and their works responsible for the making and development of botanical scientific illustration are reviewed, and three times are subdivided for the history of botanical scientific illustration, i.e. ancient times (herbal study), modern times (introducing the Western botany) and contemporary times (modern botany). Meanwhile, the representative works and main research characteristics in respective times are expounded briefly.

The Panax bipinnatifidus species complex (P. bipinnatifidus and its close relatives) in the Sino-Himalayan region has been taxonomically difficult. Evolutionary analyses using amplified fragment length polymorphism (AFLP) markers were carried out on 125 individuals representing 11 populations of the P. bipinnatifidusspecies complex and one population of P. stipuleanatus Tsai & Feng as an outgroup. The populations from the eastern Himalayan region, sampled from Nepal and eastern Tibet, formed two main groups in the neighbor-joining and split network analyses. The Pailong population (Tibet-PL) in eastern Tibet showed a highly distinct AFLP profile and was placed as the most basally branched group in the neighbor-joining tree. The remaining Himalayan populations showed three subgroups: the Nepal-HB and Nepal-HS subgroup, the Nepal HH subgroup, and the Tibet-BY subgroup. The three Himalayan subgroups had very limited gene flow among them and showed subtle morphological differences. The populations in eastern, central, and western China showed clear geographic patterns and can be sorted into several geographical groups. Each major group in the species complex has strong bootstrap support, but relationships among them are poorly resolved, which is consistent with a pattern of evolutionary radiation. The strong geographic grouping, high Nei's population differentiation index, and limited gene flow among populations in different regions support the importance of geographic isolation in the diversification of the P. bipinnatifidus species complex in the Sino-Himalayan region.

Plant species shift ranges in response to climate fluctuation over time. However, differentiation related to heterogeneity in space has been illustrated only rarely. Here we selected Hippophaë neurocarpa S. W. Liu & T. N. Ho (Elaeagnaceae), a shrub endemic to the Qinghai–Tibet Plateau, to exemplify this process. We characterized the genotypic, phenotypic, and climatic variations among 27 populations of this species sampled across its entire distribution. Genotype analyses revealed six highly differentiated groups that may have resulted from expansions in spatial range. Despite recent fluctuation in size, it is likely that most groups survived the last glacial maximum in situ. Instead of two previously described subspecies, we identified four morphotypes (stellate, peltate, and two additional types) that can be characterized based on leaf trichomes. This phenotypic subdivision is consistent with a climate gradient defined by temperature and precipitation, although similar phenotypes may derive from distinct genotypes. Collectively, we propose that the demographic history of H. neurocarpa is characteristic of an early spatial range expansion combined with a recent bottleneck, subsequently subdivided into multiple morphotypes following local adaption to heterogeneous climates.

Salvia L. (family Lamiaceae) a large genus of over 1,000 species is widely distributed in tropical and temperate regions of the world. Among them 84 species are native to China. There remain, however, many taxonomic uncertainties at the sub-generic level. Diterpenoids are a class of secondary metabolites with a large variety of structures and they have been used as chemotaxonomic markers at infra and super-generic levels. For the sake of further chemotaxonomic understanding of Salvia, this paper describes an investigation on the distribution of tanshinones, a group of biologically active diterpenes, which are known to be present in some Chinese members of the genus. Using HPLC with DAD detector, tanshinones in various Salvia species were determined and the distribution supported the circumscription of the sect. Drymosphare in the original sense of Bentham. The distribution of tanshinones, therefore, provides a valuable chemotaxonomic tool for determining infra-generic differences within Salvia.

The aim of the present study was to examine the phylogeographic and evolutionary history of Picea likiangensis, a dominant species of the conifer forests in the eastern declivity of the Qinghai–Tibetan Plateau. We collected 422 individuals from 42 natural populations of three major varieties classified under this species. In conifers, mitochondrial (mt) DNA and chloroplast (cp) DNA dispersed by seeds or pollen experience very different levels of gene flow. To this end, we examined the sequence variation of two mtDNA fragments (nad5 intron 1 and nad1 intron b/c) and three cpDNA fragments (trnL–trnF, trnS–trnG and nadhK/C). We found that cpDNA probably introgressed from P. purpurea into remote populations of P. likiangensis through long-distance dispersal. Multiple refugia seem to have been maintained for P. likiangensis during the Last Glacial Maximum because the cpDNA and mtDNA haplotypes recovered were fixed in the different regions. Postglacial expansions were only detected at the distributional edges of this species where a single cpDNA or mtDNA haplotype was fixed in adjacent populations. However, genetic imprints of postglacial expansions from these two sets of markers were different in the western and southeastern regions, which may result from the long-distance dispersal of the cpDNA, as well as its fast lineage sorting during intraspecific divergences. Analysis of molecular variance further suggested that genetic differentiation between the three varieties is higher at cpDNA markers than at mtDNA markers, which supports the previous viewpoint that cpDNA markers with a high rate of gene flow may be more effective in delimitating closely related taxa. Together, the results of the present study highlight the evolutionary complexity of a widely distributed species owing to interactions among local and edge expansion, long-distance dispersal, and intraspecific divergences at two sets of DNA genomes with different rates of gene flow.

Adiantum × meishanianum F. S. Hsu ex Y. C. Liu & W. L. Chiou was regarded as an endemic species in Meishan Village, Kaohsiung, Taiwan, China and a hybrid between A. malesianum Ghatak (the maternal parent) and a sexually reproducing diploid cryptic species of A. philippense L. (the paternal parent), as revealed by chloroplast and nuclear markers. However, morphological research revealed that A. × meishanianum is also disjunctively distributed in Yunnan and that its paternal parent is possibly A. menglianense Y. Y. Qian. Thus, this study aimed to confirm these findings by using two chloroplast regions and a low-copy nuclear marker in DNA barcoding and phylogenetic analyses, spore measurement, and flow cytometry. Our results indicated that A. × meishanianum in Yunnan is triploid and abortive, the same as A. × meishanianum in Taiwan, and they both originated from the hybridization between the maternal parent of A. malesianum and the paternal parent ofA. menglianense, but not A. philippense. In conclusion, A. × meishanianum probably originated from multiple hybridizations in Taiwan and Yunnan.

DNA barcoding is a tool to provide rapid and accurate taxonomic identification using a standard DNA region. A two-marker combination of matK+rbcL was formally proposed as the core barcode for land plants by the Consortium for the Barcode of Life Plant Working Group. However, there are currently no barcoding primers for matK showing high universality in gymnosperms. We used 57 gymnosperm species representing 40 genera, 11 families and four subclasses to evaluate the universality of nine candidate matK primers and one rbcL primer in this study. Primer (1F/724R) of rbcL is proposed here as a universal primer for gymnosperms due to high universality. One of the nine candidate matK primers (Gym_F1A/Gym_R1A) is proposed as the best “universal”matK primer for gymnosperms because of high polymerase chain reaction success and routine generation of high quality bidirectional sequences. A specific matK primer for Ephedra was newly designed in this study, which performed well on the sampled species. The primers proposed here for rbcL and matK can be easily and successfully amplified for most gymnosperms.

Synthetic hexaploid wheat (SHW) that combines novel and elite genes from the tetraploid wheat Triticum turgidum L. and wild ancestor Aegilops tauschii Coss., has been used to genetically improve hexaploid common wheat. The abundant genetic diversity in SHW can effectively make breakthroughs in wheat genetic improvement through the inclusion of increased variation. In this paper, we reviewed the current advances in research and utilization of the primary SHW lines and SHW-derived wheat varieties that have enhanced evolution of modern wheat under conditions of natural and artificial selection in southwestern China. Using primary SHW lines, four high-yielding wheat varieties have been developed. In addition, using the SHW-derived varieties as breeding parents, 12 new wheat varieties were also developed. Results of genotype–phenotype and fingerprint analysis showed that the introgressed alleles from SHW lines have contributed a great number of elite characters to the new wheat varieties, and these elite characters include disease resistance, more spikes per plant, more grains per spike, larger grains, and higher grain-yield potential. We found that the primary SHW lines and SHW-derived varieties have identifiable effects to enhance genetic variation and adaptive evolution of modern hexaploid wheat, which significantly increased the grain yields of hexaploid wheat in recent years. These findings have significant implications in the breeding of high-yielding wheat varieties resistant to biotic and abiotic stresses using SHW as genetic resources.

The history of MADS box genes is well-known in angiosperms. While duplication events and gene losses occur frequently, gene structure and intron positions are very conserved. We investigated all six introns in a duplicated MADS box gene (deficiens, def) in selected Impatiens taxa, thereby assessing intron features. For the first time, our study provides a comparison of molecular changes in all introns of a gene from a phylogenetic perspective. Interestingly, a uniform pattern of molecular evolution in the introns of each copy was not observed, but intron length increases, decreases, and size retention can be found in each copy. A tendency to accumulate long autapomorphic indels is also present, thus, a longer intron length does not reflect a higher number of parsimony-informative characters. Substitution rates vary between introns of each gene copy. While four of the six introns of def1 exhibit a change in their substitution rate, five of the six def2 introns maintain their rates throughout the genus albeit at different levels. In MADS box genes several regulatory sequences are found residing in introns. Thus, presence of putative regulatory motifs was investigated. Most of them are not conserved in position and usually present in only one of the gene copies. In addition, the potential for phylogenetic reconstruction of introns in both def copies is shortly discussed.

Orchid pollination and evolution are common topics in evolutionary biology. China has approximately 1400 orchid species distributed in diverse habitats and account for approximately 5% of the orchid species in the world. These orchids provide us with materials to explore coevolution and organic evolution. We summarized 53 Chinese orchid pollination studies and synthesized their main findings and common patterns. Bees and flies are the main pollinators of Chinese orchids and drive the diversification of Paphiopedilum and Cypripedium. In addition, the patterns are consistent with phylogenetic evolution studies. Almost half of the Chinese orchids use a common food-deceptive pollination strategy to transfer their pollens. Other orchids use Batesian mimicry, brood-site imitation, and green-leaf volatile imitation, which is rare. Holcoglossum amesianum (Rchb. f.) Christenson and Paphiopedilum parishii (Rchb. f.) Stein, which live in insect-scarce habitats, use self-pollination strategies to ensure their reproductive success. However, studies on pollination are in the early stages and comprehensive studies are scarce. Therefore, future studies should involve additional disciplines and techniques, such as chemecologic, electrophysiologic, genomic, transcriptomic, and proteomic methods, to evaluate the floral features that attract specific pollinators and to elucidate the patterns of Chinese orchid pollination, evolutionary history, diversification, and speciation between orchids and their pollinators.

Beimu, one of the most commonly used Chinese Materia Medica (CMM), is
derived from the bulbs of some fritillaries. In recent years, a large number of new species and
infraspecific taxa of the genus Fritillaria have been described from China, with total number
of taxa of 80 species, 52 varieties, and 6 forms. The dramatic increase of new taxa of the
Chinese fritillaries has influenced the investigation, application, quality control and
commodities circulation of the CMM “Beimu”. We undertook a comprehensive study of the
morphological, geographical, phytochemical and historical aspects of Chinese medicinal
fritillaries, as well as their current application. We treated the source plants of “Beimu” from a
pharmacophylogenetic point of view as the following six groups. (l) Zhebeimu (浙贝母) is a
general name of bulbs mainly derived from the cultivated Fritillaria thunbergii in Zhejiang
and Jiangsu provinces. It contains D/E trans cevanine group alkaloids, predominantly
verticine, isoverticine, and verticinone. No D/E cis cevanine group alkaloids were detected.
(2) Yibeimu (伊贝母) consists of F. walujewii and F. pallidiflora, which are distributed in
Xingjiang Uygur Autonomous Region. Unlike Zhebeimu, Yibeimu contains D/E cis cevanine
group alkaloids, of which imperaline is representative; no D/E trans form of cevanine group
alkaloids has so far been found. (3) Pingbeimu (平贝母) is obtained from cultivated F.
ussuriensis in northeastern China. It contains both D/E trans and cis forms of cevanine group
alkaloids. (4) Chuanbeimu (川贝母) is the most important medicinally used Beimu; it is
derived mainly from F. cirrhosa, F. przewalskii, and F. unibracteata in the Hengduan
mountains and their adjacent regions. These three species all have smaller bulbs than the other
species and are the main source of “Qingbei” (青贝), a kind of Beimu of the highest quality.
Fritillaria cirrhosa, distributed in Xizang, Yunnan, Sichuan, and Qinghai, shows many
morphological variations, and towards its northwestern limit is replaced by a very closely
related species, F. taipaiensis. In addition, the bulbs of F. delavayi, called Lubei (炉贝), are
also in the group of Chuanbeimu. All kinds of Chuanbeimu contain both D/E trans and D/E
cis cevanine group alkaloids. (5) Hubei Beimu (湖北贝母) is obtained mainly from bulbs of
cultivated F. hupehensis, which is very closely related to F. monantha. It contains both D/E
trans and cis forms of cevanine group alkaloids; verticine and isoverticine are representative
of the D/E trans form, and hupehenine, hupeheninoside, hupehenrine, and hupehenizine are
representative of the D/E cis form. (6) Anhui Beimu (安徽贝母) is derived from F. anhuiensis
and contains only D/E trans cevanine group alkaloids. The six groups of fritillaries have six
“Dao-di” (genuine) localities of origin. This is in accordance with current application and
marketing. All except Anhui Beimu are recorded in the latest edition of Pharmacopoeia of the
People’s Republic of China (2005 ed., Vol. 1). As a result of this study, we advocate that the
publication and naming of new taxa of the most important economic plants should be more
prudent.

In 2009, the Consortium for the Barcode of Life (CBOL) recommended the combination of rbcL and matK as the plant barcode based on assessments of recoverability, sequencing quality, and levels of species discrimination. Subsequently, based on a study of more than 6600 samples belonging to 193 families from seven phyla, the internal transcribed spacer (ITS) 2 locus was proposed as a universal barcode sequence for all major plant taxa used in traditional herbal medicine. Neither of these two studies was based on a detailed analysis of a particular family. Here, Zingiberaceae plants, including many closely related species, were used to compare the genetic divergence and species identification efficiency of ITS2, rbcL, matK, psbK–psbI, trnH–psbA, and rpoB. The results indicate that ITS2 has the highest interspecific divergence and significant differences between inter- and intraspecific divergence, whereas matK and rbcL have much lower divergence values. Among 260 species belonging to 30 genera in Zingiberaceae, the discrimination ability of the ITS2 locus was 99.5% at the genus level and 73.1% at the species level. Thus, we propose that ITS2 is the preferred DNA barcode sequence for identifying Zingiberaceae plants.