基于rbcL序列试论鸢尾属部分物种间的系统发育关系

选用叶绿体rbcL基因对鸢尾属植物的分类和系统发育进行了分析。以雄黄兰为外类群,对21份鸢尾属材料和GenBank下载的共49条序列采用最大简约法构建系统进化树,探讨了鸢尾属的分类系统。针对有争议的物种,聚类结果表明：马蔺与白花马蔺关系较远;扁竹兰和蝴蝶花亲缘关系较扇形鸢尾近;细锐果鸢尾和锐果鸢尾亲缘关系近,大锐果鸢尾较之远;四川鸢尾和薄叶鸢尾聚类近;西伯利亚鸢尾系内物种间聚类复杂,亲缘关系不清楚。     

鳞毛蕨科植物的系统发育: 叶绿体rbcL序列的证据

运用MEGA2和MrBayes 3.0b4软件包对105种鳞毛蕨类及近缘植物(其中新测定36种)的叶绿体DNA rbcL基因序列进行系统发育分析, 探讨了其主要分类群(属级水平)的系统演化关系。用最大简约法、邻接法和贝叶斯分析方法构建的系统树基本一致, 结果显示: (1)秦仁昌系统所定义的鳞毛蕨科Dryopteridaceae, 除了拟贯众属Cyclopeltis外, 均包含在两个单系群之中, 支持鳞毛蕨族Dryopterideae和耳蕨族Polysticheae的成立; 但是鳞毛蕨族还包含秦仁昌系统所定义的球盖蕨科Peranemaceae和三叉蕨科Tectariaceae肋毛蕨属Ctenitis的部分种类; 耳蕨族还包含产于美洲的Phanerophlebia属和Polystichopsis属; 确认石盖蕨属Lithostegia属鳞毛蕨族的成员, 且与复叶耳蕨属Arachniodes具有较近的亲缘关系。(2)拟贯众属与所分析的其他任何鳞毛蕨类植物的关系都比较疏远, 单独为一支。(3)秦仁昌系统所定义的球盖蕨科与肉刺蕨属Nothoperanema聚成一个分支, 属于鳞毛蕨族的成员。(4)鳞毛蕨属Dryopteris为多系类群, 耳蕨属Polystichum和贯众属Cyrtomium均为并系类群。(5)黔蕨属Phanerophlebiopsis、毛枝蕨属Leptorumohra和石盖蕨属与复叶耳蕨属构成一支; 柳叶蕨属Cyrtogonellum与Polystichum属和Cyrtomium属的部分种类聚成一支; 肉刺蕨属与球盖蕨科及鳞毛蕨属的部分种类聚成一支。对鳞毛蕨科的系统关系、球盖蕨科与鳞毛蕨科的系统关系、肋毛蕨属与鳞毛蕨科的系统关系以及中国或亚洲特有属(拟贯众属、肉刺蕨属、黔蕨属、毛枝蕨属、石盖蕨属和柳叶蕨属)的系统位置进行了讨论。     

Phylogenetic relationships within Araucariaceae based on rbcL gene sequences

Phylogenetic relationships were determined in the Araucariaceae, which are now found mainly in the Southern Hemisphere. This conifer family was well diversified and widely distributed in both hemispheres during the Mesozoic era. The sequence of 1322 bases of the rbcL gene of cpDNA was determined from 29 species of Araucariaceae, representing almost all the species of the family. Phylogenetic trees determined by the parsimony method indicate that Araucariaceae are well defined by rbcL sequences and also that the monophyly of Agathis or Araucaria is well supported by high bootstrap values. The topology of these trees revealed that Wollemia had derived prior to Agathis and Araucaria. The rbcL phylogeny agrees well with the present recognition of four sections within Araucaria: Araucaria, Bunya, Eutacta, and Intermedia. Morphological characteristics of the number of cotyledons, position of male cone, and cuticular micromorphologies were evaluated as being phylogenetically informative. Section Bunya was found to be derived rather than to be the oldest taxon. Infrageneric relationships of Agathis could not be well elucidated because there are few informative site changes in the rbcL gene, suggesting the more recent differentiation of the species as their fossil records indicate. The New Caledonian Araucaria and Agathis species each formed a monophyletic group with very low differentiation in rbcL sequences among them, indicating rapid adaptive radiation to new edaphic conditions, i.e., ultramafic soils, in the post-Eocene era.     

九子母属的系统位置：来自叶绿体rbcL序列及核核糖体ITS序列的证据

九子母属Dobinea Buch-Ham.ex D.Don是一个东亚特有属,包含贡山九子母D.vulgaris Buch-Ham.ex D.Don和羊角天麻D.delavayi(Baill.)Baill.两种,主要分布于中国两南地区.有关九子母属的系统位置长期存在争议,小同的学者曾将其归入漆树科Anacardiaceae、无忠子科sapindaceae和九子母科Podoaceae.本文基于rbcL和ITs探讨了其系统位置,结果表明,九子母属的两个种自成单系,并且是漆树科的成员.     

Phylogenetic relationships of Salix (Salicaceae) based on rbcL sequence data

Nucleotide sequences of the chloroplast-encoded rbcL gene were used to examine phylogenetic relationships of the genus Salix together with other allied genera of the family Salicaceae. Phylogenetic analyses of rbcL sequences strongly suggest the monophyly of three commonly recognized genera (Chosenia, Salix, and Toisusu). Two monophyletic groups are recognized within the larger monophyletic group. They do not correspond with any infrageneric taxa proposed so far. With regard to character evolution, it is thought that the reduction of stamen number from more than two stamens to two might occur in at least three lineages and that fused bud scales evolved several times and/or the reverse evolution occurred from fused to free. Some types of pollen surfaces are considered to have evolved independently.     

Convergent evolution of morphology and habitat use in the explosive Hawaiian fancy case caterpillar radiation

Species occurring in unconnected, but similar habitats and under similar selection pressures often display strikingly comparable morphology, behaviour and life history. On island archipelagos where colonizations and extinctions are common, it is often difficult to separate whether similar traits are a result of in situ diversification or independent colonization without a phylogeny. Here, we use one of Hawaii's most ecologically diverse and explosive endemic species radiations, the Hawaiian fancy case caterpillar genus Hyposmocoma, to test whether in situ diversification resulted in convergence. Specifically, we examine whether similar species utilizing similar microhabitats independently developed largely congruent larval case phenotypes in lineages that are in comparable, but isolated environments. Larvae of these moths are found on all Hawaiian Islands and are characterized by an extraordinary array of ecomorphs and larval case morphology. We focus on the ‘purse cases’, a group that is largely specialized for living within rotting wood. Purse cases were considered a monophyletic group, because morphological, behavioural and ecological traits appeared to be shared among all members. We constructed a phylogeny based on nuclear and mitochondrial DNA sequences from 38 Hyposmocoma species, including all 14 purse case species and 24 of non‐purse case congeners. Divergence time estimation suggests that purse case lineages evolved independently within dead wood and developed nearly identical case morphology twice: once on the distant Northwest Hawaiian Islands between 15.5 and 9 Ma and once on the younger main Hawaiian Islands around 3.0 Ma. Multiple ecomorphs are usually found on each island, and the ancestral ecomorph of Hyposmocoma appears to have lived on tree bark. Unlike most endemic Hawaiian radiations that follow a clear stepwise progression of colonization, purse case Hyposmocoma do not follow a pattern of colonization from older to younger island. We postulate that the diversity of microhabitats and selection from parasitism/predation from endemic predators may have shaped case architecture in this extraordinary endemic radiation of Hawaiian insects.     

Molecular Phylogeny of Rhizophoraceae Based on rbcL Gene Sequences

rbcL sequences to clarify the inter- and intrarelationships of Rhizophoraceae which have been variously discussed. The analyses included 12 of the 15 genera of Rhizophoraceae (4/7 of Macarisieae, 4/4 of Gynotrocheae, and 4/4 of Rhizophoreae) and a few putatively related taxa, including two of the four genera of Anisophylleaceae. The most parsimonious trees supported the monophyly of Rhizophoraceae as well as each of the three traditionally recognized tribes Macarisieae, Gynotrocheae, and Rhizophoreae. The family Rhizophoraceae is a sister taxon to Erythroxylum (Erythroxylaceae) and is further closely related to Byrsonima (Malpighiaceae), Passiflora (Passifloraceae), Turnera (Turneraceae), Ochna (Ochnaceae), Drypetes (Euphorbiaceae), and Humiria (Humiriaceae). Anisophylleaceae, which have often been included in Rhizophoraceae as a tribe or subfamily, are placed in a common clade with Begonia (Begoniaceae), Cucurbita (Cucurbitaceae), Coriaria (Coriariaceae), Corynocarpus (Corynocarpaceae), Datisca (Datiscaceae), Tetrameles (Datiscaceae), and Octomeles (Datiscaceae). Within Rhizophoraceae the mangrove tribe Rhizophoreae is sister to the inland tribe Gynotrocheae, with inland tribe Macarisieae positioned as a sister taxon to these two tribes. This pattern of relationships within the family basically agrees with those suggested by cladistic analyses based on morphological characters, except that Gynotrocheae are monophyletic with Crossostylis as a derived taxon within the tribe in the present study. Based on this cladogram for Rhizophoraceae, we discuss evolutionary trends of a few ecological and morphological characters, including the formation of aerial roots and the ovary position. Received 12 August 1999/ Accepted in revised form 11 October 1999     

Molecular Phylogeny of Casuarinaceae Based on rbcL and matK Gene Sequences

rbcL (1310 bp) and matK (1014 bp), using 15 species representing the family. The study included analyses of Ticodendron (Ticodendraceae) and three species of Betulaceae as close relatives, and one species each of Juglandaceae and Myricaceae as outgroups. Analyses based on matK gene sequences, which provided a much better resolution than the analyses based on rbcL gene sequences alone, resulted in a single most parsimonious tree whose topology is almost identical with the strict consensus tree generated by the combined data set of rbcL and matK gene sequences. Results showed that Casuarinaceae are monophyletic, comprising four distinct genera, Allocasuarina, Casuarina, Ceuthostoma and Gymnostoma, which were not recognized until recently. Within the family, Gymnostoma is positioned at the most basal position and sister to the remainder. Within the remainder Ceuthostoma is sister to the Allocasuarina-Casuarina clade. Morphologically the basalmost position of Gymnostoma is supported by plesiomorphies such as exposed stomata in the shallow longitudinal furrows of the branchlets, a basic chromosome number x=8 and the gynoecium composed of two fertile, biovulate carpels. The three other genera, Allocasuarina, Casuarina, and Ceuthostoma, have invisible stomata in the deep longitudinal furrows of the branchlets, a higher basic chromosome number x=9 or 10–14 (unknown in Ceuthostoma), the gynoecium composed of one fertile and one sterile carpel with a single ovule (unknown in Ceuthostoma). The diversity of infructescence morphology found in the latter three genera suggests that they may have evolved in close association with the elaboration of fruit dispersal mechanisms. Received 14 September 2001/ Accepted in revised form 12 October 2001     

Phylogenetic position of the genus Dobinea: Evidence from nucleotide sequences of the chloroplast gene rbcL and the nuclear ribosomal ITS region

Dobinea Buch.-Ham. ex D. Don, a genus with two species endemic to east Asia, has been placed in three different families, the Podoaceae, tribe Acerineae of the Sapindaceae, and tribe Dobineeae of the Anacardiaceae. In this paper, phylogenetic relationships of the genus were examined based on DNA sequences of the chloroplast rbcL gene and the ITS region of nuclear ribosomal DNA. Our data support the monophyly of Dobinea and its placement in the Anacardiaceae.     

用叶绿体rbcL和rps4-trnS区序列确定亚洲特有单型属——篦齿蕨属的系统位置

篦齿蕨属Metapolypodium Ching是亚洲大陆特有植物, 仅含篦齿蕨Metapolypodium manmeiense (Christ) Ching 1种, 分布于中国西南及其邻近地区, 其系统位置一直是一个有待解决的问题。本文用叶绿体rbcL和rps4-trnS区序列探讨篦齿蕨属的系统位置。我们对篦齿蕨及其近缘类群的叶绿体rbcL和rps4-trnS区进行PCR扩增和序列测定。用最大简约法、邻接法和贝叶斯推断法对自测序列结合由GenBank下载的rbcL和rps4-trnS区序列进行独立和联合的系统发育分析, 所构建的系统发生树的拓扑结构基本一致。结果显示: 篦齿蕨属与多足蕨属Polypodium L. emend. Ching的关系较疏远, 而与水龙骨属Polypodiodes Ching和拟水龙骨属Polypodiastrum Ching的成员聚成一个支系, 与栗柄水龙骨Polypodiodes microrhizoma (C. B. Clarke ex Baker) Ching的关系最近。根据本文的研究结果, 我们赞成秦仁昌1978年的分类系统, 即分别承认多足蕨属、篦齿蕨属、水龙骨属、拟水龙骨属和棱脉蕨属Schellolepis J. Sm.为独立的类群。根据分子系统学证据, 宜将栗柄水龙骨转移到篦齿蕨属中。     

中国沿海浒苔属rbcL和ITS序列比较及系统进化分析

为阐明中国沿海浒苔的亲缘关系及地理分布特点,采集青岛栈桥、盐城弶港、宁波象山、温州平阳四地浒苔样本,克隆测序得到ITS1、5.8SrDNA和ITS23种不同长度序列片段。四个地区的rbcL目的片段,长度均为1201bp。分析核苷酸差异和遗传距离,采用邻接法建立系统发生树。结果显示,ITS序列进化速率较快,rbcL序列相当保守。ITS区较短,GC含量均在65%以上,5.8SrDNA的CG含量在50%左右,ITS1区的序列差异大于ITS2区。四个地区的浒苔存在一定的地理差异,盐城和青岛的样本间的亲缘关系较近;宁波和温州的样本间的亲缘关系较近。石莼属(Ulva)和浒苔属(Enteromorpha)的物种没有聚成各自独立的分枝,而是相互混合在一起,应是两个亲缘关系相近的属。引起青岛绿潮的海藻很可能是来自盐城海域的Enteromorpha linza或Enteromorpha prolifera。     

Phylogeny of Osmundaceae Inferred from rbcL Nucleotide Sequences and Comparison to the Fossil Evidences

rbcL sequences of 11 of 15 extant species of Osmundaceae which represent all three genera, Osmunda, Todea and Leptopteris. Our phylogenetic analysis concluded: 1) Osmunda subg. Osmunda and subg. Plenasium are monophyletic groups, but subg. Osmundastrum is not. The genus Osmunda is not monophyletic because Todea and Leptopteris are positioned within Osmunda. 2) Osmunda cinnamomea is the most basally positioned species in Osmundaceae, and it can be called as “a living fossil” because a fossil species (O. claytoniites) with almost the same morphology as this species was recorded from the Triassic. 3) Osmunda japonica and O. regalis are very closely related with only one nucleotide difference in the rbcL gene. 4) Greater nucleotide variation (5–7 nucleotides) was found between conspecific samples of O. cinnamomea and O. claytoniana collected from Japan and United States. Each of these two species may comprise more than two biologically differentiated species. Received 7 July 1999/ Accepted in revised form 25 August 1999     

Phylogenetic position of Dunaliella acidophila (Chlorophyceae) based on ITS and rbcL sequences

Dunaliella acidophila is one of the most extreme acidophiles on earth and is able to survive in highly acidic habitats. This characteristic has made this organism the universal model for the study of abiotic stress. Although D. acidophila is currently circumscribed to the subgenus Pascheria within Dunaliella Teodoresco (Chlorophyceae), its taxonomic position has stirred controversy. The comparison of D. acidophila CCAP19/35 internal transcribed spacers (including ITS2 secondary structure analysis) and RuBisCo large subunit (rbcL) sequences with other Dunaliella species confirms that D. acidophila should maintain its phylogenetic position within the genus Dunaliella, suggesting its inclusion within the subgenus Dunaliella. Furthermore, the ITS1 and ITS2 data revealed that D. acidophila was highly divergent from the other freshwater species assessed, D. lateralis, with which it barely shares a 56.8% similarity.     

Phylogenetic relationships of Eurasian pines (Pinus, Pinaceae) based on chloroplast rbcL, MATK, RPL20-RPS18 spacer, and TRNV intron sequences

The sequence divergence of chloroplast rbcL, matK, trnV intron, and rpl20-rps18 spacer regions was analyzed among 32 Pinus species and representatives of six other genera in Pinaceae. The total aligned sequence length is 3570 bp. Of the four sequences examined, matK evolved much faster than rbcL in Pinus and in other Pinaceae genera. The two noncoding regions did not show more divergence than the two coding regions, especially within each Pinus subgenus. Phylogenetic analyses based on these four sequences gave consistent results and strongly supported the monophyly hypothesis for the genus Pinus and its two recognized subgenera. Pinus krempfii, the two-flat-needle pine endemic to Vietnam, was placed in subgen. Strobus and showed closer affinity to subsect. Gerardianae. The ancient character of sect. Parrya is further confirmed. However, monophyly of the sect. Parrya is not supported by our data. Among the Eurasian pines of subgen. Pinus, Mediterranean pines formed one clade and the Asian members of subsect. Sylvestres formed another. The Himalayan P. roxburghii showed considerable divergence from all the other hard pines from both regions. Pinus merkusii was distinctly separated from all the Asian members of subsect. Sylvestres. The implications of our results for Pinus classification are discussed.     

New evidence of ectomycorrhizal fungi in the Hawaiian Islands associated with the endemic host Pisonia sandwicensis (Nyctaginaceae)

Ectomycorrhizal plants and fungi are ubiquitous in mainland forests, but because of dispersal limitations are predicted to be less common on isolated islands. For instance, no native ectomycorrhizal plants or fungi have ever been reported from Hawaii, one of the most remote archipelagos on Earth. Members of the plant tribe Pisonieae are common on many islands, and prior evidence shows that some species associate with ectomycorrhizal fungi. However, until now, the Pisonieae species of Hawaii had yet to be examined for their mycorrhizal status. Here we sampled roots from members of the genus Pisonia growing on the Hawaiian islands of Oahu, Maui and Hawaii. We used molecular and microscopic techniques to categorize trees with respect to their mycorrhizal associations. We report that the Hawaiian endemic Pisonia sandwicensis forms ectomycorrhizas with at least five fungal operational taxonomic units (corresponding closely to species) belonging to four genera. We also report that this tree species is monophyletic with other ectomycorrhizal Pisonia species. We suggest that in light of the newly discovered Hawaiian ectomycorrhizal fungal community and other island ectomycorrhizal communities, dispersal limitations do not prevent the colonization of remote islands by at least some ectomycorrhizal fungi.     

Extinction patterns in the avifauna of the Hawaiian islands

Through the continuing accumulation of fossil evidence, it is clear that the avifauna of the Hawaiian Islands underwent a large‐scale extinction event around the time of Polynesian arrival. A second wave of extinctions since European colonization has further altered this unique avifauna. Here I present the first systematic analysis of the factors characterizing the species that went extinct in each time period and those that survived in order to provide a clearer picture of the possible causal mechanisms. These analyses were based on mean body size, dietary and ecological information and phylogenetic lineage of all known indigenous, non‐migratory land and freshwater bird species of the five largest Hawaiian Islands. Extinct species were divided into ‘prehistoric’ and ‘historic’ extinction categories based on the timing of their last occurrence. A model of fossil preservation bias was also incorporated. I used regression trees to predict probability of prehistoric and historic extinction based on ecological variables. Prehistoric extinctions showed a strong bias toward larger body sizes and flightless, ground‐nesting species, even after accounting for preservation bias. Many small, specialized species, mostly granivores and frugivores, also disappeared, implicating a wide suite of human impacts including destruction of dry forest habitat. In contrast, the highest extinction rates in the historic period were in medium‐sized nectarivorous and insectivorous species. These differences result from different causal mechanisms underlying the two waves of extinction.     

Phylogenetic relationships of Cornaceae and close relatives inferred from matK and rbcL sequences

Phylogenetic relationships were inferred using nucleotide sequences of the chloroplast gene matK for members of Cornales, a well-supported monophyletic group comprising Cornaceae and close relatives. The shortest trees resulting from this analysis were highly concordant with those based on previous phylogenetic analysis of rbcL sequences. Analysis of a combined matK and rbcL sequence data set (a total of 2652 bp [base pairs]) provided greater resolution of relationships and higher internal support for clades compared to the individual data sets. Four major clades (most inclusive monophyletic groups) of Cornales are indicated by both sets of genes: (1) Cornus-Alangium, (2) nyssoids (Nyssa-Davidia-Camptotheca)- mastixioids (Mastixia, Diplopanax), (3) Curtisia, and (4) Hydrangeaceae-Loasaceae. The combined evidence indicates that clades 2 and 3 are sisters, with clade 4 sister to the remainder of Cornales. These relationships are also supported by other lines of evidence, including synapomorphies in fruit and pollen morphology and gynoecial vasculature. Comparisons of matK and rbcL sequences based on one of the most parsimonious rbcL-matK trees indicate that matK has a much higher A-T content (66.9% in matK vs. 55.8% in rbcL) and a lower transition:transversion ratio (1.23 in matK vs. 2.21 in rbcL). The total number of nucleotide substitutions per site for matK is 2.1 times that of rbcL in Cornales. These findings are similar to recent comparisons of matK and rbcL in other dicots. Variable sites of matK are almost evenly distributed among the three codon positions (1.0:1.0:1.3), whereas variable sites of rbcL are mostly at the third position (1.8:1.0 :7.5). Among- lineages rates of nucleotide substitutions in rbcL are basically homogeneous throughout Cornales, but are more heterogeneous in matK.     

金粉蕨属的分子系统学研究——基于5种叶绿体DNA序列片段

金粉蕨属（Onychium Kaulfuss）隶属广义凤尾蕨科中的凤尾蕨亚科。迄今为止,该属属下分组及种间界定等仍有诸多问题亟待解决。本研究选取5个叶绿体DNA 序列片段 （rbcL/atpA/matK/trnL-trnF/trnG-trnR）,采用最大似然法（ML）和贝叶斯法（BI）构建金粉蕨属的系统发育树。结果表明：（1）金粉蕨属的9个成员被分置于两大支上。其中野雉尾金粉蕨（Onychium japonicum(Thunberg) Kunze）、西藏金粉蕨（O.tibeticum Ching & S.K.Wu）、木坪金粉蕨（O.moupinense Ching）、湖北金粉蕨（O.moupinense var. ipii(Ching) K.H.Shing）、栗柄金粉蕨（O.japonicum var. lucidum(D.Don) Christ）、黑足金粉蕨（O.cryptogrammoides Christ）、繁羽金粉蕨（O.plumosum Ching）聚为一支;而金粉蕨（O.siliculosum(Desvaux) C.Christensen）和蚀盖金粉蕨（O.tenuifrons Ching）则聚为另一支,可为该属的属下分组提供分子系统学证据;（2）野雉尾金粉蕨与栗柄金粉蕨在系统树中并没有聚在一起,而是被其它类群分割开来,不支持将后者作为野雉尾金粉蕨的变种,建议将栗柄金粉蕨提升为种的等级;（3）系统树上木坪金粉蕨与湖北金粉蕨的样本聚在一个细支上,支持《中国植物志》将湖北金粉蕨作为木坪金粉蕨变种的分类处理;（4）西藏金粉蕨与野雉尾金粉蕨聚在一起,并得到较高的支持,说明两者的关系近缘。     

线蕨属（水龙骨科）的系统发育研究：来自叶绿体rbcL和rps4-trnS序列的证据

线蕨属Colysis 植物主要分布于亚洲热带和亚热带地区,少数种类分布至非洲、澳大利亚(昆士兰)及新几内亚地区.自1849年成立以来,线蕨属的分类范畴和系统位置一直有待确定.本文利用叶绿体基因组的rbcL、rps4基因和rps4-trnS基凶间隔区序列,运用最大简约法和贝叶斯方法分析了线蕨属及其近缘类群的系统演化关系.研究结果显示:(1)线蕨属和薄唇蕨属Leptochilus(含似薄唇蕨属Paraleptochilus)组成一个支持率很高的单系分支(C-L Clade),但是薄唇蕨属的成员位于线蕨属的不同支系内,支持线蕨属和薄唇蕨属合并为一个属;(2)瘤蕨属Phymatosorus单独形成一个单系分支;(3)星蕨属Microsorum是一个多系类群,除Microsorium linguiforme、M.varians和M.pustulatum与马来群岛的Lecanopteris聚在一起外,其他的星蕨属成员均位于不同的支系上.本文的系统发育分析结果为线蕨属和薄唇蕨属的分类处理提供了分子系统学的证据.