SYSTEMATIC STATUS AND PHYLOGENETIC RELATIONSHIPS OF THE FRESHWATER GENUS BALBIANIA (RHODOPHYTA)

The freshwater rhodophyte Balbiania investiens (Lenormand) Sirodot was collected as an epiphyte of Batrachospermum in small streams in England, Ireland, and Germany. Unialgal cultures and field collections of Balbiania were analyzed in terms of their morphology, ultrastructure, and the DNA sequences of the genes coding for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase ( rbc L) and 18S ribosomal RNA (rRNA), as well as the first internal transcribed spacer region (ITS1) of the rRNA genes. One of the major distinguishing features of this genus is the production of spermatangia on the tips of specialized, elongate cells. The spermatangia are cut off in a cluster together with similar nonspermatangial cells that are packed with starch granules. The only other rhodophyte genus with this feature is Rhododraparnaldia ; the two genera are differentiated from each other by the pattern of branching, substratum of attachment, and type of diploid phase. In the parsimony and distance trees inferred from the two gene sequences as well as in a combined parsimony tree, Balbiania and Rhododraparnaldia grouped together on a well-supported branch separate from other taxa of the Batrachospermales, Acrochaetiales, Nemaliales, and Palmariales. However, the two genera are positioned within a clade containing the last three orders. Based on these findings, it is clear that the genus Balbiania is a valid taxon and that it is phylogenetically associated with Rhododraparnaldia. A new order is proposed, the Balbianiales. The two specimens of Balbiania analyzed from England and Germany have identical sequences for all regions of DNA analyzed.     

A molecular systematic investigation of the Acrochaetiales (Florideophycidae,Rhodophyta) and related taxa based on nuclear small-subunit ribosomal DNA sequence data

Small-subunit ribosomal DNA (SSU) sequences for 14 members of the rhodophyte order Acrochaetiales were used to generate phylogenetic trees to determine whether the Acrochaetiales is monophyletic and to assess the relationships of acrochaetioid algae to closely related taxa. Within the Acrochaetiales, two strongly supported groups are recognized: one group that includes, in addition to three other species, the type species of the genera Acrochaetium, Audouinella and Rhodochorton; and a second group that includes an unequivocal representative of Colaconema and nine additional species. The relationships of these groups with the Batrachospermales, Palmariales and Nemaliales were not resolved and the possibility that the Acrochaetiales is polyphyletic was not eliminated. Resolution of relationships for species within these groups was strong in only a few cases, with many of the phylogenetic issues at this level remaining equivocal. Our results do not position Camontagnea in the Acrochaetiales, as has recently been suggested, but strongly ally this genus to the family Rhodothamniellaceae of the Palmariales. The phylogenetic position of Rhododraparnaldia, an alga intermediate between the Acrochaetiales and Batrachospermales, remains unresolved. These molecular results provide a foundation for assessing the taxonomic significance of phenotypic characters (e.g. anatomy, life histories, morphology, phycoerythrin type and plastid details) variously considered taxonomically significant in the Acrochaetiales.     

串珠藻目植物的系统发育-基于rbcL序列的证据

世界范围内报道的全部串珠藻目种类均生活于淡水中,而在淡水红藻中,70%约有130种属于串珠藻目。研究以目前获取的来自世界各大洲串珠藻目植物43种的rbcL基因序列,结合其形态和生物地理特征,构建了该目的系统发育关系,以期探讨整个串珠藻目植物的系统发育关系及发生途径,进而为研究该目以至淡水红藻的起源提供基本资料。运用PAUP*4.0b10和MrBayes 3.0b4等软件对43种串珠藻目植物的叶绿体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)基于分子数据分析结果显示,红索藻目植物均独立于串珠藻目植物,构成一个单独的分支,支持红索藻目的建立。(2)鱼子菜科属于串珠藻目植物中较为进化的类群。(3)串珠藻属扭曲组与杂生组的差异度较小,结合其形态特点,倾向于将杂生组并入扭曲组。(4)串珠藻科属于串珠藻目中最大的科,包括较多的种类,其系统关系也较为复杂。因此,串珠藻科系统发育关系的明确有待于进一步结合更多的分子数据和形态学特征加以分析研究。       

A PROPOSAL FOR A NEW RED ALGAL ORDER,THE THOREALES1

Representatives of the freshwater red algal family Thoreaceae were studied to resolve their taxonomic and phylogenetic status. Three specimens of Nemalionopsis and five collections of Thorea were examined for pit plug ultrastructure and analyzed for the sequences of the genes coding for the large subunit of RUBISCO (rbcL) and the small subunit of rRNA (18S rRNA). The phylogenetic trees generated from the two genes, and a combined tree all showed the Thoreaceae to be contained in a well‐supported monophyletic clade that is separate from the other two families currently classified in the Batrachospermales, the Batrachospermaceae and the Lemaneaceae. In addition, secondary structure elements of the 18S rRNA gene were observed at positions 650 and 1145 (Escherichia coli numbering system) that are not present in other members of the Rhodophyta. The pit plugs of the gametophytic and chantransia stages of the Thoreaceae contain two cap layers, the outer one of which is typically plate‐like, though occasionally inflated ones have been seen. No pit plug cap membrane has been observed. These findings indicate the Thoreaceae has been misclassified in the Batrachospermales and should be placed in its own order, the Thoreales. This order is characterized by having freshwater representatives with multiaxial gametophytes, a uniaxial chantransia stage, and pit plugs with two cap layers, the outer one of which is usually plate‐like.     

基于叶绿体psaA和psbA基因的中国熊野藻属植物系统发育分析

以中国产熊野藻属Kumanoa的两个种, 绞扭熊野藻K. intorta (=绞扭串珠藻Batrachospermum intortum), 弯形熊野藻K. curvata (=弯形串珠藻B. curvatum)和其他6种淡水红藻为实验材料, 对其psaA和psbA基因进行扩增和测序, 并与GenBank中相近序列进行比对分析, 以贝叶斯法、最大似然法和邻接法分别构建了单基因和联合基因系统发育树. 结果表明, 3种方法构建的系统树具有相似的拓扑结构, 反映的系统发育关系基本一致, 熊野藻属中的两个种聚为一支, 与串珠藻属相分离, 支持该属的建立; 中国产的熊野藻属分子学研究结果与来自南美洲及澳洲的该属植物结果一致, 说明该属的建立具有广泛的地理适用性. 系统发育树聚类结果也明确反映了熊野藻属与串珠藻属较近的亲缘关系, 根据果胞枝形态特点, 推测熊野藻属进化地位晚于串珠藻属植物, 而早于顶丝藻目和红索藻目. 此外, 胶串珠藻与其他串珠藻组植物分离, 支持将其单独分组, 红索藻目植物与串珠藻目植物分离, 支持红索藻目的建立. 同时也表明psaA和psbA基因用于淡水红藻分析, 能够较好地反映其系统发育关系.       

A plastid DNA phylogeny of the genus Acacia Miller (Acacieae, Leguminoseae)

Past classifications of the tribe Acacieae Rchb. are outlined and the confusion concerning the relationships of the three subgenera of Acacia Mill. are highlighted. A plastid DNA analysis of Acacieae shows that the genus Acacia is not monophyletic. Furthermore subgenera Acacia Vassal and Aculeiferum Vassal are sister taxa and neither appear closely related to subgenus Phyllodineae (DC.) Ser. Subgenera Acacia and Aculeiferum form a clade that is basal to a well-supported clade consisting of tribe Ingeae Benth. taxa, Faidherbia albida (Del.) A. Chev. and subgenus Phyllodineae. The series of relationships suggested by the cpDNA data contradicts previous investigations of the tribe. Possible explanations of this conflict are explored, and the taxonomic implications of the plastid DNA data set are considered.     

Phylogenetic relationships of the Cochliopinae (Rissooidea: Hydrobiidae): an enigmatic group of aquatic gastropods

Phylogenetic analysis based on a partial sequence of the mitochondrial cytochrome c oxidase subunit I gene was performed for 26 representatives of the aquatic gastropod subfamily Cochliopinae, 6 additional members of the family Hydrobiidae, and outgroup species of the families Rissoidae and Pomatiopsidae. Maximum-parsimony analysis yielded a single shortest tree which resolved two monophyletic groups: (1) a clade containing all cochliopine taxa with the exception of Antroselates and (2) a clade composed of Antroselates and the hydrobiid genus Amnicola. The clade containing both of these monophyletic groups was depicted as more closely related to members of the family Pomatiopsidae than to other hydrobiid snails which were basally positioned in our topology. New anatomical evidence supports recognition of the cochliopine and Antroselates-Amnicola clades, and structure within the monophyletic group of cochliopines is largely congruent with genitalic characters. However, the close relationship between the Pomatiopsidae and these clades is in conflict with commonly accepted classifications and suggests that a widely accepted scenario for genitalic evolution in these snails is in need of further study.     

Molecular systematics of four endemic Batrachospermaceae (Rhodophyta) species in China with multilocus data

Four endemic Batrachospermaceae species in China, Batrachospermum hongdongense Xie & Feng, Batrachospermum longipedicellatum Hua & Shi, Kumanoa curvata (Shi) Vis et al., and Kumanoa intorta (Jao) Entwisle et al., were analyzed with multilocus data in order to assess their phylogenetic placement. Multilocus molecular data from one nuclear gene (the ribosomal SSU), one chloroplast gene (rbcL), and two mitochondrial genes (COI and the cox2-3 spacer) as well as morphological studies were used to determine the phylogenetic relationships of these endemic species within the Batrachospermales. Batrachospermum hongdongense and B. longipedicellatum had previously been placed in Batrachospermum section Batrachospermum, but based on the data from this study they should be transferred into section Helminthoidea. Kumanoa curvata and K. intorta clearly belong to the newly established genus Kumanoa.     

基于线粒体基因cyt b的鹟亚科部分鸟类系统发育

采用分子系统学方法对鹟亚科(Muscicapinae)6属31种鸟类的cytb基因序列992bp进行系统发生分析。以荒漠伯劳(Lanius isabellinus)和发冠卷尾(Dicrurus hottentottus)为外群,采用贝叶斯法(Bayesian,BI)、最大似然法(Maximum-likelihood,ML)和最大简约法(Maximumparsimony,MP)分别构建鹟亚科的系统发育树。结果支持:寿带属(Terpsiphone)、扇尾鹟属(Rhipidura)与方尾鹟属(Culicicapa)可从鹟亚科中移出,其中寿带属归入王鹟科(Monarchidae),扇尾鹟属与方尾属归入扇尾鹟科(Rhipiduridae);鹟属(Muscicapa)、仙鹟属(Niltava)为单系发生,并聚为姐妹群,亲缘关系较近;姬鹟属(Ficedula)并非单系发生,白眉姬鹟(Ficedulazanthopygia)在3种系统发生树中的位置差别较大,研究结果未能确定其分类地位;铜蓝(Muscicapa thalassina)与白腹蓝(Cyanoptila cyanomelana)亲缘关系较近,前者应从属中移出,后者应从姬属移出,共同归入仙属或列为仙属的姐妹属。上述结论解决了亚科部分有争议属、种间的进化关系,为亚科分类系统提供了DNA水平证据。     

An evaluation of support for order-level monophyly and interrelationships within the class Demospongiae using partial data from the large subunit rDNA and cytochrome oxidase subunit I

Large subunit ribosomal DNA (LSU rDNA) sequence data from 120 taxa and cytochrome oxidase subunit 1(COI) sequence data from 27 taxa are analyzed separately and together to estimate the internal phylogeny of the class Demospongiae and to evaluate how consistent these data are with pre-existing hypotheses of relationship concerning order-level monophyly and relationships. The monophyly of Porifera is only slightly inconsistent with LSU data, which do not support the monophyly of the class Demospongiae regardless of the inclusion or exclusion of Homoscleromopha (this result is likely due to the placement of a single hexactinellid taxon within the Demospongiae), however, no LSU support is found for the monophyly of Silicea (Demospongiae+Hexactinellida) unless homoscleromorphs are excluded. Neither the subclasses Ceractinomorpha and Tetractinomorpha, nor the orders Halichondrida, Hadromerida, and Haplosclerida are supported as monophyletic under any data partition. The haplosclerid suborders Haplosclerina and Petrosina are supported as monophyletic to the exclusion of the suborder Spongillina, and the orders Dictyoceratida, Verongida, Poecilosclerida, Astrophorida, Spirophorida, Homosclerophorida, and Agelasida are largely reconstructed as monophyletic, with the exception of few anomalously placed taxa. Few inter-order relationships are strongly supported by any data partition, but there is moderate support for a verongid+chondrosid clade and a tetractinellid+halichondrid clade. Furthermore, LSU data strongly support the existence of two novel clades that do not correspond to the existing classification and that show no morphological uniformity. Finally, every data partition supports the monophyly of a clade that includes the order Agelasida, some members of the genus Axinella, and two taxa tentatively identified as belonging to the orders Hadromerida and Halichondrida.     

基于SSU序列的串珠藻目植物系统发育分析

通过18S rDNA基因(SSU)序列,构建了串珠藻目植物的系统发育关系.结果显示:SSU基因序列片段长度为1 871 bp,核苷酸变异位点有709个,占序列长度的38％;其中简约信息位点有169个,占序列长度的9％.用最大似然法、邻接法和贝叶斯法构建的系统树拓扑结构基本一致,都显示红索藻目的2个属独立于串珠藻目成单独分支,支持红索藻目的建立;胶串珠藻独立于其他串珠藻组植物,支持将其单独分组;数据同时支持将扭曲组和杂生组合并,建立Kumanoa属;但多芒组、绿色组、沼生组等因分子序列数据涉及的种类较少,其系统关系的确定还需要更多的证据.     

小麦抗白粉病相关基因GST克隆与表达

以从小麦抗白粉病相关基因差异表达分析中获得的EST-3 (Genbank序列号EX567360)为标签,采用电子克隆的方法对其进行延伸,并对电子克隆结果进行半定量RT-PCR验证,最后对白粉菌不同侵染时间进行了表达分析.经RT-PCR扩增,EST-3表达的带型变化趋势与其在抑制性消减杂交SSH-cDNA的差异显示情况一致,且RT-PCR获得的序列与电子克隆的序列一致性达98％.生物信息学分析表明,该序列是由875 bp核苷酸组成的,具有完整的开放阅读框架,编码蛋白为229个氨基酸,GenBank序列号JK841279,含有一个N端和C端谷胱甘肽硫转移酶结构域,该序列与小麦谷胱甘肽硫转移酶基因(GST)一致性较高,达97％.表达分析结果显示,白粉菌侵染24 h表达受到抑制,48 h开始表达,侵染72 h表达最强,96 h又开始下降,表明GST基因属于白粉菌诱导型相关基因,参与小麦对白粉病的应答反应.     

The RAG-1 exon in the avian order Caprimulgiformes: phylogeny, heterozygosity, and base composition

We sequenced 2.8 kb of the RAG-1 exon for most of the extant genera in the avian order Caprimulgiformes to investigate monophyly of the order and phylogeny within the traditional families. The order is not monophyletic: the Aegothelidae (owlet-nightjars) were the sister group of the Apodiformes (swifts and hummingbirds). There was no support for the monophyly of a clade containing the remaining families of Caprimulgiformes. However, the RAG-1 data strongly supported a relationship between the Podargidae (frogmouths) and Caprimulgidae (nightjars). Within the Caprimulgidae, the Australasian genus Eurostopodus was sister to the rest of the family, which in turn was composed of four major clades, three of which were restricted to the New World and primarily to the Neotropics. The Old World caprimulgids form a monophyletic clade embedded within the New World taxa; consequently, most Old World nightjars are probably the result of a single expansion out of the Neotropics. The genus Caprimulgus was not found to be monophyletic. Several species in the Caprimulgidae have both elevated heterozygosity and high GC3 content; it is likely that these are causally related.     

Phylogenetic analysis of the Sphaeriidae (Mollusca: Bivalvia) based on partial mitochondrial 16s rDNA gene sequences

Abstract. We have constructed molecular phylogenetic trees for members of the Sphaeriidae in order to test proposed generic level relationships, and to reconstruct the evolutionary pattern of parental care, in this exclusively freshwater family of heterodont bivalves. An ∼480 nucleotide fragment of the mitochondrial large ribosomal subunit (16s rDNA) was sequenced for 4 corbiculid outgroups in addition to 19 sphaeriid ingroup taxa. Ingroup species were obtained from North and South America, Europe, and Australasia and included representatives of the main sphaeriid genera. Our analyses support four primary conclusions: 1) the Sphaeriinae are robustly monophyletic with respect to Eupera platensis ; 2) the genus Pisidium is paraphyletic and P. sterkianum is sister to the 17 other sphaeriine taxa in our dataset; 3) synchronous brooding is the ancestral reproductive pattern in the Sphaeriinae; 4) the sequential brooders form a clade in which Musculium taxa are monophyletic and nested among lineages of Sphueriunz. Our gene trees reveal an evolutionary progression in parental care complexity from the relatively simple pattern in the Euperinae, to the origin of brood sacs and of extraoogonial embryonic nutrition in the common ancestor of the Sphaeriinae, and ultimately to the development of sequential brooding in Sphaerium/Musculium taxa.     

PHYLOGENETIC RELATIONSHIPS OF SPECIES OF UNCERTAIN TAXONOMIC POSITION WITHIN THE ACROCHAETIALES-PALMARIALES COMPLEX (RHODOPHYTA): INFERENCES FROM PHENOTYPIC AND 18S rDNA SEQUENCE DATA1

Nucleotide sequences of the small-subunit ribosomal RNA gene ( 18S rDNA ) were newly determined for four members of the related rhodophyte orders Palmariales and Acrochaetiales and were compared by neighbor-joining and parsimony analyses with four previously published sequences from these orders. A published rDNA sequence from Nemalion helminthoides ( Velley in Withering ) Batters ( Nemaliales ) and a gene sequence determined herein for Nothocladus nodosus Skuja ( Batrachospermales ) were used as outgroups. Sequences were very similar within the Palmariales with a maximum difference of 13 nucleotides out of 1772 between members of the families Palmariaceae and Rhodophysemataceae. Despite similarities in life history, the acrochaetioid algae Rhodo-chorton purpureum ( Lightfoot ) Rosenvinge and Rhodothamniella floridula ( Dillwyn ) J. Feldmann in Christensen were phylogenetically separated with R. purpureum affiliated weakly with Acrochaetiales, and R. floridula forming a sister branch unequivocally to palmarialean algae of the families Rhodophysemataceae and Palmariaceae . Rhodothamniella floridula is postulated on both molecular and phenotypic grounds ( encompassing biochemical and anatomical characters, and life history features ) to represent an early lineage, Rhodothamniellaceae fam. nov., in the Palmariales. The family Rhodophysemataceae appeared paraphyletic in the sequence analyses, but a monophyletic Rhodophysemataceae could not be rejected by Templeton-Felsenstein or Kishino-Husegawa tests, and the family was clearly monophyletic in analysis of the phenotypic data. The earlier tentative placement of Rhodophysemataceae in the Palmariales rather than Acrochaetiales was confirmed .     

Phylogenetic relationships of the genus Paramecium inferred from small subunit rRNA gene sequences

The genus Paramecium includes species that are well known and very common in freshwater environments. Species of Paramecium are morphologically divided into two distinct groups: the "bursaria" subgroup (foot-shaped) and the "aurelia" subgroup (cigar-shaped). Their placement within the class Oligohymenophorea has been supported by the analysis of the small subunit rRNA gene sequence of P. tetraurelia. To confirm the stability of this placement and to resolve relationships within the genus, small subunit rRNA gene sequences of P. bursaria, P. calkinsi, P. duboscqui, P. jenningsi, P. nephridiatum, P. primaurelia, and P. polycaryum were determined and aligned. Trees constructed using distance-matrix, maximum-likelihood, and maximum-parsimony methods all depicted the genus as a monophyletic group, clustering with the other oligohymenophorean taxa. Within the Paramecium clade, P. bursaria branches basal to the other species, although the remaining species of the morphologically defined "bursaria" subgroup do not group with P. bursaria, nor do they form a monophyletic subgroup. However, the species of the "aurelia" subgroup are closely related and strongly supported as a monophyletic group.     

The nature of the ancestral red alga: inferences from a cladistic analysis

A cladistic analysis of the orders of Rhodophyta is presented. Sixteen taxa and 34 characters comprise the data matrix. Included in the analysis are biochemical and ultrastructural features of pigments, cell walls, cell organelles, mitosis and pit connections as well as vegetative and reproductive characters. The traditional recognition of two classes or subclasses, Bangiophycidae and Florideophycidae, is not supported regardless of whether Porphyridiales, Rhodochaetales or Bangiales is designated the outgroup. Florideophycidae, however, appears to be monophyletic with Bangiales as its sister group. Relationships among taxa with one or two plug cap layers, i.e. Acrochaetiales, Palmariales, Corallinales, Nemaliales, Batrachospermales, Gelidiales and Hildenbrandiales are unresolved. Rhodochaetales, Bangiales and possibly Erythropeltidales are monophyletic, but Porphyridiales is polyphyletic. The class Cyanidiophyceae is not recognized and the included genera are considered to be unicellular red algae belonging to Porphyridiales. Taxa that have been proposed as sister groups for red algae, including Cyanobacteria, Cryptophyta, Glaucophyta and Chlorophyta, and Ascomycetes and Basidiomycetes are discussed in relation to the proposed phylogeny of Rhodophyta.