Monophyly of the family Desmoscolecidae (Nematoda,Demoscolecida) and Its Phylogenetic position inferred from 18S rDNA sequences

To infer the monophyletic origin and phylogenetic relationships of the order Desmoscolecida, a unique and puzzling group of mainly free-living marine nematodes, we newly determined nearly complete 18S rDNA sequences for six marine desmoscolecid nematodes belonging to four genera (Desmoscolex, Greeffiella, Tricoma and Paratricoma). Based on the present data and those of 72 nematode species previously reported, the first molecular phylogenetic analysis focusing on Desmoscolecida was done by using neighbor joining (NJ), maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) methods. All four resultant trees consistently and strongly supported that the family Desmoscolecidae forms a monophyletic group with very high node confidence values. The monophyletic clade of desmocolecid nematodes was placed as a sister group of the clade including some members of Monhysterida and Araeolaimida, Cyartonema elegans (Cyartonematidae) and Terschellingia longicaudata (Linhomoeidae) in all the analyses. However, the present phylogenetic trees do not show any direct attraction between the families Desmoscolecidae and Cyartonematidae. Within the monophyletic clade of the family Desmoscolecidae in all of the present phylogenetic trees, there were consistently observed two distinct sub-groups which correspond to the subfamilies Desmoscolecinae [Greeffiella sp. + Desmoscolex sp.] and Tricominae [Paratricoma sp. + Tricoma sp].     

Phylogenetic analyses of various euglenoid taxa (euglenozoa) based on 18s rdna sequence data

18S rRNA genes (SSU rDNA) of five newly sequenced species were used as molecular markers to infer phylogenetic relationships within the euglenoids. Two members of the order Euglenales ( Lepocinclis ovata Playfair , Phacus similis Christen), two of the order Eutreptiales ( Distigma proteus Ehrenberg, , D. curvata Pringsheim) and Gyropaigne lefévrei Bourelly et Georges of the order Rhabdomonadales were used in parsimony, maximum likelihood, and distance analyses. All trees derived from SSU rRNA data strongly supported the monophyletic origin of the Euglenozoa, with kinetoplastids as sister clade to the euglenoids and Petalomonas cantuscygni Cann et Pennick diverging at the base of the monophyletic euglenoid lineage. The data also supported the theory that phagotrophic euglenoids arose prior to osmotrophs and phototrophs. A lineage of Peranema trichophorum Ehrenberg and all sequenced Euglenales formed a sister clade to the osmotrophs. This suggests that the evolution of phototrophy within the euglenoids radiated from a single event.     

Phylogenetic relationships of mullets (Mugilidae) in China Seas based on partial sequences of two mitochondrial genes

Phylogenetic analyses of Mugilidae species from the China coast were carried out based on 16S and 12S rRNA mitochondrial gene sequences by maximum parsimony, maximum likelihood, Bayesian inference and neighbor joining analysis in the present study. The results suggested that Mugil cephalus is the most genetically divergent species among the Mugilidae. The four Liza species clustered together and formed a monophyletic group. The genera Osteomugil showed closer affiliation with Valamugil than with Ellochelon; these three genera then grouped together to form a monophyletic clade presenting as the sister group to Liza. Analyses of phylogenetic and genetic distance indicated that Southern and Northern lineages of Liza haematocheila may be two different species; likewise, strong genetic divergence existed between Southern and Northern M. cephalus lineages. In addition, our results supported the Southern origin of Chinese Mugilids, which is contrary to the hypothesis based on morphological characters.     

A molecular phylogeny of fleas (Insecta: Siphonaptera): origins and host associations

Siphonaptera (fleas) is a highly specialized order of holometabolous insects comprising ～2500 species placed in 16 families. Despite a long history of extensive work on flea classification and biology, phylogenetic relationships among fleas are virtually unknown. We present the first formal analysis of flea relationships based on a molecular matrix of four loci (18S ribosomal DNA, 28S ribosomal DNA, Cytochrome Oxidase II, and Elongation Factor 1‐alpha) for 128 flea taxa from around the world representing 16 families, 25 subfamilies, 26 tribes, and 83 flea genera with eight outgroups. Trees were reconstructed using direct optimization and maximum likelihood techniques. Our analysis supports Tungidae as the most basal flea lineage, sister group to the remainder of the extant fleas. Pygiopsyllomorpha is monophyletic, as are the constituent families Lycopsyllidae, Pygiopsyllidae, and Stivaliidae, with a sister group relationship between the latter two families. Macropsyllidae is resolved as sister group to Coptopsyllidae with moderate nodal support. Stephanociricidae is monophyletic, as are the two constituent subfamilies Stephanocircinae and Craneopsyllinae. Vermipsyllidae is placed as sister group to Jordanopsylla. Rhopalopsyllidae is monophyletic as are the two constituent subfamilies Rhopalopsyllinae and Parapsyllinae. Hystrichopsyllidae is paraphyletic with Hystrichopsyllini placed as sister to some species of Anomiopsyllini and Ctenopariini placed as sister to Carterettini. Ctenophthalmidae is grossly paraphyletic with the family broken into seven lineages dispersed on the tree. Most notably, Anomiopsyllini is paraphyletic. Pulicidae and Chimaeropsyllidae are both monophyletic and these families are sister groups. Ceratophyllomorpha is monophyletic and includes Ischnopsyllidae, Ceratophyllidae, and Leptopsyllidae. Leptopsyllidae is paraphyletic as are its constituent subfamilies Amphipsyllinae and Leptopsyllinae and the tribes Amphipsyllini and Leptopsyllini. Ischnopsyllidae is monophyletic. Ceratophyllidae is monophyletic, with a monophyletic Dactypsyllinae nested within Ceratophyllinae, rendering the latter group paraphyletic. Mapping of general host associations on our topology reveals an early association with mammals with four independent shifts to birds. © The Willi Hennig Society 2008.     

基于18S rDNA序列的蝽次目(半翅目：异翅亚目)

利用18SrDNA分子约1 912 bp的序列对蝽次目21个科53个种进行系统发育分析。运用MP法、ML法和NJ法分析后的结果表明:蝽次目的单系性得到很高的支持;扁蝽总科成为毛点类的姐妹群;毛点类基本确定为两大分支:一支包含蝽总科和红蝽总科;另一支主要由长蝽总科、缘蝽总科和南蝽总科组成;长蝽总科和缘蝽总科都是多系;长蝽总科中,跷蝽科和皮蝽科的关系最近,构成姐妹群,位于整个毛点类的基部;与长蝽总科中另外两个科长蝽科和地长蝽科的关系很远。说明利用18SrDNA分子对研究蝽次目的系统发育关系是适合的,能够重建蝽次目;扁蝽总科和蝽总科单系性的结果与形态学的研究以及Li et al (2005)的研究一致;但较Li et al(2005)的研究更进一步把红蝽总科从广义的缘蝽总科中分出来;并建议皮蝽科作为一个独立的总科更合适。     

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.     

Description of Phaeobola aeris gen. nov., sp. nov (Rhizaria,Cercozoa, Euglyphida) Sheds Light on Euglyphida’s Dark Matter

The majority of Euglyphida species are characterised by shells with imbricated silica scales. Environmental surveys indicate a large unexplored diversity and recent efforts hinted at a certain diversity of yet undescribed, inconspicuous, scale-lacking Euglyphida. Here we describe Phaeobola aeris gen. nov., sp. nov. that shows a variety of morphological characters typical for the Euglyphida but lacks silica scales-instead, this species bears an agglutinated test. Neither its morphology nor phylogenetic placement allows its assignment to any currently described family. We erected the yet monospecific genus Phaeobola gen. nov., which with yet available data remain Euglyphida incertae sedis.     

Insights into the Evolution of Nuclear Dualism in the Ciliates Revealed by Phylogenetic Analysis of rRNA Sequences

The small subunit rRNA gene sequences of the karyorelictean ciliates, Loxodes striatus and Protocruzia sp., and the heterotrichian ciliates, Climacostomum virens and Eufolliculina uhligi , were used to test the evolution of nuclear dualism in the Phylum Ciliophora. Phylogenies derived using a least squares distance method, neighbour joining, and maximum parsimony demonstrate that the karyorelictean ciliates sensu Small and Lynn, 1985 do not form a monophyletic group. However, Loxodes and the heterotrich ciliates form the first branch in the ciliate lineage, and Protocruzia branches, in distance methods, basal to the spirotrich lineage. It is proposed that Protocruzia be removed from the Class Karyorelictea, and placed in closer taxonomic association with the spirotrich lineage. The distribution of nuclear division types along the phylogenetic tree is consistent with the notion that macronuclei incapable of division represent a derived rather than a primitive or "karyorelictid" character trait.     

Multigene analysis of lophophorate and chaetognath phylogenetic relationships

Maximum likelihood and Bayesian inference analyses of seven concatenated fragments of nuclear-encoded housekeeping genes indicate that Lophotrochozoa is monophyletic, i.e., the lophophorate groups Bryozoa, Brachiopoda and Phoronida are more closely related to molluscs and annelids than to Deuterostomia or Ecdysozoa. Lophophorates themselves, however, form a polyphyletic assemblage. The hypotheses that they are monophyletic and more closely allied to Deuterostomia than to Protostomia can be ruled out with both the approximately unbiased test and the expected likelihood weights test. The existence of Phoronozoa, a putative clade including Brachiopoda and Phoronida, has also been rejected. According to our analyses, phoronids instead share a more recent common ancestor with bryozoans than with brachiopods. Platyhelminthes is the sister group of Lophotrochozoa. Together these two constitute Spiralia. Although Chaetognatha appears as the sister group of Priapulida within Ecdysozoa in our analyses, alternative hypothesis concerning chaetognath relationships could not be rejected.     

Analysis of Ribosomal RNA Genes Suggests That Trypanosomes Are Monophyletic

To further investigate the phylogeny of protozoa from the order Kinetoplastida we have sequenced the small subunit (SSU) and a portion of the large subunit (LSU) nuclear rRNA genes. The SSU and LSU sequences were determined from a lizard trypanosome, Trypanosoma scelopori and a bodonid, Rhynchobodo sp., and the LSU sequences were determined from an insect trypanosomatid, Crithidia oncopelti, and a bodonid, Dimastigella trypaniformis. Contrary to previous results, in which trypanosomes were found to be paraphyletic, with Trypanosoma brucei representing the earliest-diverging lineage, we have now found evidence for the monophyly of trypanosomes. Addition of new taxa which subdivide long branches (such as that of T. brucei) have helped to identify homoplasies responsible for the paraphyletic trees in previous studies. Although the monophyly of the trypanosome clade is supported in the bootstrap analyses for maximum likelihood at 97% and maximum parsimony at 92%, there is only a small difference in ln-likelihood value or tree length between the most optimal monophyletic tree and the best suboptimal paraphyletic tree. Within the trypanosomatid subtree, the clade of trypanosomes is a sister group to the monophyletic clade of the nontrypanosome genera. Different groups of trypanosomes group on the tree according to their mode of transmission. This suggests that the adaptation to invertebrate vectors plays a more important role in the trypanosome evolution than the adaptation to vertebrate hosts. Received: 5 July 1996 / Accepted: 26 September 1996     

Molecular phylogeny and evogenomics of heterocystous cyanobacteria using rbcl gene sequence data

Taxonomic affiliations and molecular diversity of 41 heterocystous cyanobacteria representing 12 genera have been assessed on an evolutionary landscape using rbcl gene sequence data-based phylogenomics and evogenomics approaches. Phylogenetic affiliations have clearly demonstrated the polyphyly of the true branching cyanobacteria, along with a frequent intermixing amongst the heterocystous cyanobacteria. The monophyletic origin of the heterocystous cyanobacteria was also quite evident from maximum parsimony and neighbor joining analyses. Incongruency with the traditional scheme of cyanobacterial taxonomy was frequently observed, thus advocating towards some re-amendments in the cyanobacterial classificatory schemes. Evogenomics analyses of gene sequence data gave a clear indication about the greater evolutionary pace of the unbranched cyanobacteria as compared to the branched forms. It was evident that the order Nostocales would be controlling the future pace of evolution of heterocystous cyanobacteria. The cyanobacteria Nostoc was found to have the greatest genetic heterogeneity amongst the studied genera, along with some evidence towards events of lateral gene transfer amongst the heterocystous cyanobacteria in case of the rbcl gene. Thus, heterocystous cyanobacteria were found to be a fast evolving group, with estimates of gene conversion tracts pointing towards the unbranched heterocystous cyanobacteria being at the base of evolutionary diversifications of the complete heterocystous lineage.     

Complete Mitochondrial Genome of a Neotropical Fruit Bat, Artibeus jamaicensis, and a New Hypothesis of the Relationships of Bats to Other Eutherian Mammals

The complete mitochondrial genome was obtained from a microchiropteran bat, Artibeus jamaicensis. The presumptive amino acid sequence for the protein-coding genes was compared with predicted amino acid sequences from several representatives of other mammalian orders. Data were analyzed using maximum parsimony, maximum likelihood, and neighbor joining. All analyses placed bats as the sister group of carnivores, perissodactyls, artiodactyls, and cetaceans (e.g., 100% bootstrap value with both maximum parsimony and neighbor joining). The data strongly support a new hypothesis about the origin of bats, specifically a bat/ferungulate grouping. None of the analyses supported the superorder Archonta (bats, flying lemurs, primates, and tree shrews). Our hypothesis regarding the relationship of bats to other eutherian mammals is concordant with previous molecular studies and contrasts with hypotheses based solely on morphological criteria and an incomplete fossil record. The A. jamaicensis mitochondrial DNA control region has a complex pattern of tandem repeats that differs from previously reported chiropteran control regions. Received: 22 January 1998 / Accepted: 3 June 1998     

Phylogeny of West AfricanCaryedon(Coleoptera: Bruchidae): Congruence between Molecular and Morphological Data

Seed beetles belonging to the Old World genusCaryedonfeed in the seeds of various Caesalpinioideae, Mimosoideae, and Combretaceae. In an attempt to resolve broad phylogenetic relationships within the genus, we obtained 332 base pair sequences of mitochondrial 12S ribosomal DNA and morphological data for the 16 West AfricanCaryedonspecies. Morphological characters were analyzed under maximum parsimony and sequences were compared under maximum parsimony, maximum likelihood, and neighbor joining. Using a partition homogeneity test, we determined that morphological and molecular data sets were combinable. Combined data were analyzed under maximum parsimony. Morphological and molecular trees were congruent at the species group level and total evidence analyses yielded the same topologies as molecular data with each of the three outgroups used. Four main terminal clades are recognized, each corresponding with a group of species generally feeding on the same host plant family, subfamily, genus, or species. The monophyly of legume feedingCaryedonis supported by both data sets, and Combretaceae feeders split in two monophyletic assemblages.     

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     

The robustness of two phylogenetic methods: four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining

The robustness (sensitivity to violation of assumptions) of the maximum- likelihood and neighbor-joining methods was examined using simulation. Maximum likelihood and neighbor joining were implemented with Jukes- Cantor, Kimura, and gamma models of DNA substitution. Simulations were performed in which the assumptions of the methods were violated to varying degrees on three model four-taxon trees. The performance of the methods was evaluated with respect to ability to correctly estimate the unrooted four-taxon tree. Maximum likelihood outperformed neighbor joining in 29 of the 36 cases in which the assumptions of both methods were satisfied. In 133 of 180 of the simulations in which the assumptions of the maximum-likelihood and neighbor-joining methods were violated, maximum likelihood outperformed neighbor joining. These results are consistent with a general superiority of maximum likelihood over neighbor joining under comparable conditions. They extend and clarify an earlier study that found an advantage for neighbor joining over maximum likelihood for gamma-distributed mutation rates.      

基于16S rRNA序列的角蟾科部分属间系统关系

采用最大似然法(ML法)、最大简约法(MP法)、邻接法(NJ法)对来自角蟾科Megophryidae(Anura)8属17种及外群2种共25条400bp左右的线粒体16S rRNA序列进行系统发育关系分析。结果表明,用于分析的所有角蟾科物种形成两大支,第一支包括Megophrys,Brachytarsophrys和Atympanophrys,第二支包括Leptobrachium,Leptolalax,Scutiger,Oreolalax和Vibrissaphora。支持将角蟾科划分为两大类群,即第一支属于Megophryini族．第二支属于Leptobrachiini族。根据分子钟模型初步推测两类群问的分歧时间大致为14．2～18．7百万年前。在Megophryini族中,基因树的拓扑结构不支持Atympanophrys建立后的Megophrys为单系;而在Leptobrachiini族中,Leptolalax为一有效属,其系统发生较早。     

Family-level relationships of Onagraceae based on chloroplast rbcL and ndhF data

Despite intensive morphological and molecular studies of Onagraceae, relationships within the family are not fully understood. One drawback of previous analyses is limited sampling within the large tribe Onagreae. In addition, the monophyly of two species-rich genera in Onagreae, Camissonia and Oenothera, has never been adequately tested. To understand relationships within Onagraceae, test the monophyly of these two genera, and ascertain the affinities of the newly discovered genus Megacorax, we conducted parsimony and maximum likelihood analyses with rbcL and ndhF sequence data for 24 taxa representing all 17 Onagraceae genera and two outgroup Lythraceae. Results strongly support a monophyletic Onagraceae, with Ludwigia as the basal lineage and a sister-taxon relationship between Megacorax and Lopezia. Gongylocarpus is supported as sister to Epilobieae plus the rest of Onagreae, although relationships within the latter clade have limited resolution. Thus, we advocate placement of Gongylocarpus in a monogeneric tribe, Gongylocarpeae. Most relationships within Onagreae are weakly resolved, suggesting a rapid diversification of this group in western North America. Neither Camissonia nor Oenothera appears to be monophyletic; however, increased taxon sampling is needed to clarify those relationships. Morphological characters generally agree with the molecular data, providing further support for relationships.     

Phylogeny and classification of the Grimmiaceae/Ptychomitriaceae complex (Bryophyta) inferred from cpDNA

Phylogenetic relationships within the Grimmiaceae/Ptychomitriaceae were studied using a plastid tRNA cluster, including four tRNAs (trnS, trnT, trnL, trnF), a fast evolving gene (rps4), four spacers separating the coding regions, as well as one group I intron. Secondary structure analyses of the spacers as well as the trnL intron P8 domain identified several homoplastic inversions. Tracing the structural evolution of P8 we were able to identify lineage specific modifications that are mainly explained by inversions often in combination with large indel events. Phylogenetic analyses using maximum parsimony, maximum likelihood, and Bayesian methods indicate that Jaffueliobryum and Indusiella are closely related to Ptychomitrium and form the Ptychomitriaceae s. str. As Campylostelium is neither resolved within Ptychomitriaceae s. str. nor Grimmiaceae s. str., we prefer to treat it in its own family, Campylosteliaceae De Not. The systematic position of Glyphomitrium, as also found by other authors, should be considered in a broader analysis of haplolepidous mosses as our analyses indicate that it is not part of Campylosteliaceae, Grimmiaceae, or Ptychomitriaceae. Within Grimmiaceae s. str., Racomitrium is recognized as a monophyletic group sister to a clade including Dryptodon, Grimmia, and Schistidium. Coscinodon species appear disperse in Grimmia s. str. next to species sharing the same gametophyte morphology, and thus the genus is synonymized with Grimmia. Finally, Schistidium is resolved monophyletic with high statistical support, and seems to represent a rapidly evolving group of species. Our results are not fully congruent with recently published treatments splitting Grimmiaceae in a fairly high number of genera, neither with a comprehensive Grimmia including Dryptodon and Grimmia s. str.     

A comprehensive molecular phylogeny of tiger beetles (Coleoptera,Carabidae, Cicindelinae)

Tiger beetles are a remarkable group that captivates amateur entomologists, taxonomists and evolutionary biologists alike. This diverse clade of beetles comprises about 2300 currently described species found across the globe. Despite the charisma and scientific interest of this lineage, remarkably few studies have examined its phylogenetic relationships with large taxon sampling. Prior phylogenetic studies have focused on relationships within cicindeline tribes or genera, and none of the studies have included sufficient taxon sampling to conclusively examine broad species patterns across the entire subfamily. Studies that have attempted to reconstruct higher‐level relationships of Cicindelinae have yielded conflicting results. Here, we present the first taxonomically comprehensive molecular phylogeny of Cicindelinae to date, with the goal of creating a framework for future studies focusing on this important insect lineage. We utilized all available published molecular data, generating a final concatenated dataset including 328 cicindeline species, with molecular data sampled from six protein‐coding gene fragments and three ribosomal gene fragments. Our maximum‐likelihood phylogenetic inferences recover Cicindelinae as sister to the wrinkled bark beetles of the subfamily Rhysodinae. This new phylogenetic hypothesis for Cicindelinae contradicts our current understanding of tiger beetle phylogenetic relationships, with several tribes, subtribes and genera being inferred as paraphyletic. Most notably, the tribe Manticorini is recovered nested within Platychilini including the genera Amblycheila Say, Omus Eschscholtz, Picnochile Motschulsky and Platychile Macleay. The tribe Megacephalini is recovered as paraphyletic due to the placement of the monophyletic subtribe Oxycheilina as sister to Cicindelini, whereas the monophyletic Megacephalina is inferred as sister to Oxycheilina, Cicindelini and Collyridini. The tribe Collyridini is paraphyletic with the subtribes Collyridina and Tricondylina in one clade, and Ctenostomina in a second one. The tribe Cicindelini is recovered as monophyletic although several genera are inferred as para‐ or polyphyletic. Our results provide a novel phylogenetic framework to revise the classification of tiger beetles and to encourage the generation of focused molecular datasets that will permit investigation of the evolutionary history of this lineage through space and time.