Tree of life for the genera of Chinese vascular plants

We reconstructed a phylogenetic tree of Chinese vascular plants (Tracheophyta) using sequences of the chloroplast genes atpB, matK, ndhF, and rbcL and mitochondrial matR. We produced a matrix comprising 6098 species and including 13?695 DNA sequences, of which 1803 were newly generated. Our taxonomic sampling spanned 3114 genera representing 323 families of Chinese vascular plants, covering more than 93% of all genera known from China. The comprehensive large phylogeny supports most relationships among and within families recognized by recent molecular phylogenetic studies for lycophytes, ferns (monilophytes), gymnosperms, and angiosperms. For angiosperms, most families in Angiosperm Phylogeny Group IV are supported as monophyletic, except for a paraphyletic Dipterocarpaceae and Santalaceae. The infrafamilial relationships of several large families and monophyly of some large genera are well supported by our dense taxonomic sampling. Our results showed that two species of Eberhardtia are sister to a clade formed by all other taxa of Sapotaceae, except Sarcosperma. We have made our phylogeny of Chinese vascular plants publically available for the creation of subtrees via SoTree (http://www.darwintree.cn/flora/index.shtml), an automated phylogeny assembly tool for ecologists.     

基于孢子形态和分子证据探讨鳞盖蕨属(碗蕨科)系统分类

孢粉学是解决植物分类中疑难类群物种微形态分化的重要方法, 随着分子系统学的发展, 结合这两门学科的优势可以更加有效地解决疑难类群的分类学问题。鳞盖蕨属(Microlepia)是一个分类困难的疑难类群, 采用孢粉学与分子系统学一一对应的方法, 以及居群取样方式, 选取280份样本, 联合4个叶绿体片段(rbcL、trnL-F、psbA-trnH和rps4), 采用最大似然法和贝叶斯法构建该属的系统发生关系, 在此基础上对凭证标本中100份材料的孢子进行观察和分析。综合分子系统学和孢粉学的研究结果, 得出结论: (1) 在形态学研究中广泛被接受的15个物种得到了单系支持, 并厘清了分类困难的复合群; (2) 发现边缘鳞盖蕨(M. marginata)可能存在隐性种; (3) 建议恢复过去归并处理为异名的瑶山鳞盖蕨(M. yaoshanica)、罗浮鳞盖蕨(M. lofoushanensis)、四川鳞盖蕨(M. szechuanica)以及滇西鳞盖蕨(M. subspeluncae); (4) 提出鳞盖蕨属可能存在杂交现象; (5) 提出鳞盖蕨属完整的属下分类建议。     

石松类和蕨类植物的主要分类系统的科属比较

石松类和蕨类植物在秦仁昌（1978）系统、《中国蕨类植物科属志》、《中国植物志》、Christenhusz维管植物线性排列系统中和“FloraofChina”的科属组成、数量存在很大差异。秦仁昌（1978）系统收录63科223属,《中国蕨类植物科属志》63科226属,《中国植物志》61科220属、Chnstenhusz线性排列系统38科163属和“FloraofChina”38科177属。本文通过比较石松类和蕨类植物的几个主要分类系统中科属的变动情况,拟为新一代植物志（iFlora）中石松类和蕨类植物的编研提供依据。同时,还指出了几个主要的分类系统中关于中文名、拉丁名以及命名人的不一致和错误．为进一步研究提供检索和鉴定参考。     

香港蕨类植物分布新记录和名称修订(三)

报道了近年在香港再发现的两个属－黄腺蕨属（叉蕨科）和网藤蕨属（藤蕨科）,并对港产的黄腺蕨、有盖黄腺蕨和网藤蕨的标本和文献进行整理,及对国产的相近种类作分类处理,把钩形黄腺羽蕨和广西黄腺羽蕨归并于黄腺蕨中。此外,亦对网藤蕨进行了长期观察,证实了Holtum关于该种的叶轴顶端的形态修正。黄腺蕨属和网藤蕨属在香港的再发现,对华南蕨植物地理区系的研究具有一定的意义。由于这两属在本地均为罕见之种类,故可考虑到入得法珍稀蕨类名单之内。     

广东蕨类植物新资料

报道了2个新异名,1个新等级和35种蕨类植物在广东的分布新记录。正安肋毛蕨（Ctenitis changanensis Ching）和信宜铁角蕨（Asplenium xinyiense Ching et S.H.Wu）分别作直鳞肋毛蕨（Ctenitis eatoni (Bak.) Ching）和厚叶铁角蕨（Asplenium griffithianum Hook）的异名处理;齿翅井栏凤尾蕨（Pteris serralata（Miau）Y. H. Yan）被提升到种的等级;假芒萁属（Sticherus Presl）、柄盖蕨属（Peranema D. Don）、蛾眉蕨属（Lunathyrium Koidz.）和革舌蕨属（Scleroglossum Alderw）等4个属为广东分布新记录,小笠原卷柏（Selaginella boninensis Baker）为中国大陆分布新记录。广东现有蕨类已达到56科144属502种。     

Exploring the pteridophyte flora of the Eastern Afromontane biodiversity hotspot

In this review, we explore our current understanding of the fern and lycophyte diversity occurring in the Eastern Afromontane Biodiversity Hotspot (EABH). The review explores the species diversity of this region in the context of the Afromadagascan pteridophyte diversity based on an exhaustive species list assembled in the synopsis of Afromadagascan pteridophytes published by Roux in 2009. The list was updated by incorporating recent progress in our understanding of the taxonomy and phylogeny of these plants. Evidence for a distinct pteridophyte flora occurring in the East African mountain region was discovered using ordination and clustering analyses. This EABH floras shares links to other Afromadagascan pteridophyte floras such as the one in the tropical lowland forests of central and western Africa. These floras share the dominance of species that preferably occur in humid climates whereas other African pteridophyte floras tend to contain a higher proportion of xeric adapted ferns. The phylogenetic composition of the EABH pteridophyte flora was assessed by comparing global versus local proportion of orders, families, and genera. This analysis revealed distinct patterns that are partly caused by the radiation of Blotiella and Triplophyllum besides selective colonization of species pre-adapted to Afromadagascan climates. In situ speciation in the East African tropical mountains may have contributed to the global diversity of widespread genera such as Asplenium and Pteris. In summary, this is the first comprehensive attempt to assess the pteridophyte diversity of the East African mountains providing the framework for future studies on their conservation, ecology, and evolution.     

An updated Chinese vascular plant tree of life: Phylogenetic diversity hotspots revisited

Large‐scale phylogenies provide a framework for interdisciplinary investigations in taxonomy, evolutionary biology, biogeography, ecology, and conservation. Integration of regional tree of life and species distribution data has greatly promoted spatial phylogenetic studies on biodiversity, floristic assembly, and biogeographic regionalization. In this study, we updated the phylogenetic tree of Chinese vascular plants by integrating data from public databases and sequences newly generated by our laboratory, to facilitate the exploration of floristic and ecological questions at a country scale. A phylogenetic tree with 15 092 tips and 14 878 species was obtained, including 13 663 species (44.0%) and 2953 genera (95.7%) native to China. Only two families (Corsiaceae and Mitrastemonaceae) and 133 genera native to China are not sampled in this study. Low proportion of sampling is detected in orders with high species diversity and those with low species diversity. The Hengduan Mountains, plus the western Qinghai–Tibet Plateau and western Xinjiang, show the greatest gap of target molecular data for angiosperms. Our phylogeny of Chinese vascular plants recovers relationships among and within major lineages that are highly congruent with published phylogenies at a broader scale. Most families (98.7%) are supported as monophyletic, and 573 genera (17.9%) are recognized as non‐monophyletic. Finally, hotspots of phylogenetic diversity for the Chinese angiosperms at both the genus and species levels are identified based on our phylogram, implicating conservation priorities for phylogenetic diversity. The updated phylogeny of Chinese vascular plants is publically available to generate subtrees through our automated phylogeny assembly tool SoTree in the DarwinTree platform ( http://www.darwintree.cn/flora-sotree-v2/index.shtml ).     

Chloroplast phylogenomics resolves key relationships in ferns

Studies on chloroplast genomes of ferns and lycophytes are relatively few in comparison with those on seed plants. Although a basic phylogenetic framework of extant ferns is available, relationships among a few key nodes remain unresolved or poorly supported. The primary objective of this study is to explore the phylogenetic utility of large chloroplast gene data in resolving difficult deep nodes in ferns. We sequenced the chloroplast genomes from Cyrtomium devexiscapulae(Koidz.) Ching (eupolypod I) and Woodwardia unigemmata (Makino) Nakai (eupolypod II), and constructed the phylogeny of ferns based on both 48 genes and 64 genes. The trees based on 48 genes and 64 genes are identical in topology, differing only in support values for four nodes, three of which showed higher support values for the 48-gene dataset. Equisetum L. was resolved as the sister to the Psilotales–Ophioglossales clade, and Equisetales–Psilotales–Ophioglossales clade was sister to the clade of the leptosporangiate and marattioid ferns. The sister relationship between the tree fern clade and polypods was supported by 82% and 100% bootstrap values in the 64-gene and 48-gene trees, respectively. Within polypod ferns, Pteridaceae was sister to the clade of Dennstaedtiaceae and eupolypods with a high support value, and the relationship of Dennstaedtiaceae–eupolypods was strongly supported. With recent parallel advances in the phylogenetics of ferns using nuclear data, chloroplast phylogenomics shows great potential in providing a framework for testing the impact of reticulate evolution in the early evolution of ferns.     

河南太行山蕨类植物区系的研究

初步探讨了河南太行山蕨类植物区系的特点。该区系有蕨类植物 1 0 4种 ,隶属于 2 3科 4 8属 ,优势成分以蹄盖蕨科、鳞毛蕨科等系统演化上比较高级的类群为主。组成本区系的成分来源不同 ,以温带成分占优势 ,与河北、山西、北京地区的蕨类区系关系密切 ,与山东、秦岭、长白山、黄山、鼎湖山的相似程度渐低。这与中国现代蕨类植物地理分布规律相吻合     

中国现代石松类和蕨类的系统发育与分类系统

石松类和蕨类植物是以孢子繁殖的维管植物,在陆地植物演化上占据重要地位。随着分子系统学研究的开展,各大类群间的系统发育关系得以阐明,传统上的概念得以修正,新的现代石松类和蕨类植物的分类系统也被提出,并不断得到完善。该文介绍国内外在蕨类植物系统发育方面的研究成果,重点讨论中国分布的类群的分类处理。文中提出了一个完整的中国现代石松类和蕨类植物的分类系统,包括5亚纲、14目、39科及12亚科、约140余属。     

Phylogeny of Gastrotricha: a morphology-based framework of gastrotrich relationships

Currently, the phylum Gastrotricha is divided into the orders Macrodasyida and Chaetonotida, with the structure of the myoepithelial pharynx being an important distinguishing feature. Macrodasyida currently has six recognized families, and Chaetonotida comprises seven families. However, within-group relationships are poorly understood. To arrive at a better understanding of gastrotrich systematics and phylogeny, we performed the first cladistic analysis of nearly all known gastrotrich genera using 71 morphological characters. Results suggest that the Gastrotricha is a monophyletic group (supported by 82% of bootstrap replications) with its most primitive taxa distributed among the families Dactylopodolidae and Neodasyidae. Monophyly of Macrodasyida and Chaetonotida was supported by 90% and 52% bootstrap replications, respectively. Within the Macrodasyida, the families Dactylopodolidae, Turbanellidae, Macrodasyidae, and Thaumastodermatidae all formed monophyletic clades. The families Planodasyidae and Lepidodasyidae were paraphyletic. Among the Chaetonotida, the marine family Xenotrichulidae was monophyletic, supported by 51% of bootstrap replications. A second clade containing all freshwater families was supported by 62% bootstrap values. However, Chaetonotidae were paraphyletic. Using this analysis as a framework, we now can explore possible patterns of evolution within it, and arrive at a consensus of the gastrotrich ground pattern. Moreover, in future molecular studies of metazoan phylogeny, we will be able to select gastrotrich species that are more appropriate representatives of the phylum.     

First insights into fern matK phylogeny

MatK, the only maturase gene in the land plant plastid genome, is a very popular phylogenetic marker that has been extensively applied in reconstructing angiosperm phylogeny. However, the use of matK in fern phylogeny is largely unknown, due to difficulties with amplification: ferns have lost the flanking trnK exons, typically the region used for designing stable priming sites. We developed primers that are either universal or lineage-specific that successfully amplify matK across all fern families. To evaluate whether matK is as powerful a phylogenetic marker in ferns as in angiosperms, we compared its sequence characteristics and phylogenetic performance to those of rbcL and atpA. Among these three genes, matK has the highest variability and substitution evenness, yet shows the least homoplasy. Most importantly, applying matK in fern phylogenetics better resolved relationships among families, especially within eupolypods I and II. Here we demonstrate the power of matK for fern phylogenetic reconstruction, as well as provide primers and extensive sequence data that will greatly facilitate future evolutionary studies of ferns.     

湖北恩施地区蕨类植物区系研究

蕨类植物是森林植被中草本层的重要组成部分,对森林的生长发育有重大影响。本研究在搜集文献、野外调查和采集标本的基础上,对湖北恩施地区蕨类植物区系成分及特点进行研究。结果显示:(1)恩施地区蕨类植物共有39科96属380种,其中中国特有种106种;该地区蕨类植物起源古老,物种分化水平较高,优势科属明显、物种丰富、组成多样,是蕨类植物物种多样性的典型代表地区之一。(2)该地区稀子蕨属、荚果蕨属、黔蕨属和骨牌蕨属种类齐全、分布广泛,是这些属的分化和分布中心。(3)该地区蕨类植物生活类型齐全,以土生为主(占81.36%)。(4)恩施地区在中国蕨类植物地理区系中占有重要地位,该地区蕨类植物科属以泛热带区系成分相对较多,总体偏热带区系成分;物种以温带亚洲、东亚和中国特有分布型为主(占60.79%),具有显著的亚热带性质。(5)恩施蕨类植物区系与其他地区联系广泛,过渡性比较明显,尤其与四川地区联系紧密。     

中国粟米草科分类修订

粟米草科(Molluginaceae)隶属于石竹目,是一个分类极为困难的被子植物类群,关于该科的分类学界定在众多不同被子植物分类系统中争议颇大。在最近的分子系统学研究中,粟米草科的范围被准确界定,全球共包含11属。在此基础上对中国粟米草科类群进行了分类修订,最终确认中国产粟米草科植物5属7种,其中线叶漆姑粟草[Hypertelis umbellata (Forssk.)Thulin]为中国分布新记录种。更新了分种检索表,并提供了各属形态描述及相关物种的地理分布图。     

Evolution of the Mitochondrial Cytochrome Oxidase II Gene in Collembola

The sequence of the mitochondrial COII gene has been widely used to estimate phylogenetic relationships at different taxomonic levels across insects. We investigated the molecular evolution of the COII gene and its usefulness for reconstructing phylogenetic relationships within and among four collembolan families. The collembolan COII gene showed the lowest A + T content of all insects so far examined, confirming that the well-known A + T bias in insect mitochondrial genes tends to increase from the basal to apical orders. Fifty-seven percent of all nucleotide positions were variable and most of the third codon positions appeared free to vary. Values of genetic distance between congeneric species and between families were remarkably high; in some cases the latter were higher than divergence values between other orders of insects. The remarkably high divergence levels observed here provide evidence that collembolan taxa are quite old; divergence levels among collembolan families equaled or exceeded divergences among pterygote insect orders. Once the saturated third-codon positions (which violated stationarity of base frequencies) were removed, the COII sequences contained phylogenetic information, but the extent of that information was overestimated by parsimony methods relative to likelihood methods. In the phylogenetic analysis, consistent statistical support was obtained for the monophyly of all four genera examined, but relationships among genera/families were not well supported. Within the genus Orchesella, relationships were well resolved and agreed with allozyme data. Within the genus Isotomurus, although three pairs of populations were consistently identified, these appeared to have arisen in a burst of evolution from an earlier ancestor. Isotomurus italicus always appeared as basal and I. palustris appeared to harbor a cryptic species, corroborating allozyme data. Received: 12 January 1996 / Accepted: 10 August 1996     

Global versus Chinese perspectives on the phylogeny of the N-fixing clade

There has been increasing interest in integrating a regional tree of life with community assembly rules in the ecological research. This raises questions regarding the impacts of taxon sampling strategies at the regional versus global scales on the topology. To address this concern, we constructed two trees for the nitrogen-fixing clade: (i) a genus-level global tree including 1023 genera; and (ii) a regional tree comprising 303 genera, with taxon sampling limited to China. We used the supermatrix approach and performed maximum likelihood analyses on combined matK, rbcL, and trnL-F plastid sequences. We found that the topology of the global and the regional tree of the N-fixing clade were generally congruent. However, whereas relationships among the four orders obtained with the global tree agreed with the accepted topology obtained in focused analyses with more genes, the regional topology obtained different relationships, albeit weakly supported. At a finer scale, the phylogenetic position of the family Myricaceae was found to be sensitive to sampling density. We expect that internal support throughout the phylogeny could be improved with denser taxon sampling. The taxon sampling approach (global vs. regional) did not have a major impact on fine-level branching patterns of the N-fixing clade. Thus, a well-resolved phylogeny with relatively dense taxon sampling strategy at the regional scale appears, in this case, to be a good representation of the overall phylogenetic pattern and could be used in ecological research. Otherwise, the regional tree should be adjusted according to the correspondingly reliable global tree.