Morphological convergence characterizes the evolution of Xanthophyceae (Heterokontophyta): evidence from nuclear SSU rDNA and plastidial rbcL genes

Xanthophyceae are a group of heterokontophyte algae. Few molecular studies have investigated the evolutionary history and phylogenetic relationships of this class. We sequenced the nuclear-encoded SSU rDNA and chloroplast-encoded rbcL genes of several xanthophycean species from different orders, families, and genera. Neither SSU rDNA nor rbcL genes show intraspecific sequence variation and are good diagnostic markers for characterization of problematic species. New sequences, combined with those previously available, were used to create different multiple alignments. Analyses included sequences from 26 species of Xanthophyceae plus three Phaeothamniophyceae and two Phaeophyceae taxa used as outgroups. Phylogenetic analyses were performed according to Bayesian inference, maximum likelihood, and maximum parsimony methods. We explored effects produced on the phylogenetic outcomes by both taxon sampling as well as selected genes. Congruent results were obtained from analyses performed on single gene multiple alignments as well as on a data set including both SSU rDNA and rbcL sequences. Trees obtained in this study show that several currently recognized xanthophycean taxa do not form monophyletic groups. The order Mischococcales is paraphyletic, while Tribonematales and Botrydiales are polyphyletic even if evidence for the second order is not conclusive. Botrydiales and Vaucheriales, both including siphonous taxa, do not form a clade. The families Botrydiopsidaceae, Botryochloridaceae, and Pleurochloridaceae as well as the genera Botrydiopsis and Chlorellidium are polyphyletic. The Centritractaceae and the genus Bumilleriopsis also appear to be polyphyletic but their monophyly cannot be completely rejected with current evidence. Our results support morphological convergence at any taxonomic rank in the evolution of the Xanthophyceae. Finally, our phylogenetic analyses exclude an origin of the Xanthophyceae from a Vaucheria-like ancestor and favor a single early origin of the coccoid cell form.     

介形纲丽足目和速足目及相关类群18S rDNA分子系统发育的研究

文中分析现生介形类 (Ostracoda) 4目 2 1科 2 9属的 18SrDNA部分序列 ,采用最大似然法 (ML)、邻接法 (NJ)和最大简约法 (MP) ,尝试构建介形类的分子系统树 ;结合介形类的形态特征和化石记录 ,主要对速足目(Podocopida)、丽足目 (Myodocopida)及其超科级分类阶元的系统发生关系进行探讨。 3种分析方法均支持形态学上Podocopida ,Myodocopida和海萤超科 (Cypridinacea)的界定 ;但对Podocopida目土菱介超科 (Bairdiacea)的系统地位提出质疑 ,该类群可能不是单系发生的自然类群。上述分析显示 ,Podocopida,Myodocopida,Platycopida和Halo cypridina组成一个单系群 ;介形类在目、超科、科和属的水平上可能发生过多次辐射分化     

Phylogenetic relationships of tachinid flies in subfamily Exoristinae (Tachinidae: Diptera) based on 28S rDNA and elongation factor-1α

Abstract The phylogenetic relationships within the largest subfamily of Tachinidae, Exoristinae, were explored using nucleotide sequences of two genes (EF-1α and 28S rDNA). A total of fifty-five and forty-three taxa were represented in the analyses for each gene, respectively, representing forty-three genera. Neighbour joining, parsimony and maximum likelihood inference methods were employed to reconstruct phylogenetic relationships in separate analyses of each gene, and parsimony was used to analyse the combined dataset. Although certain taxa were highly mobile, phylogenetic reconstructions generally supported recent classification schemes based on reproductive habits and genitalia. Generally, the monophyly of Tachinidae and Exoristinae was supported. Tribes Winthemiini, Exoristini and Blondeliini were repeatedly constructed as monophyletic groups, with the former two clades often occupying a basal position among Exoristinae. Goniini and Eryciini generally clustered together as a derived clade within Exoristinae; however, they were never reconstructed as two distinct clades. These results suggest that the possession of unembryonated eggs is plesiomorphic within the subfamily and that there may have been multiple transitions between microtype and macrotype egg forms.     

A molecular phylogeny of celtidaceae and ulmaceae (Urticales) based onrbcL Nucleotide sequences

On the basis of 1,290 bp sequences of the chloroplast generbcL, a molecular phylogeny of seven of nine genera of the Celtidaceae and four of six genera of the Ulmaceae was produced. These data were analyzed together with some other urticalean genera using three methods (i.e., maximum parsimony, maximum likelihood, and neighbor joining methods). Maximum likelihood topology among 18 trees obtained indicated that the Urticales are monophyletic with its common clade splitting basally into two: one leading to a line comprisingAmpelocera (traditionally placed in Celtidaceae) and Ulmaceae, and the other leading to a line comprising the remaining genera of Celtidaceae, Moraceae, and other Urticales. Ulmaceae, to whichAmpelocera is a sister group, are monophyletic, as supported by many lines of morphological evidence. In contrast to Ulmaceae, the monophyly of Celtidaceae (excludingAmpelocera) was not supported, and resolution of relationships of Celtidaceae with other Urticales, as well as of those within the family, is left for future study.     

Molecular biological study on speciation and phylogeny of the order Entomobryomorpha (Collembola: Hexapoda)

In order to elucidate the phylogenetic relationship among groups of the order Entomobryomorpha (Collembola), the sequences on the ITS 1 to ITS 2 fragments of the rRNA gene were analyzed in 11 species of three families. In order to avoid the potential risks and inconsistencies of a single method or data set, the phylogenetic reconstructions were based on three different approaches: methods of maximum parsimony, maximum likelihood and neighbor joining. The inferred phylogenies supported monophyly of the order Entomobryomorpha. The relationships between families were different, but the orders of branching within each family were the same. Entomobryidae and Isotomidae were paraphyletic, whereas Tomoceridae was monophyletic. Tomoceridae was subdivided into two branches; the molecular analysis provided results distinctive enough to separate the two genera by the high bootstrap value. On the other hand, two different populations of putative Homidia koreana appeared to be different species, although their chaetotaxy is identical. A wide coverage of characters, including not only morphological characters but also genetic data such as allozymes and DNA sequences, will give a more accurate picture of the classification and phylogeny of the studied group.     

Molecular Phylogeny of Conjugating Green Algae (Zygnemophyceae,Streptophyta) Inferred from SSU rDNA Sequence Comparisons

Nuclear-encoded SSU rDNA sequences have been obtained from 64 strains of conjugating green algae (Zygnemophyceae, Streptophyta, Viridiplantae). Molecular phylogenetic analyses of 90 SSU rDNA sequences of Viridiplantae (inciuding 78 from the Zygnemophyceae) were performed using complex evolutionary models and maximum likelihood, distance, and maximum parsimony methods. The significance of the results was tested by bootstrap analyses, deletion of long-branch taxa, relative rate tests, and Kishino-Hasegawa tests with user-defined trees. All results support the monophyly of the class Zygnemophyceae and of the order Desmidiales. The second order, Zygnematales, forms a series of early-branching clades in paraphyletic succession, with the two traditional families Mesotaeniaceae and Zygnemataceae not recovered as lineages. Instead, a long-branch Spirogyra/Sirogonium clade and the later-diverging Netrium and Roya clades represent independent clades. Within the order Desmidiales, the families Gonatozygaceae and Closteriaceae are monophyletic, whereas the Peniaceae (represented only by Penium margaritaceum) and the Desmidiaceae represent a single weakly supported lineage. Within the Desmidiaceae short internal branches and varying rates of sequence evolution among taxa reduce the phylogenetic resolution significantly. The SSU rDNA-based phylogeny is largely congruent with a published analysis of the rbcL phylogeny of the Zygnemophyceae (McCourt et al. 2000) and is also in general agreement with classification schemes based on cell wall ultrastructure. The extended taxon sampling at the subgenus level provides solid evidence that many genera in the Zygnemophyceae are not monophyletic and that the genus concept in the group needs to be revised.     

Molecular phylogeny of Pamphagidae (Acridoidea,Orthoptera) from China based on mitochondrial cytochrome oxidase II sequences

Abstract Phylogenetic relationships of Pamphagidae were examined using cytochrome oxidase subunit II (COII) mtDNA sequences (684 bp). Twenty‐seven species of Acridoidea from 20 genera were sequenced to obtain mtDNA data, along with four species from the GenBank nucleotide database. The purpose of this study was analyzing the phylogenetic relationships among subfamilies within Pamphagidae and interpreting the phylogenetic position of this family within the Acridoidea superfamily. Phylogenetic trees were reconstructed using neighbor‐joining (NJ), maximum parsimony (MP) and Bayesian inference (BI) methods. The 684 bp analyzed fragment included 126 parsimony informative sites. Sequences diverged 1.0%–11.1% between genera within subfamilies, and 8.8%–12.3% between subfamilies. Amino acid sequence diverged 0–6.1% between genera within subfamilies, and 0.4%–7.5% between subfamilies. Our phylogenetic trees revealed the monophyly of Pamphagidae and three distinct major groups within this family. Moreover, several well supported and stable clades were found in Pamphagidae. The global clustering results were similar to that obtained through classical morphological classification: Prionotropisinae, Thrinchinae and Pamphaginae were monophyletic groups. However, the current genus Filchnerella (Prionotropisinae) was not a monophyletic group and the genus Asiotmethis (Prionotropisinae) was a sister group of the genus Thrinchus (Thrinchinae). Further molecular and morphological studies are required to clarify the phylogenetic relationships of the genera Filchnerella and Asiotmethis.     

Identifying clades in Asian Annonaceae: monophyletic genera in the polyphyletic Miliuseae

The tribe Miliuseae (Annonaceae) comprises six genera distributed in Asia: Alphonsea, Mezzettia, Miliusa, Orophea, Platymitra, and Phoenicanthus. A phylogenetic study to investigate the putative monophyly of the tribe and the intergeneric relationships is presented here. Nucleotide sequences of the plastid gene rbcL, trnL intron, and trnL-trnF intergenic spacer were analyzed from 114 Annonaceae taxa, including 24 Miliuseae species and two outgroups using maximum parsimony and Bayesian inference. The two data sets (rbcL and the trnL-trnF regions) were analyzed separately and in combination. Miliuseae were found to be polyphyletic due to the position of Mezzettia and are part of a large, predominantly Asian and Central-American clade (miliusoid clade). Although intergeneric relationships were poorly resolved, all genera, except Polyalthia, were monophyletic, supporting previous generic delimitation based on morphology. A group of three Polyalthia species seems the most likely sister group of Miliusa. Several infrageneric groups of Miliusa, Orophea, and Polyalthia are supported by both molecular and morphological data. No morphological synapomorphies have yet been found for the miliusoid clade. Molecular clades within the miliusoid clade, however, can be characterized by size and the shape of the outer petals, number of ovules per carpel, and the size of the fruits.     

Evidence for host-specific clades of tetraphyllidean tapeworms (Platyhelminthes: Eucestoda) revealed by analysis of 18S ssrDNA

Sequence data from the V4 and V7-V9 variable regions of the 18S small subunit ribosomal DNA (ssrDNA) gene were used to examine relationships among 26 tetraphyllidean and two lecanicephalidean taxa. Newly collected specimens of 21 of the tetraphyllidean species were used to generate ssrDNA sequences that were combined with sequences previously available, including those of two diphyllidean taxa used for outgroup rooting. The sequences were aligned by eye according to secondary structural motifs of the conserved core of the molecule. Of the 1520 sites in the alignment, 874 (58%) were excluded from analysis due to alignment gaps and lack of positional homology as inferred by manual inspection. Genetic variability of the ssrDNA gene regions compared was greater than would be expected, based on the present taxonomy of the ingroup species, and the genetic divergences among tetraphyllidean 'families' and genera were comparable to that among tapeworm orders. Phylogenetic hypotheses were generated by the methods of maximum parsimony and maximum likelihood (GTR + I + Gamma nucleotide substitution model). Four most parsimonious trees resulted from analysis by maximum parsimony. Strict consensus of the four trees supported the monophyly of the Tetraphyllidea, with the lecanicephalidean taxa forming a sister lineage. Among the tetraphyllidean taxa included in the analysis were three major clades: a basal clade including species of the phyllobothriid genera Anthocephalum, Echeneibothrium, Rhinebothrium, Rhodobothrium and Spongiobothrium; a clade uniting the phyllobothriids of the genus Duplicibothrium with the dioecotaeniid genus Dioecotaenia; and a larger sister clade to the Duplicibothrium + Dioecotaenia clade that included the phyllobothriid genera Caulohothrium, Ceratobothrium, Clistobothrium, Paraoryigmatobothrium and Prosobothrium, the litobothriid genus Litobothrium and the onchobothriid genera Acanthobothrium, Calliobothrium, Phoreiobothrium and Platybothrium. Maximum likelihood analysis resulted in a topology that was congruent where nodes were strongly supported by parsimony analysis, but differed in the relative positions of the well-supported clades. In addition,maximum likelihood analysis grouped the lecanicephalidean taxa among the tetraphyllidean taxa, indicating paraphyly of the order Tetraphyllidea as currently defined. Relationships suggested by both methods of analysis reflected common host associations of the taxa better than their current classification, suggesting that coevolution has had a significant role in the evolution of the group.     

Phylogeny and evolution of Cervidae based on complete mitochondrial genomes

Mitochondrial DNA sequences can be used to estimate phylogenetic relationships among animal taxa and for molecular phylogenetic evolution analysis. With the development of sequencing technology, more and more mitochondrial sequences have been made available in public databases, including whole mitochondrial DNA sequences. These data have been used for phylogenetic analysis of animal species, and for studies of evolutionary processes. We made phylogenetic analyses of 19 species of Cervidae, with Bos taurus as the outgroup. We used neighbor joining, maximum likelihood, maximum parsimony, and Bayesian inference methods on whole mitochondrial genome sequences. The consensus phylogenetic trees supported monophyly of the family Cervidae; it was divided into two subfamilies, Plesiometacarpalia and Telemetacarpalia, and four tribes, Cervinae, Muntiacinae, Hydropotinae, and Odocoileinae. The divergence times in these families were estimated by phylogenetic analysis using the Bayesian method with a relaxed molecular clock method; the results were consistent with those of previous studies. We concluded that the evolutionary structure of the family Cervidae can be reconstructed by phylogenetic analysis based on whole mitochondrial genomes; this method could be used broadly in phylogenetic evolutionary analysis of animal taxa.     

Utility of plastid psaB gene sequences for investigating intrafamilial relationships within Orchidaceae

DNA sequences of the plastid gene psaB were completed for 182 species of Orchidaceae (representing 150 different genera) and outgroup families in Asparagales. These data were analyzed using parsimony, and resulting trees were compared to a rbcL phylogeny of Orchidaceae for the same set of taxa after an additional 30 new rbcL sequences were added to a previously published matrix. The psaB tree topology is similar to the rbcL tree, although the psaB data contain less homoplasy and provide greater bootstrap support than rbcL alone. In combination, the two-gene tree recovers the five monophyletic subfamilial clades currently recognized in Orchidaceae, but fails to resolve the positions of Cypripedioideae and Vanilloideae. These new topologies help to clarify some of the anomalous results recovered when rbcL is analyzed alone. Both genes appear to be absent from the plastid genome of several achlorophyllous orchids, but are present in the form of presumably non-functional pseudogenes in Cyrtosia. This study is the first to document the utility of psaB sequences for phylogenetic studies of plants below the family level.     

基于18S rRNA基因序列分析唇口目苔藓动物主要类群的系统发生关系

对隶属于3亚目、5次目、20科、23属共25个种类的唇口目(裸唇纲)苔藓虫18S rRNA基因部分序列进行了序列测定.结合从GenBank中获得的该类群其它7个种类的18S rRNA基因同源序列,以序列分析软件对其序列组成和变异进行了比较分析;同时,以羽苔虫(被唇纲)和管孔苔虫(窄唇纲)为外类群,以邻接法和最大简约法重建了它们的系统发生树,分析了该目主要类群系统发生关系.序列分析结果显示:经比对后序列长度为884 bp,其中保守位点241个,可变位点643个,简约信息位点357个;A,T,C和G 4碱基平均含量分别为23.8%、22.8%、24.4%和28.9%.分子系统树表明:本研究所有有囊类构成1个单系群,其中檐胞次目的几种苔虫位于皮壳次目内部;无囊类形成1个多系群,其中的亚目级(新唇口亚目)和次目级分类阶元(枝室次目、假软壁次目和隐壁次目)也都为多系发生,这些结果与前人的分子系统学研究结果大体一致,而与传统的形态分类体系间存在明显的冲突.     

PHYLOGENETIC UTILITY OF rbc S SEQUENCES: AN EXAMPLE FROM ANTITHAMNION AND RELATED GENERA (CERAMIACEAE, RHODOPHYTA)

We report the potential phylogenetic utility of the small RUBISCO subunit ( rbc  S) sequences from a sampling of Antithamnion and related genera in ceramiacean algae. The size of rbc  S was 417 bp for all taxa examined. Analyses of the DNA sequence data indicated that pairwise divergences of rbc  S sequences were 3.3%–9.8% among species of Antithamnion , and ranged from 13.6% to 18.0% between Antithamnion and related genera. Phylogenetic analyses fully resolved relationships at the intrageneric level with statistical significance supported by high bootstrap values. Two subgenera of Antithamnion , Pteroton and Antithamnion , were clearly distinguished in the molecular tree. In the clade of subgenus Pteroton , A. aglandum was allied with A. callocladum and separated from A. nipponicum. In the pairwise distance comparison of sequence variation, Ceramium showed the greatest genetic distances among genera examined in the study. All phylogenetic trees generated by the maximum parsimony, neighbor joining, and maximum likelihood were completely congruent in topology with high confidence.     

Molecular evolution and phylogeny of the atpB-rbcL spacer of chloroplast DNA in the true mosses.

The nucleotide variation of a noncoding region between the atpB and rbcL genes of the chloroplast genome was used to estimate the phylogeny of 11 species of true mosses (subclass Bryidae). The A+T rich (82.6%) spacer sequence is conserved with 48% of bases showing no variation between the ingroup and outgroup. Rooted at liverworts, Marchantia and Bazzania, the monophyly of true mosses was supported cladistically and statistically. A nonparametric Wilcoxon Signed-Ranks test Ts statistic for testing the taxonomic congruence showed no significant differences between gene trees and organism trees as well as between parsimony trees and neighbor-joining trees. The reconstructed phylogeny based on the atpB-rbcL spacer sequences indicated the validity of the division of acrocarpous and pleurocarpous mosses. The size of the chloroplast spacer in mosses fits into an evolutionary trend of increasing spacer length from liverworts through ferns to seed plants. According to the relative rate tests, the hypothesis of a molecular clock was supported in all species except for Thuidium, which evolved relatively fast. The evolutionary rate of the chloroplast DNA spacer in mosses was estimated to be (1.12 +/- 0.019) x 10(-10) nucleotides per site per year, which is close to the nonsynonymous substitution rates of the rbcL gene in the vascular plants. The constrained molecular evolution (total nucleotide substitutions, K approximately 0.0248) of the chloroplast DNA spacer is consistent with the slow evolution in morphological traits of mosses. Based on the calibrated evolutionary rate, the time of the divergence of true mosses was estimated to have been as early as 220 million years ago.     

Value of recN sequences for species identification and as a phylogenetic marker within the family "Leuconostocaceae"

The genera Leuconostoc, Oenococcus, and Weissella (family "Leuconostocaceae") constitute a group of lactic acid bacteria of great interest in food microbiology. From the taxonomic point of view, they are considered phylogenetically coherent according to their 16S rRNA gene sequences and other macromolecules. These three genera were the focus of the present study; specifically, the resolution and discriminatory power of recN (encoding a DNA repair and genetic recombination protein) as a molecular marker at the species level were investigated. For this purpose, partial sequences (about 1200 nt) were obtained from 23 type strains and from several additional strains following direct amplification of recN and subsequent sequencing. Phylogeny was evaluated according to different treeing methods (neighbor joining, maximum likelihood, and maximum parsimony) and the inclusion of variability filters. The results showed that recN, used either alone or in combination with 16S rRNA data, can serve as a phylogenetic marker as well as a tool for species identification.     

Phylogeny of the Polytrichales (Bryophyta) based on simultaneous analysis of molecular and morphological data

Phylogenetic analyses of Polytrichales were conducted using morphology and sequence data from the chloroplast genes rbcL and rps4 plus the trnL-F gene region, part of the mitochondrial nad5 and the nuclear-encoded 18S rDNA. Our analyses included 46 species representing all genera of Polytrichales. Phylogenetic trees were constructed with simultaneous parsimony analyses of all sequences plus morphology and separate combinations of sequence data only. Results lend support for recognition of Polytrichales as a monophyletic entity. Oedipodium griffithianum appears as a sister taxon to Polytrichales or as a sister taxon of all mosses excluding Sphagnales and Andreaeles. Within Polytrichales, Alophosia and Atrichopsis, species without the adaxial lamellae (in Atrichopsis present but poorly developed on male gametophyte) otherwise typical of the group are sister to the remaining species followed by a clade including Bartramiopsis and Lyellia, species with adaxial lamellae covering only the central portion of the leaves. Six taxa with an exclusively Southern Hemisphere distribution form a grade between the basal lineages and a clade including genera that are mostly confined to the Northern Hemisphere.     

Tribal and intergeneric relationships of Mesechiteae (Apocynoideae, Apocynaceae): evidence from three noncoding plastid DNA regions and morphology

The Neotropical tribe Mesechiteae (Apocynaceae) is currently considered to include nine genera: Allomarkgrafia, Galactophora, Macrosiphonia, Mandevilla, Mesechites, Quiotania, Secondatia, Telosiphonia, and Tintinnabularia. Tribal and intergeneric relationships, however, are in dispute. To test the monophyly of the tribe and evaluate intratribal relationships, a maximum parsimony analysis was conducted based on DNA sequences from the plastid rpl16 intron, rps16 intron, and trnS-G intergenic spacer region as well as morphological data for 23 taxa of Mesechiteae and 11 taxa from other tribes of Apocynoideae. Mesechiteae, as currently circumscribed, was found to be polyphyletic. Only removal of Secondatia and Galactophora and inclusion of Forsteronia rendered the tribe monophyletic. Thus defined, Mesechiteae forms a strongly supported clade including seven genera in three subclades: the Mesechites subclade (comprising Tintinnabularia, Allomarkgrafia, and Mesechites), the Forsteronia subclade (containing only Forsteronia) and the Mandevilla subclade (comprising Macrosiphonia, Mandevilla, and Telosiphonia). Allomarkgrafia is nested in Mesechites. Macrosiphonia and Telosiphonia form two distinct monophyletic clades. Both, however, are nested in Mandevilla. Results suggest upholding the following genera in Mesechiteae: Allomarkgrafia, Forsteronia, Mandevilla, Mesechites, and Tintinnabularia. The status of Quiotania could not be evaluated.     

Molecular phylogeny of pontobdelline leeches and their place in the descent of fish leeches (Hirudinea, Piscicolidae)

Phylogenetic relationships of all genera of the fish leech subfamily Pontobdellinae were investigated using mitochondrial (12S rDNA, COI, tRNA-Leu, ND1) and nuclear (28S rDNA) DNA sequences under maximum likelihood, Bayesian inference and parsimony. All methods resulted in trees that corroborated the monophyly of the family Piscicolidae, but recovered their subfamily Pontobdellinae as non-monophyletic. Based on the basal position of the giant Antarctic Megaliobdella szidati , it is hypothesized that the putative ancestor of fish leeches was a free-ranging, large bodied, muscular leech. The next branch contains parasites of cartilaginous fishes, Pontobdella muricata and Pontobdella macrothela . Two remaining genera of the subfamily (the Arctic Oxytonostoma and the Antarctic Moorebdellina ) showed weak affinities to other piscicolid taxa. The obtained phylogenetic hypothesis suggests a possible transition from an ancestral free-ranging life style and temporary parasitism, to parasitism on cartilaginous fishes, followed by parasitism on bony fishes.     

基于孕激素受体基因的类人猿亚目的分子系统学研究

通过对类人猿亚目中部分种类的孕激素受体基因进行分析,重建类人猿亚目的 系统发育关系.扩增并测定了来源于14个属的类人猿亚目物种的孕激素受体编码区序列,并基于这一序列数据,分别采用邻接法、最大简约法和最大似然法重建了系统发育关系.除了阔鼻下目,3种方法构建的系统发生树的拓扑结构类似且各节点支持率高.重建的人猿超科和猴超科内部亲缘关系支持多数人所认可的分类系统.本研究为黑猩猩和人的姐妹群关系提供了证据,提示黑猩猩比大猩猩或其他猿猴更接近人类.阔鼻下目中蜘蛛猴科、卷尾猴科和僧面猴科三者之间的系统发育关系在本研究中未得到很好辨析.