基于叶绿体TrnL- F序列和联合数据分析木通科的分子系统发育(英文)

基于叶绿体trnL_F序列单独分析以及trnL_F和rbcL序列联合分析重建了木通科的分子系统发育。本研究的系统发育拓扑结构与覃海宁和塔赫他间的族划分系统非常一致。猫儿屎族和串果藤族在系统发育树上位于本科的基部。由分布于南美的勃奎拉藤属和拉氏藤属组成的拉氏藤族得到了trnL_F序列分析 (10 0 % )和联合序列分析 (99% )的很好支持。木通族在两个分析里都得到了 10 0 %的靴带支持率。新建立的长萼木通属在trnL_F树上嵌套在木通属内 ;然而 ,在联合分析的树上 ,它与木通属形成姐妹群并得到很高的支持率。在系统发育上关系密切的 3个属 :牛藤果属、八月瓜属和野木瓜属之间的关系仍未解决。牛藤果与八月瓜在两个分析里都形成姐妹群 ,但支持率低。小花鹰爪枫嵌套在野木瓜属内 ,并与西南野木瓜形成姐妹群。木通族内这 3个属可能都不是单系 ,它们的属间界限和属的界定需要更多的分子和形态数据的进一步研究。     

PHYLOGENETIC RELATIONSHIPS OF THE BROWN ALGAL ORDERS ECTOCARPALES, CHORDARIALES, DICTYOSIPHONALES, AND TILOPTERIDALES (PHAEOPHYCEAE) BASED ON RUBISCO LARGE SUBUNIT AND SPACER SEQUENCES

Phylogenetic relationships among 23 species of morphologically simple brown algae belonging to the Ectocarpales sensu stricto , Chordariales, Dictyosiphonales, and Tilopteridales sensu stricto , Phaeophyceae (Fucophyceae), were analyzed using chloroplast-encoded RUBISCO large subunit gene sequences ( rbc L) and the associated RUBISCO spacer sequences. Comparison of the observed and expected sequence divergence at the three codon positions of rbc L showed that the level of mutational saturation within the brown algae is minor. Thus, rbc L is well suited for phylogenetic studies in this group. Unweighted parsimony analyses and a neighbor-joining distance analysis were performed using unambiguously aligned rbc L sequences from the above four orders, one marine raphidophyte and two Tribophyceae (Xantophyceae). Polyphyly of Tilopteridales sensu lato (i.e. including Dictyosiphonales) is verified; we therefore recommend the use of Tilopteridales in the strict sense. The Ectocarpales, Chordariales, and Dictyosiphonales are paraphyletic with respect to each other, forming a highly interwoven clade. A separate parsimony analysis of the RUBISCO spacer as well as a combined rbc L and spacer analysis supported the close relationship among the latter three orders, adding to the evidence that they should be subsumed into the Ectocarpales sensu lato.     

蹄盖蕨科的系统发育: 叶绿体DNA trnL-F区序列证据

蹄盖蕨科Athyriaceae是蕨类植物中一个复杂的大科,由于属间关系不甚清楚,该科分类系统还有一些问题,比如新蹄盖蕨、拟鳞毛蕨属、假冷蕨属、肠蕨属、短肠蕨属和菜蕨属的系统位置常有争议。根据蹄盖蕨科34种植物和3种外类群植物的叶绿体DNA trnL-F区序列建立了系统发育树,结果显示:1.trnL_F区序列分析的结果与rbcL基因序列分析的结果几乎一致。2.新蹄盖蕨属Neoathyrium Ching&Z.R.Wang不应成立,该属应与角蕨属Cornopteris Nakai合并。3.假冷蕨属Pseudo     

A revision and phylogenetic analysis of Stapeliopsis (Apocynaceae)

A survey of morphological characters is carried out for Stapeliopsis . The information obtained from this is combined with molecular data from the plastid trn L-F DNA region and ITS1 of the nuclear encoded 18S−26S rRNA cistron, to obtain a hypothesis of the evolutionary relationships among the species. It is shown that Stapeliopsis is monophyletic in a combined molecular and morphological analysis. Stapeliopsis is sister to a clade containing Huernia , Orbea and Tromotriche . The species of Stapeliopsis group into two clades. One contains S. khamiesbergensis , S. neronis and S. urniflora , and this is highly supported. The remaining species fall into an unsupported clade in which S. exasperata is sister to the others. The genera Hermanschwartzia Plowes and Neopectinaria Plowes are rejected. It is shown that a synapomorphy for Stapeliopsis is the laterally flattened inner corona-lobes, which touch the anthers only at their bases. Eight species of Stapeliopsis are recognized, with no subgeneric divisions.  © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society , 2005, 148 , 125–155.     

Molecular phylogeny and biogeography of the Neotropical cichlid fish tribe Cichlasomatini (Teleostei: Cichlidae: Cichlasomatinae)

We have conducted the first comprehensive molecular phylogeny of the tribe Cichlasomatini including all valid genera as well as important species of questionable generic status. To recover the relationships among cichlasomatine genera and to test their monophyly we analyzed sequences from two mitochondrial (16S rRNA, cytochrome b) and one nuclear marker (first intron of S7 ribosomal gene) totalling 2236 bp. Our data suggest that all genera except Aequidens are monophyletic, but we found important disagreements between the traditional morphological relationships and the phylogeny based on our molecular data. Our analyses support the following conclusions: (a) Aequidens sensu stricto is paraphyletic, including also Cichlasoma (CA clade); (b) Krobia is not closely related to Bujurquina and includes also the Guyanan Aequidens species A. potaroensis and probably A. paloemeuensis (KA clade). (c) Bujurquina and Tahuantinsuyoa are sister groups, closely related to an undescribed genus formed by the 'Aequidens'pulcher-'Aequidens'rivulatus groups (BTA clade). (d) Nannacara (plus Ivanacara) and Cleithracara are found as sister groups (NIC clade). Acaronia is most probably the sister group of the BTA clade, and Laetacara may be the sister group of this clade. Estimation of divergence times suggests that the divergence of Cichlasomatini started around 44Mya with the vicariance between coastal rivers of the Guyanas (KA and NIC clades) and remaining cis-andean South America, followed by evolution of the Acaronia-Laetacara-BTA clade in Western Amazon, and the CA clade in the Eastern Amazon. Vicariant divergence has played importantly in evolution of cichlasomatine genera, with dispersal limited to later range extension of species within genera.     

单种属弥勒苣苔属系统位置研究：基于分子和细胞学数据

弥勒苣苔属是苦苣苔科的单种属,仅分布于中国西南部。为探讨弥勒苣苔在苦苣苔亚科中的系统位置,我们选择了苦苣苔亚科116个类群,外类群为苦苣苔亚科以外的7个物种。用最大简约法（MP）和贝叶斯分析（BI）,对以上类群的核基因ITS以及两个叶绿体基因trnL-F、atpB-rbcL数据进行了独立和联合分析。在三个片段联合分析的结果中,弥勒苣苔与马铃苣苔属、后蕊苣苔属、金盏苣苔属、直瓣苣苔属以及川鄂粗筒苣苔构成一个强烈支持的分枝。MP树中,此分枝为并系,而在BI分析中,弥勒苣苔与川鄂粗筒苣苔、直瓣苣苔属互为姐妹类群。同时,第一次报道了弥勒苣苔的染色体数目（2n=34）。根据前人报道,马铃苣苔属、后蕊苣苔属、粗筒苣苔属和直瓣苣苔属的染色体数目同为2n=34,这进一步支持我们的分子系统发育分析。     

Phylogenetic relationships in Taxodiaceae and Cupressaceae sensu stricto based on matK gene, chlL gene, trnL-trnF IGS region, and trnL intron sequences

Nucleotide sequences from four chloroplast genes, the matK, chlL, intergenic spacer (IGS) region between trnL and trnF, and an intron of trnL, were determined from all species of Taxodiaceae and five species of Cupressaceae sensu stricto (s.s.). Phylogenetic trees were constructed using the maximum parsimony and the neighbor-joining methods with Cunninghamia as an outgroup. These analyses provided greater resolution of relationships among genera and higher bootstrap supports for clades compared to previous analyses. Results indicate that Taiwania diverged first, and then Athrotaxis diverged from the remaining genera. Metasequoia, Sequoia, and Sequoiadendron form a clade. Taxodium and Glyptostrobus form a clade, which is the sister to Cryptomeria. Cupressaceae s.s. are derived from within Taxodiaceae, being the most closely related to the Cryptomeria/Taxodium/Glyptostrobus clade. These relationships are consistent with previous morphological groupings and the analyses of molecular data. In addition, we found acceleration of evolutionary rates in Cupressaceae s.s. Possible causes for the acceleration are discussed.     

Evolution and biogeography of Alectryon (Sapindaceae).

Phylogenetic analysis of nucleotide sequences from four plastid loci (matK, partial trnK-matK introns, rps16 intron) and one nuclear locus (the internal transcribed spacer of rDNA; ITS-1) was conducted for 14 species of Alectryon and five related genera in Sapindaceae. Both matK and rps16 intron provide few informative characters within Alectryon, whereas ITS-1 provides the largest number of parsimony-informative characters and has the greatest sequence divergence between taxa. Support for branches in cladograms produced in PAUP increased markedly upon inclusion of ITS-1 data to matK and rps16 intron data. Analyses of each region alone or combined produced congruent results, suggesting that the regions are complementary. Phylogenetic analysis indicates that there are two main lineages within Alectryon, with A. subcinereus sister to the remaining sampled Alectryon taxa. Two morphological characters, presence/absence of petals and aril patterning, are congruent with the molecular phylogeny. One robustly supported clade is characterized by smooth arils and petals, in contrast to the taxa in the other major clade which have patterned arils and an absence of petals. These analyses also support a number of revised subgeneric groupings for Alectryon. The decision to submerge Heterodendrum in Alectryon is supported, although taxa belonging to Heterodendrum do not form a clade. The majority of the Australian Alectryon appear to belong to the tropical monsoonal/arid flora with species from both lineages being found in representative vine thickets across northern Australia. It appears that the seasonally dry rainforest communities comprise a number of elements that do not share common evolutionary histories within this genus.     

Phylogeny of Gardenieae (Rubiaceae) based on chloroplast DNA sequences from the rps16 intron and trnL(UAA)-F(GAA) intergenic spacer

Chloroplast DNA (cpDNA) sequences of the rps 16 intron and the trn L (UAA)-F(GAA) intergenic spacer were obtained from 59 species, to evaluate phylogenetic relationships among members of the Gardenieae, Rubiaceae. The results indicate that Gardenieae is polyphyletic and that genera included in the subtribe Diplosporinae should be transferred to the Coffeeae and Octotropideae. The Octotropideae tribe may also be polyphyletic. It is also demonstrated that the tribe Pavetteae is polyphyletic. In addition, the present data support a basal position for the disputed genus Bertiera within the Coffeeae clade. Of the informal groups proposed by Robbrecht & Puff within the Gardenieae, the Alibertia group is strongly supported, and is estimated to also include Ibetralia, Genipa aff. williamsii , and one undescribed taxon. However, Genipa americana was not part of this clade suggesting that Genipa is polyphyletic. The Tetrad group is not supported, and character optimisations suggest that pollen released in tetrads may have arisen three times. Most of these genera appear in the same clade as the three neotropical genera Sphinctanthus, Rosenbergiodendron , and Tocoyena , all of which bear pollen in monads. Atractogyne, Mitriostigma , and Oxyanthus form the second group with pollen in tetrads, whereas Gardenia is embedded in a third group. Massularia , with polyads, occurs either singly on a large polytomy or at the base of the Atractocarpus-Porterandia-Trukia clade.     

由5个DNA片段推断极度濒危植物五针白皮松的系统位置

五针白皮松(Pinus squamata X．W．Li)是上世纪90年代描述的一种中国特有松树,目前野外只有立木32株,处于极度濒危状态。前人认为这个种可能是白松亚属(subgen．Strobus)的白皮松(P．bungeana Zucc．ex Endl．)与松亚属(subgen．Pinus)的云南松(P．yunnanensis Franch．)的过渡类型,并将其归入白皮松组狐尾松亚组(subsect．Balfourianae)。本文试图在前人分子系统学工作的基础上,检测五针白皮松5个DNA片段,叶绿体基因rbcL、matK、rpl20-rps18间隔区和trn V内含子以及核糖体ITS,将五针白皮松放在整个松属中探讨其系统位置。4个叶绿体基因单独分析结果和它们的联合数据分析结果以及根据ITS得到的系统树均表明,五针白皮松是白皮松亚组(subsect．Gerardianae)的一个稳定成员,其可能的姐妹群是西藏白皮松(P．gerardiana Wall．)。对白皮松亚组的地理分布作了初步探讨。     

CLOSTERIUM MONILIFERUM-EHRENBERGII (CHAROPHYCEAE, CHLOROPHYTA) SPECIES COMPLEX VIEWED FROM THE 1506 GROUP I INTRON AND ITS2 OF NUCLEAR rDNA

To assess phylogenetic relationships and speciation modes in Closterium , we sequenced two noncoding regions of the nuclear ribosomal cistron, the 1506 group I intron in small subunit and the internal transcribed spacer 2, for a total of 58 strains of the Closterium moniliferum-ehrenbergii species complex. These include both homothallic and heterothallic C. moniliferum Erenberg ex Ralfs v. moniliferum , heterothallic C. moniliferum v. submoniliferum (Woronichin) Krieger, and heterothallic C. ehrenbergii Meneghini ex Ralfs that can be divided into several mating groups. We found no or very little sequence divergence within single mating groups of C. ehrenbergii and among all heterothallic strains of C. moniliferum v. moniliferum or C. moniliferum v. submoniliferum. Nevertheless, sequence divergence was much greater between those mating groups of C. ehrenbergii and also among the three traditional taxa . Maximum parsimony and maximum likelihood analyses showed that the taxon C. ehrenbergii was not monophyletic. The two varieties of C. moniliferum appeared as a sister clade to certain mating groups of C. ehrenbergii . Among the clades that were recovered in different trees by maximum parsimony and maximum likelihood analyses, we consistently found two large conspicuous clades: clade I consisted of mating groups A, B, C, H, K, and L of C. ehrenbergii whose zygospores have smooth-walls, and clade II contained the mating groups D, E, I, J, and S whose zygospores are scrobiculate. Phylogenetic incongruences observed are discussed from the viewpoints of the different molecular nature of the group I intron and internal transcribed spacer 2, as well as putative rapid diversification of the mating groups and probable ancient ancestral hybridization.     

ANALYSIS OF CLONAL CULTURES OF THE BROWN TIDE ALGAE AUREOCOCCUS AND AUREOUMBRA (PELAGOPHYCEAE) USING 18S rRNA, rbcL, AND RUBISCO SPACER SEQUENCES

Variability among clonal cultures of the brown tide algae Aureococcus anophagefferens Hargraves et Sieburth and Aureoumbra lagunensis Stockwell, DeYoe, Hargraves et Johnson was examined by DNA sequence comparisons. Nuclear-encoded 18S rRNA and plastid-encoded rbc L gene sequences were determined for six Aureococcus strains. RUBISCO spacer sequences were determined for 14 strains of Aureococcus. No differences among Aureococcus strains were found in the DNA regions examined. The rbc L and RUBISCO spacer sequences for three Aureoumbra strains were identical but differed from those of Aureococcus. These data indicate that blooms of these species are comprised of cells that are very similar and also imply that Aureococcus and Aureoumbra do not contain varieties or cryptic species. Separate and combined phylogenetic analyses of the 18S rRNA and rbc L gene sequences were performed. Results confirm that the brown-tide-causing algae of Long Island Sound, New York ( Aureococcus ), and Laguna Madre, Texas ( Aureoumbra ), are best classified in separate genera within the Pelagophyceae. Phylogenetic trees place Aureococcus and Aureoumbra within the Pelagomonadales and Sarcinochrysidales, respectively.     

A Phylogenetic Analysis of the Plastid matK Gene with Emphasis on Melanthiaceae sensu lato

Abstract: The presented mat K tree primarily agrees well with the previously presented rbc L tree and combined rbc L + atp B + 18SrDNA tree. According to the mat K tree, the monocotyledons are monophyletic with 100 % bootstrap support. Acorus diverges first from all other monocotyledons (90 % bootstrap support) in which two major clades are recognized: one (89 %) consisting of Alismatanae and Tofieldia (Nartheciaceae), and the other (< 50 %) comprising Lilianae, Commelinanae and Nartheciaceae other than Tofieldia. Within the latter major clade, Petrosavia and Japonolirion (Nartheciaceae) (82 %) diverge first from the remaining taxa (< 50 %) in which two clades are formed: one (81 %) consisting of Pandanales, Dioscoreales and Nartheciaceae-Narthecioideae, and the other (< 50 %) comprising Liliales, Asparagales and Commelinanae. In the former clade, Dioscoreales and Narthecioideae are grouped together (88 %). In the latter clade, Asparagales and Commelinanae are grouped together (< 50 %). Differences between the mat K and rbc L tree topologies appear in the positions of Tricyrtis (Calochortaceae) and Dracaenaceae. Differences between the mat K and combined rbc L + atp B + 18SrDNA tree topologies exist in the positions of the Petrosavia-Japonolirion pair (Nartheciaceae) and Pandanales. The stop codon position of the mat K gene appears to be highly variable among the monocotyledons, especially in the Liliales.     

Phylogenetic analysis of the grape family (Vitaceae) based on three chloroplast markers

Seventy-nine species representing 12 genera of Vitaceae were sequenced for the trnL-F spacer, 37 of which were subsequently sequenced for the atpB-rbcL spacer and the rps16 intron. Phylogenetic analysis of the combined data provided a fairly robust phylogeny for Vitaceae. Cayratia, Tetrastigma, and Cyphostemma form a clade. Cyphostemma and Tetrastigma are each monophyletic, and Cayratia may be paraphyletic. Ampelopsis is paraphyletic with the African Rhoicissus and the South American Cissus striata nested within it. The pinnately leaved Ampelopsis form a subclade, and the simple and palmately leaved Ameplopsis constitutes another with both subclades containing Asian and American species. Species of Cissus from Asia and Central America are monophyletic, but the South American C. striata does not group with other Cissus species. The Asian endemic Nothocissus and Pterisanthes form a clade with Asian Ampelocissus, and A. javalensis from Central America is sister to this clade. Vitis is monophyletic and forms a larger clade with Ampelocissus, Pterisanthes, and Nothocissus. The eastern Asian and North American disjunct Parthenocissus forms a clade with Yua austro-orientalis, a species of a small newly recognized genus from China to eastern Himalaya. Vitaceae show complex multiple intercontinental relationships within the northern hemisphere and between northern and southern hemispheres.     

Phylogeny of Melaleuca, Callistemon, and Related Genera of the Beaufortia Suballiance (Myrtaceae) Based on 5S and ITS-1 Spacer Regions of nrDNA

A phylogenetic analysis of genera within the informal suballiance Beaufortia (family Myrtaceae), largely endemic to Australia and New Caledonia, is presented based on separate and combined data sets for 5S and ITS-1 spacer regions of nuclear ribosomal DNA. The two sets were not in conflict but the 5S data set was more informative. Data were analysed using conventional parsimony, jackknife parsimony, and three-item parsimony analyses. Three-item analysis gave more resolved trees than conventional parsimony analysis. The Beaufortia suballiance includes two major clades, with all Australian representatives of Callistemon (shown to be monophyletic) and most Australian representatives of Melaleuca forming one of these. The sister clade comprises a well-defined group of endemic New Caledonian taxa (classified as Callistemon and Melaleuca ), some Australian species of Melaleuca , a clade including the Western Australia/Northern Territory genera Beaufortia, Lamarchea , and Regelia , and a clade including the south-west Western Australian genera Calothamnus, Eremaea, Conothamnus , and Phymatocarpus . All molecular analyses sup port the monophyly of Conothamnus and of Regelia , genera for which a number of species were included. Three-item analysis of the combined data set supports the monophyly of Beaufortia . The findings have implications for both taxonomy and biogeography.     

Systematics of Amaryllidaceae based on cladistic analysis of plastid sequence data

Cladistic analyses of plastid DNA sequences rbcL and trnL-F are presented separately and combined for 48 genera of Amaryllidaceae and 29 genera of related asparagalean families. The combined analysis is the most highly resolved of the three and provides good support for the monophyly of Amaryllidaceae and indicates Agapanthaceae as its sister family. Alliaceae are in turn sister to the Amaryllidaceae/Agapanthaceae clade. The origins of the family appear to be western Gondwanaland (Africa), and infrafamilial relationships are resolved along biogeographic lines. Tribe Amaryllideae, primarily South African, is sister to the rest of Amaryllidaceae; this tribe is supported by numerous morphological synapomorphies as well. The remaining two African tribes of the family, Haemantheae and Cyrtantheae, are well supported, but their position relative to the Australasian Calostemmateae and a large clade comprising the Eurasian and American genera, is not yet clear. The Eurasian and American elements of the family are each monophyletic sister clades. Internal resolution of the Eurasian clade only partially supports currently accepted tribal concepts, and few conclusions can be drawn on the relationships of the genera based on these data. A monophyletic Lycorideae (Central and East Asian) is weakly supported. Galanthus and Leucojum (Galantheae pro parte) are supported as sister genera by the bootstrap. The American clade shows a higher degree of internal resolution. Hippeastreae (minus Griffinia and Worsleya) are well supported, and Zephyranthinae are resolved as a distinct subtribe. An Andean clade marked by a chromosome number of 2n = 46 (and derivatives thereof) is resolved with weak support. The plastid DNA phylogenies are discussed in the context of biogeography and character evolution in the family.     

Phylogenetic relationships in Cyperus L. s.l. (Cyperaceae) inferred from plastid DNA sequence data

The phylogeny of Cyperus and allied genera has been reconstructed using cladistic analysis of plastid rbcL gene, rps16 intron, trnL intron, and trnL-F intergenic spacer sequence data in 40 species of tribe Cypereae. Cyperus s.s. as currently circumscribed is not monophyletic because ten cyperoid genera are embedded within it. Eucyperoid Cyperus species (with a C₃ anatomy, e.g. C. involucratus ) and the genera Courtoisina , Kyllingiella and Oxycaryum form a clade that is sister to a clade comprising chlorocyperoid species (with a C₄ anatomy, e.g. C. papyrus ) and the genera Alinula , Ascolepis , Kyllinga , Lipocarpha , Pycreus , Remirea and Sphaerocyperus . The position of two species is uncertain; C . tenellus is resolved in a clade together with Isolepis although with typical cyperoid spikelets, whereas I. humillima is not resolved near either Isolepis or Cyperus s . l . © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 138 , 145–153.     

A nuclear DNA phylogeny and proposed taxonomic revision of African greenbuls (Aves, Passeriformes, Pycnonotidae)

The Pycnonotidae (bulbuls and greenbuls) comprise approximately 130 species and are widely distributed across Africa and Asia, mainly in evergreen thickets and forest. Recent molecular findings suggest a basal split between the African and the Asian species, although the three African Pycnonotus species are part of the Asian radiation and represent a relative recent immigration to Africa. In this study we investigate the phylogenetic relationships within the African clade, which with the exclusion of Pycnonotus contains approximately 50 species, of which the majority are placed in three large genera Andropadus , Phyllastrephus and Chlorocichla . We use three nuclear markers (myoglobin intron 2, ODC introns 6 and 7 along with intervening exon 7, and β-fibrinogen intron 5), together encompassing 2072 aligned positions, to infer the relationships within the African clade. The resulting tree is generally well supported and indicates that none of the three largest currently recognized genera are monophyletic. For instance, the species included in Andropadus represent three different clades that are not each other's closest relatives. The montane species currently placed in that genus form a strongly supported clade, which is sister to Ixonotus , Thescelocichla, Baeopogon and Chlorocichla , although within this clade the genus Chlorocichla is polyphyletic. The remaining Andropadus species fall into two groups, one of these with A . importunus and A . gracilirostris , which along with Calyptocichla serina form a basal branch in the African greenbul radiation. In support of some previous studies the Leaf-love ( Pyrrhurus scandens ) is placed within Phyllastrephus . We also propose a new classification that reflects the phylogenetic relationships among African greenbuls.