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     

Systematic affinities of Rhizophoraceae and Anisophylleaceae, and intergeneric relationships within Rhizophoraceae, based on chloroplast DNA, nuclear ribosomal DNA, and morphology

A cladistic analysis of sequences from the chloroplast gene rbcL was used to determine the systematic affinities of Rhizophoraceae and Anisophylleaceae. This analysis rejects close relationships of Rhizophoraceae with Celastraceae or Elaeocarpaceae, suggested previously, and identifies Erythroxylaceae as sister group within the Malpighiales, supported by several morphological and anatomical characters. Our molecular results also indicate that Anisophylleaceae are nested within Cucurbitales. Although this placement is novel, this affinity is also well supported by shared morphological characters. Tribal and generic relationships within Rhizophoraceae are evaluated with a combination of six molecular data sets (rbcL, atpB-rbcL intergenic spacer, trnL-trnF intergenic spacer, ITS1, ITS2, and 5.8S) and a morphological data set. These relationships are compared with results from previous morphological cladistic analyses. Against the background of the molecular results, we briefly discuss the evolution of morphological characters traditionally used for tribal subdivision as well as characters presumably significant for adaptation to mangrove habitats, namely, aerial stilt roots and vivipary.     

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     

基于叶绿体trnL-F,rbcL序列和核核糖体ITS序列探讨蓼属（蓼科）头状蓼组的系统发育

选用叶绿体基因trnL-F,rbc-L序列和核核糖体ITS序列对蓼属头状蓼组的分类和系统发育进行了分析。以药用大黄为外类群,用最大简约法对3个片段的单独和联合矩阵分别构建系统发育树。结果表明,头状蓼组是一个较自然的类群,与春蓼组、刺蓼组和金线草属的亲缘关系较近;支持头状蓼组作为一组放在春蓼属,细茎蓼和蓝药蓼从头状蓼组转移至冰岛蓼属;不支持将刺蓼组并入头状蓼组;对于小叶蓼的系统学位置有待于进一步研究。     

基于线粒体控制区序列的猕猴属系统发育研究

通过线粒体部分控制区DNA序列数据探讨7种猕猴属物种的分子系统发育关系。结果表明熊猴的核苷酸多样度最高,而藏酋猴核苷酸多样度较低。基于控制区序列数据所构建的最大似然树,不考虑食蟹猴的位置,7种猕猴物种可粗略地分为3个种组,即狮尾猴组(包括北平顶猴)、头巾猴组(包括红面猴、熊猴和藏酋猴)和食蟹猴组(包括恒河猴和台湾猴)。与前人(Fooden＆Lanyon,1989;Tosi et al,2003a;Deinard＆Smith,2001;Evans et al,1999;Hayasaka et al,1996;Morales＆Melnick,1998)的结果不同,我们的结果支持食蟹猴比北平顶猴分化早的假设;东部恒河猴(相对于台湾猴)和东部熊猴(相对于藏酋猴)出现并系。与Y染色体、等位酶、核基因以及部分形态学数据推测的结果(Delson,1980;Fooden＆Lanyon。1989;Fooden,1990;Tosi et al,2000,2003a,b;Deinard＆Smith,2001)一致,红面猴应归于头巾猴组,但此结论与前人(Hayasaka et al,1996;Morales＆Melnick,1998;Tosi et al,2003a)依据线粒体得到的结果有较大分歧。     

Molecular Phylogeny of the Suborder Leucodontineae (Musci; Leucodontales) Inferred from rbcL Sequence Data

rbcL sequence data (1324 bp on average). Our analyses indicate (1) that Antitrichia is distantly related to the other members of Leucodontaceae and should be excluded from the family, (2) that Cryphaeaceae form a monophyletic clade, not with Anomodontaceae and Leptodontaceae, but with Leucodontaceae, refuting the placement of Leucodontaceae and Cryphaeaceae in different superfamilies, (3) that Forsstroemia, variously classified in Leucodontaceae, Cryphaeaceae or Leptodontaceae, forms a monophyletic clade with Neckera (Neckeraceae), and (4) that the presumed monophyly of Anomodon and that of Anomodontaceae are not supported. Received 18 September 1999/ Accepted in revised form 27 December 1999     

Molecular phylogeny of mangroves VIII: Analysis of mitochondrial DNA variation for species identification and relationships in Indian mangrove Rhizophoraceae

Ten species belonging to four genera of the mangrove tribe Rhizophoreaefound in the Indian subcontinent were analysed for species identification andgenetic relationship using nine mitochondrial gene probes. RFLP patternobservedwith 27 probe enzyme combinations the genera Rhizophora,Bruguiera, Ceriops andKandelia differentiated these species into three classesofmitotypes with further resolution within them. Clustering of these mitotypesindicated that Rhizophora was more closely related toCeriops-Kandelia than to theBruguiera. Though the component species of each genusclustered together, a high degree of heterogeneity was observed among fourspecies of the genus Rhizophora and three species of genusBruguiera. The variation between two species ofCeriops was minimal. Species-specific profiles wereobserved for all the species in some probe-enzyme combination. Though themonotypic genus Kandelia shared a number of loci withgenusCeriops, it remained distinct. The putative parents of thenaturally occuring interspecific hybrid in Pichavaram were reconfirmed to beR. apiculata and R. mucronata. Theresults are discussed with regard to the taxonomic and phylogeneticrelationships between different species and genera of the tribe Rhizophoreae.     

基于三个DNA片段讨论菖蒲科的分子系统学

菖蒲属长期以来被置于天南星科,但近年来分子系统学的研究表明菖蒲属与天南星科的关系较远,应成立一个单型科,即菖蒲科（Acoraceae)。本文选择菖蒲科3个种及1个变种即金钱蒲（Acorus gramineus),石菖蒲（A.ttrinowii)。金边菖蒲（A.tatarinowii),金边菖蒲（A.tatarinowii var.flawo-marginatus)和菖蒲（A.calamus)不同染色体倍性的4个居群进行了核糖体RNA内源转录间隔段（ITS）进行测序。并据此讨论了菖蒲属的属下系统关系,结果表明,菖蒲科为一个自然的单系类群,不同倍性的菖蒲构成一个自展数据支持率为100%的分支,无中肋的金钱蒲,石菖蒲和金边石菖蒲构成另一个自展数据支持率为100%的分支,通过比较分析菖蒲科与其相关类群之间18S和rbcL两段DNA序列,对菖蒲科的系统位置进行了讨论,在基于18S和rbcL的系统树中,菖蒲均处于单子叶植物中较为孤立的位置。     

从rbcL序列探讨单室茱萸属的系统位置

为了探讨单室茱萸属Mastixia的系统位置,本文对八蕊单室萸（Mastixia euony moides),云南单室茱萸（M.pentandra subsp,chinensis)及近缘物种云南紫树（Nyssa yunnanensis)和毛八角枫（Alangium kurzii)的cpDNA中编码1,5－二磷酸核酸糖羧化酶大亚基的rbcL基因序列进行了双脱氧测定。通过对这些序列与广义山茱萸科Cornaceae和Mastixia曾被归入的科的类群的rbcL序列进行PAUP（Phylogenetic Analysis Using Parsimony)分析,得到24棵最简约的分支树图。PAUP分析表明单室茱萸属与马蹄参属Diplopanax,紫树属Nyssa,喜树属Camptotheca和珙桐属Davidia的亲缘关系最近,并由分支图支持可以将Mastixia提升为山茱萸目Cornales中的一个科－单室萸科Masstixiaceae。     

百合目叶绿体rbcL基因核苷酸替代速率检测

分析了百合目主要类群叶绿体中编码核酮糖1,5二磷酸羧化氧化酶大亚基rbcL基因的42条序列,使用RRTree相对速率检测方法,详细研究rbcL基因在百合目7科间同义替代速率和非同义替代速率的变化.相对速率检测显示:百合目内秋水仙科(Colchicaceae)的同义替代速率和非同义替代速率均最快,金梅草科(Campynemat-aceae)同义替代速率最慢,百合科(Liliaceae)的非同义替代速率最慢,但在百合目各科间,无论同义替代速率还是非同义替代速率差异均不显著.     

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。     

基于5.8SrDNA序列论三白草科的系统发育

三白草科（Saururaceae)是古草本的一个核心类群,它的研究对被子植物起源和早期演化具有重要意义,本文采用最大简约法（maximum parsimony method)和邻接法（neighbor-joining method)等不同的分析方法,对三白草科及其外类群齐头绒（Zippelia begoniaefolia Blume)的5.85rDNA序列进行分析,得到一致的结论：Anemopsis最早从三白草科中分离出来,Saururus chinensis和S.cernuus是一对姐群,由于5.85rDNA序列的变异位点和信息位点相对比较少,Gymnotheca chinensis-G.involucrata-Houttuynia-Saururus之间难以通过5.8SrDNA序列的比较进行分辨。     

用细胞色素b部分序列研究斑马鱼的分子分类与系统发育

用细胞色素b特异性引物,对长尾斑马鱼、短尾斑马鱼、豹纹斑马鱼、食蚊鱼和青石斑鱼的总DNA进行PCR扩增、克隆、测序后与Genbank数据库的团头鲂、青鲻鱼、草鱼、金桔鱼的细胞色素6基因同源序列进行序列比较。结果显示,长度为426bp的细胞色素b同源序列的平均碱基组成是：26．7％A,26．1％c．16．6％G．30．5％T,密码子第三位点的碱基组成存在较大的偏倚,G的含量仅占6．4％。长尾斑马鱼、短尾斑马鱼和豹纹斑马鱼之间细胞色素b DNA序列变异很小,相似性高于99%。NJ法构建的分子系统树表明：豹纹斑马鱼先与长尾斑马鱼聚在一起,再与短尾斑马鱼聚为一组。本研究结果支持Frankel和David等人认为豹纹斑马鱼应该是Danio rerio的一个亚种,而不是单独的一个种的观点。     

Phylogenetic position of the Hawaiian geraniums based on rbcL Sequences

The seven currently recognized species of Geranium endemic to the Hawaiian Islands are unusual in their shrubby or arborescent habit and unlobed, parallel-veined leaves rather than the palmately cleft or lobed leaves and herbaceous habit typical of the genus. Their placement within the genus and their biogeographic source have been obscured by this morphological distictiveness and the limited resolution of relationships on the basis of morphology in the very speciose subgenus Geranium. Phylogenetic analysis of rbcL gene sequences provides strong support for the monophyly of the Hawaiian group, and indicates that the Hawaiian clade is deeply nested within section Geranium rather than comprising a separate section. The continental relatives studied to date with the greatest similarity in sequence to the Hawaiian group are native to the Americas rather than Asia or the Pacific. The Hawaiian species are extremely similar to one another in rbcL sequence, while the tree topology obtained is consistent with a basal position for Geranium arboreum within the group.     

利用CoI基因序列对雀科鸟类的分子系统发育关系初探

基于线粒体DNA(mtDNA)中Col基因的部分序列(1300bp)对雀形目雀科(Fringillidae)36种鸟类进行系统发育分析.对数据集构建NJ树、Baycs树和ML树.对建树结果进行分析,发现铁爪鸦(Calcarius lapponicus)与鸦属(Emberiza)鸟类的亲缘关系比其他雀科的鸟类更近;支持蓝鹀(Latoucheornis siemsseni)隶属于鹀属的观点:证实了黄颈拟蜡嘴雀(Mycerobas affinis)与黑尾蜡嘴雀(Eophona migratorius)之间紧密的亲缘关系;发现长尾雀(Uragus sibiricus)和朱鸦(Urocynchramus pylzowi)之间亲缘关系很远,而与朱雀属(Carpodacus)有较近的亲缘关系:结果支持雀类与鸦类的亚科级分类水平.     

Molecular Phylogeny of Magnolia (Magnoliaceae) Inferred from cpDNA Sequences and Evolutionary Divergence of the Floral Scents

Magnolia (disjuncts), however, have similar chemical profiles. A molecular phylogeny of Magnoliaceae was constructed to reveal phylogenetic relationships of taxa by sequencing the trnK intron (including the matK coding region), psbA-trnH, and atpB-rbcL intergenic spacer regions of chloroplast DNA from 25 Magnolia, two Michelia, and two Liriodendron taxa. The psbA-trnH spacer region showed twice the sequence divergence (0.0157) of the trnK intron (0.0073) or the matK coding region (0.0077). The strict consensus tree constructed from the combined data set (ca. 3,700 bp) indicated the genus Magnolia was polyphyletic containing Michelia species as ingroup. The clade of Magnolia liliifera var. obovata, M. coco, and M. delavayi formed the first branch. Among the remaining species, two additional large clades were recognized, i.e., one comprised of American evergreen Magnolia species and another of subgenus Yulania. The relationship among sect. Rytidospermum taxa was not clearly resolved. Parsimonious mapping of the floral scent chemical characters was performed onto the molecular phylogenetic tree to discuss evolutionary trends of the floral scent chemistries. Received 7 December 1998/ Accepted in revised form 18 May 1999     

缘管浒苔Rubisco酶大亚基基因编码序列rbcL克隆及分析

主要对缘管浒苔光合作用第一关键酶Rubisco大亚基基因(rbcL)进行了克隆分离.首先通过PCR特异性扩增叶绿体基因编码的缘管浒苔大亚基编码序列rbcL部分基因序列(1035 bp).依据基因步移原理,首次克隆得到缘管浒苔rbcL5'上游非翻译区序列(224 bp).据推测,rbcL 5'上游非翻译区序列存在类似原核生物的启动子元件-10区(TAAAAT)和-35区(TTGAAA).此外,依据3'-RACE(cDNA末端快速扩增技术)原理,克隆得到缘管浒苔rbcL3'末端cDNA序列(579 bp).     

基于线粒体COI基因探讨鹟亚科部分属和种的分类地位

采用PCR扩增、测序的方法,对鹟亚科(Muscicapinae)6属16种鸟类的线粒体COI基因序列1176bp进行测定,并以荒漠伯劳和发冠卷尾作为外群构建Bayes、ML、MP3棵系统发育树。结果支持:寿带属(Terpsiphone)、扇尾鹟属(Rhipidura)、方尾鹟属(Culicicapa)3属与鹟亚科其他鸟类亲缘关系较远,扇尾鹟属与方尾鹟属亲缘关系较近;鹟属(Muscicapa)为单系发生,本研究结果未能确定它与仙鹟属、姬鹟属的进化关系;铜蓝鹟(Muscicapa thalassina)从鹟属中移出,归入仙鹟属。上述结论解决了鹟亚科部分属间的进化关系,为鹟亚科分类系统的研究提供了分子水平证据。     

Phylogeny of Plastids Based on Cladistic Analysis of Gene Loss Inferred from Complete Plastid Genome Sequences

Based on the recent hypothesis on the origin of eukaryotic phototrophs, red algae, green plants, and glaucophytes constitute the primary photosynthetic eukaryotes (whose plastids may have originated directly from a cyanobacterium-like prokaryote via primary endosymbiosis), whereas the plastids of other lineages of eukaryotic phototrophs appear to be the result of secondary or tertiary endosymbiotic events (involving a phototrophic eukaryote and a host cell). Although phylogenetic analyses using multiple plastid genes from a wide range of eukaryotic lineages have been carried out, some of the major phylogenetic relationships of plastids remain ambiguous or conflict between different phylogenetic methods used for nucleotide or amino acid substitutions. Therefore, an alternative methodology to infer the plastid phylogeny is needed. Here, we carried out a cladistic analysis of the loss of plastid genes after primary endosymbiosis using complete plastid genome sequences from a wide range of eukaryotic phototrophs. Since it is extremely unlikely that plastid genes are regained during plastid evolution, we used the irreversible Camin-Sokal model for our cladistic analysis of the loss of plastid genes. The cladistic analysis of the 274 plastid protein-coding genes resolved the 20 operational taxonomic units representing a wide range of eukaryotic lineages (including three secondary plastid-containing groups) into two large monophyletic groups with high bootstrap values: one corresponded to the red lineage and the other consisted of a large clade composed of the green lineage (green plants and Euglena) and the basal glaucophyte plastid. Although the sister relationship between the green lineage and the Glaucophyta was not resolved in recent phylogenetic studies using amino acid substitutions from multiple plastid genes, it is consistent with the rbcL gene phylogeny and with a recent phylogenetic study using multiple nuclear genes. In addition, our analysis robustly resolved the conflicting/ambiguous phylogenetic positions of secondary plastids in previous phylogenetic studies: the Euglena plastid was sister to the chlorophycean (Chlamydomonas) lineage, and the secondary plastids from the diatom (Odontiella) and cryptophyte (Guillardia) were monophyletic within the red lineage.     

Phylogenetic relationships of Combretoideae (Combretaceae) inferred from plastid,nuclear gene and spacer sequences

Phylogenetic relationships of the subfamily Combretoideae (Combretaceae) were studied based on DNA sequences of nuclear ribosomal internal transcribed spacer (ITS) regions, the plastid rbcL gene and the intergenic spacer between the psaA and ycf3 genes (PY-IGS), including 16 species of eight genera within two traditional tribes of Combretoideae, and two species of the subfamily Strephonematoideae of Combretaceae as outgroups. Phylogenetic trees based on the three data sets (ITS, rbcL, and PY-IGS) were generated by using maximum parsimony (MP) and maximum likelihood (ML) analyses. Partition-homogeneity tests indicated that the three data sets and the combined data set are homogeneous. In the combined phylogenetic trees, all ingroup taxa are divided into two main clades, which correspond to the two tribes Laguncularieae and Combreteae. In the Laguncularieae clade, two mangrove genera, Lumnitzera and Laguncularia, are shown to be sister taxa. In the tribe Combreteae, two major clades can be classified: one includes three genera Quisqualis, Combretum and Calycopteris, within which the monophyly of the tribe Combreteae sensu Engler and Diels including Quisqualis and Combretum is strongly supported, and this monophyly is then sister to the monotypic genus Calycopteris; another major clade includes three genera Anogeissus, Terminalia and Conocarpus. There is no support for the monophyly of Terminalia as it forms a polytomy with Anogeissus. This clade is sister to Conocarpus. Electronic Publication