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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Euonymus, a cosmopolitan genus of the family Celastraceae, has its species diversity centered in East Asia. It exhibits a complex pattern of morphological variation, making its taxonomy difficult. Monophyly of the genus remains uncertain, and the evolutionary implications of the infrageneric division and delimitation of many species are debatable. In this study, we sampled a total of 62 accessions representing 48 species/taxa covering a broad range of diversity of the genus and its allies. We first investigated the phylogeny of Euonymus using DNA sequences of multiple nuclear and plastid markers, and then used this phylogeny to discuss the circumscription and classification of the genus in combination with evolution of fruit characters, which has been used as an important criterion for the generic subdivision. The resultant data revealed the monophyly of Euonymus sensu lato with inclusion of Glyptopetalum, resolved the major lines of phylogeny of the genus, and clarified the echinate and winged capsules each as lineage-specific. Therefore, among the five sections accepted by Flora of China, only Sect. Echinococcus(with spiny fruits) and Sect. Kalonymus (with winged fruits) correspond to the molecular grouping. The globose capsule may represent an ancestral character state, and the other types of fruits, that is, the shallowly to deeply lobed capsules, may belong to a broad range of continuous variation derived from the globose.

The genus Ventilago Gaertn. usually occurs in hot, dry, and low-altitude tropical environments. The fossil record of this genus is meager, so its origin and geographic history are still poorly understood. We describe a fossil winged fruit species—Ventilago lincangensis K. N. Liu & S. P. Xie sp. nov. from the upper Miocene Bangmai Formation of Lincang city, Yunnan Province, China. The fossil conforms to the modern genus Ventilago in architecture of the prominent fruit wing including a prominent midvein, a set of minor longitudinally secondary veins extending the full length of the fruit and reticulate higher order venation. The elliptical fruit body at the base of the wing shows an equatorial rim and has a short pedicel. This is the first report of Ventilago fruits in China, and is significant for the investigation of the origin and evolutionary history of this genus.