PHYLOGENETIC RELATIONSHIPS WITHIN THE COLONIAL VOLVOCALES (CHLOROPHYTA) INFERRED FROM rbcL GENE SEQUENCE DATA

The chloroplast-encoded large subunit of the ribulose-1, 5-bisphosphate carboxylase / oxygenase (rbcL) gene was sequenced from 20 species of the colonial Volvocales (the Volvacaceae, Goniaceae, and Tetrabaenaceae) in order to elucidate phylogenetic relationships within the colonial Volvocales. Eleven hundred twenty-eight base pairs in the coding regions of the (rbcL) gene were analyzed by the neighbor-joining (NJ) method using three kinds of distance estimations, as well as by the maximum parsimony (MP) method. A large group comprising all the anisogamous and oogamous volvocacean species was resolved in the MP tree as well as in the NJ trees based on overall and synonymous substitutions. In all the trees constructed, Basichlamys and Tetrabaena (Tetrabaenaceae) constituted a very robust phylogenetic group. Although not supported by high bootstrap values, the MP tree and the NJ tree based on nonsynonymous substitutions indicated that the Tetrabaenaceae is the sister group to the large group comprising the Volvocaceae and the Goniaceae. In addition, the present analysis strongly suggested that Pandorina and Astrephomene are monophyletic genera whereas Eudorina is nonmonophyletic. These results are essentially consistent with the results of the recent cladistic analyses of morphological data. However, the monophyly of the Volvocaceae previously supported by four morphological synapomorphies is found only in the NJ tree based on nonsynonymous substitutions (with very low bootstrap values). The genus Volvox was clearly resolved as a polyphyletic group with V. rousseletii Pocock separated from other species of Volvox in the rbcL gene comparisons, although this genus represents a monophyletic group in the previous morphological analyses. Furthermore, none of the rbcL gene trees supported the monophyly of the Goniaceae; Astrephomene was placed in various phylogenetic positions .     

Origin and evolution of the colonial volvocales (Chlorophyceae) as inferred from multiple, chloroplast gene sequences

A combined data set of DNA sequences (6021 bp) from five protein-coding genes of the chloroplast genome (rbcL, atpB, psaA, psaB, and psbC genes) were analyzed for 42 strains representing 30 species of the colonial Volvocales (Volvox and its relatives) and 5 related species of green algae to deduce robust phylogenetic relationships within the colonial green flagellates. The 4-celled family Tetrabaenaceae was robustly resolved as the most basal group within the colonial Volvocales. The sequence data also suggested that all five volvocacean genera with 32 or more cells in a vegetative colony (all four of the anisogamous/oogamous genera, Eudorina, Platydorina, Pleodorina, and Volvox, plus the isogamous genus Yamagishiella) constituted a large monophyletic group, in which 2 Pleodorina species were positioned distally to 3 species of Volvox. Therefore, most of the evolution of the colonial Volvocales appears to constitute a gradual progression in colonial complexity and in types of sexual reproduction, as in the traditional volvocine lineage hypothesis, although reverse evolution must be considered for the origin of certain species of Pleodorina. Data presented here also provide robust support for a monophyletic family Goniaceae consisting of two genera: Gonium and Astrephomene.     

The Aceto-Carmine Technic Applied to the Colonial Volvocales

A study of nuclear structure and chromosome number in the colonial Volvocales has led to the development of an aceto-carmine technic particularly applicable to this group of plants. The genera investigated are Gonium, Volvulina, Eudorina, Pleodorina, and Volvox. Another genus, as yet undescribed in the literature, has also been investigated successfully by this method.     

PHYLOGENETIC ANALYSIS OF YAMAGISHLELLA AND PLATYDORINA (VOLVOCACEAE,CHLOROPHYTA) BASED ON rbcL GENE SEQUENCES1

Yamagishiella, based on Pandorina unicocca Rayburn et Starr, is distinguished from Eudorina by its isogamous sexual reproduction, whereas Platydorina exhibits anisogamous sexual reproduction. In the present study, we sequenced the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcL) genes from five Japanese and North American strains of Y. unicocca (Rayburn et Starr) Nozaki, two Platydorina caudata Kofoid strains, and two strains of Eudorina unicocca G. M. Smith, as well as eight related colonial and unicellular species. Phylogenetic trees were constructed based on these sequence data and on previously published rbcL gene sequences from 23 volvocalean species in order to deduce phylogenetic relationships within the colonial Volvocales, with particular regard to the phylogenetic positions and status of the genera Yamagishiella and Platydorina. Two robust monophyletic groups of the anisogamous/oogamous volvocacean species were resolved in the maximum-parsimony tree as well as in the neighbor-joining distance tree. One of the two groups comprises three species of Volvox section Volvox, whereas the other is composed of other sections of Volvox as well as of all the species of Eudorina and Pleodorina. Platydorina, however, was positioned outside these two monopliyletic groups. Therefore, derivation of the Platydorina lineage may be earlier than that of such anisogamous/oogamous groups, or orgin of “anisogamy with sperm packets” in Platydorina may be independent of sperm packet evolution in Eudorina, Pleodorina, and Volvox. It was also resolved with high bootstrap values that all of the Y. unicocca strains form a monophyletic group positioned outside the large monophyletic group including Eudorina and Pleodorina. These reject the possibility of the reverse evolution of isogamy from anisogamy to give rise to Yamagishiella within the lineage of Eudorina.     

Molecular phylogeny of the volvocine flagellates.

Phylogenetic studies of approximately 2,000 bases of sequence from the large and small nuclear-encoded ribosomal RNAs are used to investigate the origins of the genus Volvox. The colonial and multicellular genera currently placed in the family Volvocaceae form a monophyletic group that is significantly closer phylogenetically to Chlamydomonas reinhardtii than it is to the other unicellular green flagellates that were tested, including Chlamydomonas eugametos, Chlorella pyrenoidosa, and Haematococcus lacustris. Statistical analysis of 251 phylogenetically informative nucleotide positions rejects the "volvocine lineage" hypothesis, which postulates a monophyletic evolutionary progression from unicellular organisms (such as Chlamydomonas), through colonial organisms (e.g., Gonium, Pandorina, Eudorina, and Pleodorina) demonstrating increasing size, cell number, and tendency toward cellular differentiation, to multicellular organisms having fully differentiated somatic and reproductive cells (in the genus Volvox). The genus Volvox appears not to be monophyletic. Volvox capensis falls outside a lineage containing other representatives of Volvox (V. aureus, V. carteri, and V. obversus), and both of these Volvox lineages are more closely related to certain colonial genera than they are to each other. This implies either a diphyletic origin of Volvox from different colonial volvocacean ancestors, a phylogenetic derivation of some of the colonial genera from a multicellular (i.e., Volvox) ancestor, or both. Considered together with previously published observations, these results suggest that the different levels of organizational and developmental complexity found in the Volvocaceae represent alternative stable states, among which evolutionary transitions have occurred several times during the phylogenetic history of this group.     

Evolution of rbcL group IA introns and intron open reading frames within the colonial Volvocales (Chlorophyceae)

Mobile group I introns sometimes contain an open reading frame (ORF) possibly encoding a site-specific DNA endonuclease. However, previous phylogenetic studies have not clearly deduced the evolutionary roles of the group I intron ORFs. In this paper, we examined the phylogeny of group IA2 introns inserted in the position identical to that of the chloroplast-encoded rbcL coding region (rbcL-462 introns) and their ORFs from 13 strains of five genera (Volvox, Pleodorina, Volvulina, Astrephomene, and Gonium) of the colonial Volvocales (Chlorophyceae) and a related unicellular green alga, Vitreochlamys. The rbcL-462 introns contained an intact or degenerate ORF of various sizes except for the Gonium multicoccum rbcL-462 intron. Partial amino acid sequences of some rbcL-462 intron ORFs exhibited possible homology to the endo/excinuclease amino acid terminal domain. The distribution of the rbcL-462 introns is sporadic in the phylogenetic trees of the colonial Volvocales based on the five chloroplast exon sequences (6021 bp). Phylogenetic analyses of the conserved intron sequences resolved that the G. multicoccum rbcL-462 intron had a phylogenetic position separate from those of other colonial volvocalean rbcL-462 introns, indicating the recent horizontal transmission of the intron in the G. multicoccum lineage. However, the combined data set from conserved intron sequences and ORFs from most of the rbcL-462 introns resolved robust phylogenetic relationships of the introns that were consistent with those of the host organisms. Therefore, most of the extant rbcL-462 introns may have been vertically inherited from the common ancestor of their host organisms, whereas such introns may have been lost in other lineages during evolution of the colonial Volvocales. In addition, apparently higher synonymous substitutions than nonsynonymous substitutions in the rbcL-462 intron ORFs indicated that the ORFs might evolve under functional constraint, which could result in homing of the rbcL-462 intron in cases of spontaneous intron loss. On the other hand, the presence of intact to largely degenerate ORFs of the rbcL-462 introns within the three isolates of Gonium viridistellatum and the rare occurrence of the ORF-lacking rbcL-462 intron suggested that the ORFs might degenerate to result in the spontaneous intron loss during a very short evolutionary time following the loss of the ORF function. Thus, the sporadic distribution of the rbcL-462 introns within the colonial Volvocales can be largely explained by an equilibrium between maintenance of the introns by the intron ORF and spontaneous loss of introns when the introns do not have a functional ORF.     

团藻目群体鞭毛类的中国新记录

于2015年3月到7月在湖北省内多处水体采集浮游藻类样品,通过光学显微镜观察样品形态,共鉴定出团藻目群体鞭毛类3科5属8种。其中四豆藻科Tetrabaenaceae Nozaki et Itoh为中国新记录科,四豆藻属Tetra-baena（Dujardin）Fromentel和似团藻属Volvulina Playfair为中国新记录属,发现了5个新记录种分别为简单四豆藻Tetrabaena socialis（Dujardin）Nozaki et Itoh、科尔曼实球藻Pandorina colemaniae Nozaki、致密似团藻Vol-vulina compacta Nozaki、柱状空球藻Eudorina cylindrical Korshikov和单果空球藻Eudorina unicocca Smith。基于3种分子标记进行的系统发育分析验证了各样品的形态学鉴定;同时四豆藻科、盘藻科和团藻科均为单系类群,进一步支持了Nozaki的分类系统。     

Floral morphology and embryo sac development in Burretiodendron kydiifolium Y. C. Hsu et R. Zhuge (Tiliaceae) and their systematic significance

Phylogenetic analysis of rbc L and atp B gene sequences from Biebersteinia Stephan (represented by B. orphanidis Boiss.) and from selected taxa of the rosids I and II clades does not support traditional grouping of this genus in Geraniaceae s. s. nor in Geraniales, but indicates strong support for a position nested within Sapindales (as recently delimitated). The rbc L and atp B phylogenies obtained were congruent but differently resolved and do not link Biebersteinia to any other clade within Sapindales. Biebersteinia is on a long branch on its own which, given the particular combination of apomorphic morphological characters, justifies familial status.     

基于线粒体COI基因的大蚊属Tipula系统发育及长角大蚊亚属Tipula (Sivatipula)分类地位初步研究(双翅目:大蚊总科)

大蚊属Tipula Linnaeus,1758是大蚊科中种类最多的属,目前其单系性尚未得到全面验证.此外,长角大蚊亚属Tipula (Sivatipula) Alexander,1964因其极长的触角以及独有的精子泵结构,明显不同于大蚊属其他亚属,使其亚属的分类地位存在争议.本研究基于COI序列对19个大蚊属物种及5个其他属物种进行了系统发育分析,并计算了物种间的遗传距离.研究结果表明:(1)邻接树(NJ)和最大似然树(ML)均显示长角大蚊亚属与大蚊属其他亚属未形成单系,大蚊属的单系性没有得到支持;(2)基于遗传距离和系统发育分析并结合形态信息,结果显示长角大蚊亚属独立于大蚊属内其他亚属,应将其提升为属级分类单元.     

A twelve-step program for evolving multicellularity and a division of labor

The volvocine algae provide an unrivalled opportunity to explore details of an evolutionary pathway leading from a unicellular ancestor to multicellular organisms with a division of labor between different cell types. Members of this monophyletic group of green flagellates range in complexity from unicellular Chlamydomonas through a series of extant organisms of intermediate size and complexity to Volvox, a genus of spherical organisms that have thousands of cells and a germ-soma division of labor. It is estimated that these organisms all shared a common ancestor about 50 +/- 20 MYA. Here we outline twelve important ways in which the developmental repertoire of an ancestral unicell similar to modern C. reinhardtii was modified to produce first a small colonial organism like Gonium that was capable of swimming directionally, then a sequence of larger organisms (such as Pandorina, Eudorina and Pleodorina) in which there was an increasing tendency to differentiate two cell types, and eventually Volvox carteri with its complete germ-soma division of labor.     

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.     

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 WITHIN THE COLONIAL VOLVOCALES (CHLOROPHYTA) INFERRED FROM CLADISTIC ANALYSIS BASED ON MORPHOLOGICAL DATA1

A cladistic analysis was used to deduce the phylogenetic relationships within the colonial Volvocales. Forty-one pairs of characters related to gross morphology and ultrastructure of vegetative colonies as well as asexual and sexual reproduction were analyzed based on parsimony, using the PAUP 3.0 computer program, for 25 species belonging to nine volvocacean and goniacean genera of the colonial Volvocales. Chlamydomonas reinhardtii Dangeard was the outgroup. The strict consensus tree indicated the presence of two monophyletic groups, one composed of all the volvocacean species analyzed in this study and the other containing the goniacean species except for the four-celled species Gonium sociale (Dujardin) Warming. In addition, these two groups constitute a large monophyletic group, to which G. sociale is a sister group. A new combination Tetrabaena socialis (Dujardin) Nozaki et Itoh and a new family Tetrabaenaceae Nozaki et Itoh are thus proposed for G. sociale. In addition, the analysis suggests that the volvocacean genera Eudorina and Pleodorina are paraphyletic groups, respectively, and that the monotypic genus Yamagishiella has no autapomorphic characters and represents primitive features of the anisogamous and oogamous genera of the Volvocaceae. Phylogenetic relationships within the Volvocaceae and the Goniaceae, as well as the various modes of sexual reproduction exhibited by these organisms, are discussed on the basis of the analysis.     

基于Cyt b基因探讨羚羊亚科原羚属系统发生关系

原羚属物种在羚羊亚科中的分类地位尚存在很多争议。本文测定了原羚属的黄羊和藏原羚细胞色素b基因全序列(1140bp),并与牛科其它属31个种的同源序列进行比较,对其碱基组成变异情况及核苷酸序列差异进行了分析。基于细胞色素b基因全序列,用简约法(MP)、邻接法(NJ)和似然法(ML)构建了系统进化树。结果表明：黄羊和藏原羚的序列差异为3．78％,颠换数目近乎为0,其突变远未饱和;原羚属内黄羊和藏原羚为不同种,单系发生;原羚属与赛加羚羊属、犬羚属及跳羚属等并系发生,原羚属隶属于羚羊亚科,应为独立属;羚羊亚科组成属间多为并系起源。根据序列差异值2％／百万年的细胞色素6分子钟,推测黄羊和藏原羚分歧时间大约为1～2百万年;原羚属与羚羊亚科其它属分歧时间大约在5．7～8百万年。     

PHYLOGENY OF THE BATRACHOSPERMALES (RHODOPHYTA) INFERRED FROM rbcL AND 18S RIBOSOMAL DNA GENE SEQUENCES

The sequence data from the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase ( rbc L) gene and 18S ribosomal DNA (small subunit) of taxa in the freshwater rhodophyte order Batrachospermales were used to construct phylogenetic hypotheses. Taxa examined in this study represent four families, eight genera, and six sections of the genus Batrachospermum . In addition, Rhododraparnaldia oregonica Sheath, Whittick et Cole, was included in the analysis because it shares particular ultrastructural, reproductive, and morphological characteristics with members of the Batrachospermales and Acrochaetiales. The trees generated from each gene, as well as a combined data set, were largely congruent. Rhododraparnaldia consistently occurs on an early branch within the Acrochaetiales – Palmariales clade and does not appear to be a member of the Batrachospermales. In addition, Thorea violacea Bory de St. Vincent was not closely related to the other taxa of the Batrachospermales in all trees and hence the family Thoreaceae does not appear to be a natural grouping within this order. All other taxa analyzed, which are presently classified within this order, formed a monophyletic clade in most analyses. Psilosiphon scoparium Entwisle was not closely allied with the taxa of the Lemaneaceae, lending support to the newly proposed family Psilosiphonaceae. Sequence data from the remaining taxa of the Lemaneaceae support the concept of a derived monophyletic clade. The genus Batrachospermum appears to comprise many morphologically similar but distantly related taxa, which will need further investigation to resolve their taxonomic status. Tuomeya, Sirodotia and Nothocladus are retained at the generic level until further data are obtained.     

The systematic relationships of glucosinolate-producing plants and related families: a cladistic investigation based on morphological and molecular characters

A cladistic analysis is performed using 94 morphological and biochemical characters for 42 genera to compare a phylogeny based on morphological data with those obtained using different genes ( rbc L, atp B, 18S RNA, mat K) or their combination with morphological data, and to understand the floral evolution within the expanded Brassicales (Capparales) relative to Sapindales and Malvales. The tree produced with morphological data is congruent with those obtained from macromolecular studies in obtaining a well-supported glucosinolate-producing clade and an expanded Sapindales. The combined analysis of the morphological and molecular characters is generally well resolved with support for many of the relationships. The inclusion of the fossil taxon Dressiantha demonstrates the value of inserting fossil evidence in phylogenetic analyses. However, the fossil appears to be related to the Anacardiaceae and not to the Brassicales. The core Brassicales are well supported by a number of synapomorphies, although the internal position of Tovariaceae and Pentadiplandraceae is not well resolved. Emblingiaceae appears to be related to Bataceae and Salvadoraceae. Several significant morphological characters are mapped on the combined trees and their evolutionary significance is discussed. Within Brassicales and Sapindales several well supported clades can be recognized which merit ordinal or subordinal status, putting the present orders at a higher level; these include: Tropaeolales, Setchellanthales, Batidales, Brassicales (Brassiciflorae), Burserales, Sapindales and Rutales (Sapindiflorae). The present scheme of affinities within the Brassicales corresponds well with a gradual morphological evolution in the order.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 151 , 453–494.     

基于线粒体ND1和CO1基因序列探讨锯眼蝶-亚科主要类群的系统发生关系

研究测定了锯眼蝶亚科4族、10属共20个国产代表种的线粒体ND1和COI基因的部分序列,结合从GenBank中获得的4个国外产种类的同源序列,以凤蝶科的迪洛尔娟凤蝶、丝带凤蝶,以及娟蝶科的西猛娟蝶为外类群,通过邻接法、最大简约法、最大似然法和贝叶斯法重建了分子系统树,分析了该亚科及其主要类群的系统发生关系。分析结果表明：帻眼蝶族和锯眼蝶族具有较近的亲缘关系;黛眼蝶族不是单系群,该族中的黛眼蝶属、荫眼蝶属与眉眼蝶族具有较近的亲缘关系,带眼蝶属、藏眼蝶属、毛眼蝶属和帕眼蝶属聚合为一个独立的支系,其中带眼蝶属和藏眼蝶属在所有的分析方法中均以100%的置信度（BP=100%, PP=1.00）相聚合,笔者倾向于将它们合并为一属。     

Characterization of rbcL group IA introns from two colonial volvocalean species (Chlorophyceae)

Group I introns were reported for the first time in the large subunit of Rubisco (rbcL) genes, using two colonial green algae, Pleodorina californica and Gonium multicoccum (Volvocales). The rbcL gene of P. californica contained an intron (PlC intron) of 1320 bp harboring an open reading frame (ORF). The G. multicoccum rbcL gene had two ORF-lacking introns of 549 (GM1 intron) and 295 (GM2 intron) base pairs. Based on the conserved nucleotide sequences of the secondary structure, the PlC and GM1 introns were assigned to group IA2 whereas the GM2 intron belonged to group IA1. Southern hybridization analyses of nuclear and chloroplast DNAs indicated that such intron-containing rbcL genes are located in the chloroplast genome. Sequencing RNAs from the two algae revealed that these introns are spliced out during mRNA maturation. In addition, the PlC and GM1 introns were inserted in the same position of the rbcL exons, and phylogenetic analysis of group IA introns indicated a close phylogenetic relationship between the PlC and GM1 introns within the lineage of bacteriophage group IA2 introns. However, P. californica and G. multicoccum occupy distinct clades in the phylogenetic trees of the colonial Volvocales, and the majority of other colonial volvocalean species do not have such introns in the rbcL genes. Therefore, these introns might have been recently inserted in the rbcL genes independently by horizontal transmission by viruses or bacteriophage.     

THE PINGUIOPHYCEAE CLASSIS NOVA, CHROMOPHYTE ALGAE PRODUCING LARGE AMOUNTS OF OMEGA-3 FATTY ACIDS

The streptophytes comprise the Charophyceae sensu Mattox and Stewart (a morphologically diverse group of fresh-water green algae) and the embryophytes (land plants). Several charophycean groups are currently recognized. These include the Charales, Coleochaetales, Chlorokybales, Klebsormidiales and Zygnemophyceae (Desmidiales and Zygnematales). Recently, SSU rRNA gene sequence data allied Mesostigma viride (Prasinophyceae) with the Streptophyta. Complete chloroplast sequence data, however, placed Mesostigma sister to all green algae, not with the streptophytes. Several morphological, ultrastructural and biochemical features unite these lineages into a monophyletic group including embryophytes, but evolutionary relationships among the basal streptophytes remain ambiguous. To date, numerous studies using SSU rRNA gene sequences have yielded differing phylogenies with varying degrees of support dependent upon taxon sampling and choice of phylogenetic method. Like SSU data, chloroplast DNA sequence data have been used to examine relationships within the Charales, Coleochaetales, Zygnemophyceae and embryophytes. Representatives of all basal streptophyte lineages have not been examined using chloroplast data in a single analysis. Phylogenetic analyses were performed using DNA sequences of rbc L (the genes encoding the large subunit of rubisco) and atp B (the beta-subunit of ATPase) to examine relationships of basal streptophyte lineages. Preliminary analyses placed the branch leading to Mesostigma as the basal lineage in the Streptophyta with Chlorokybus , the sole representative of the Chlorokybales, branching next. Klebsormidiales and the enigmatic genus Entransia were sister taxa. Sister to these, the Charales, Coleochaetales, embryophytes and Zygnemophyceae formed a monophyletic group with Charales and Coleochaetales sister to each other and this clade sister to the embryophytes.     

Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences

Phylogenetic relationships of mushrooms and their relatives within the order Agaricales were addressed by using nuclear large subunit ribosomal DNA sequences. Approximately 900 bases of the 5' end of the nucleus-encoded large subunit RNA gene were sequenced for 154 selected taxa representing most families within the Agaricales. Several phylogenetic methods were used, including weighted and equally weighted parsimony (MP), maximum likelihood (ML), and distance methods (NJ). The starting tree for branch swapping in the ML analyses was the tree with the highest ML score among previously produced MP and NJ trees. A high degree of consensus was observed between phylogenetic estimates obtained through MP and ML. NJ trees differed according to the distance model that was used; however, all NJ trees still supported most of the same terminal groupings as the MP and ML trees did. NJ trees were always significantly suboptimal when evaluated against the best MP and ML trees, by both parsimony and likelihood tests. Our analyses suggest that weighted MP and ML provide the best estimates of Agaricales phylogeny. Similar support was observed between bootstrapping and jackknifing methods for evaluation of tree robustness. Phylogenetic analyses revealed many groups of agaricoid fungi that are supported by moderate to high bootstrap or jackknife values or are consistent with morphology-based classification schemes. Analyses also support separate placement of the boletes and russules, which are basal to the main core group of gilled mushrooms (the Agaricineae of Singer). Examples of monophyletic groups include the families Amanitaceae, Coprinaceae (excluding Coprinus comatus and subfamily Panaeolideae), Agaricaceae (excluding the Cystodermateae), and Strophariaceae pro parte (Stropharia, Pholiota, and Hypholoma); the mycorrhizal species of Tricholoma (including Leucopaxillus, also mycorrhizal); Mycena and Resinomycena; Termitomyces, Podabrella, and Lyophyllum; and Pleurotus with Hohenbuehelia. Several groups revealed by these data to be nonmonophyletic include the families Tricholomataceae, Cortinariaceae, and Hygrophoraceae and the genera Clitocybe, Omphalina, and Marasmius. This study provides a framework for future systematics studies in the Agaricales and suggestions for analyzing large molecular data sets.