Hidden among Sea Anemones: The First Comprehensive Phylogenetic Reconstruction of the Order Actiniaria (Cnidaria,Anthozoa, Hexacorallia) Reveals a Novel Group of Hexacorals

Sea anemones (order Actiniaria) are among the most diverse and successful members of the anthozoan subclass Hexacorallia, occupying benthic marine habitats across all depths and latitudes. Actiniaria comprises approximately 1,200 species of solitary and skeleton-less polyps and lacks any anatomical synapomorphy. Although monophyly is anticipated based on higher-level molecular phylogenies of Cnidaria, to date, monophyly has not been explicitly tested and at least some hypotheses on the diversification of Hexacorallia have suggested that actiniarians are para- or poly-phyletic. Published phylogenies have demonstrated the inadequacy of existing morphological-based classifications within Actiniaria. Superfamilial groups and most families and genera that have been rigorously studied are not monophyletic, indicating conflict with the current hierarchical classification. We test the monophyly of Actiniaria using two nuclear and three mitochondrial genes with multiple analytical methods. These analyses are the first to include representatives of all three currently-recognized suborders within Actiniaria. We do not recover Actiniaria as a monophyletic clade: the deep-sea anemone Boloceroides daphneae, previously included within the infraorder Boloceroidaria, is resolved outside of Actiniaria in several of the analyses. We erect a new genus and family for B. daphneae, and rank this taxon incerti ordinis. Based on our comprehensive phylogeny, we propose a new formal higher-level classification for Actiniaria composed of only two suborders, Anenthemonae and Enthemonae. Suborder Anenthemonae includes actiniarians with a unique arrangement of mesenteries (members of Edwardsiidae and former suborder Endocoelantheae). Suborder Enthemonae includes actiniarians with the typical arrangement of mesenteries for actiniarians (members of former suborders Protantheae, Ptychodacteae, and Nynantheae and subgroups therein). We also erect subgroups within these two newly-erected suborders. Although some relationships among these newly-defined groups are still ambiguous, morphological and molecular results are consistent enough to proceed with a new higher-level classification and to discuss the putative functional and evolutionary significance of several morphological attributes within Actiniaria.     

Phylogenetic relationships between spiny, slipper and coral lobsters (Crustacea, Decapoda, Achelata)

Molecular data can aid in the resolution of conflicting hypotheses generated through difficulties in the interpretation of morphological data and/or an incomplete fossil record. Moreover, the reconstruction of phylogenetic relationships using molecular data may help to trace back the origin of morphological innovations which had a major impact on the radiation of a taxonomical group. In this work, different nuclear (18S, 28S, and H3) and mitochondrial (16S and COI) gene regions were sequenced in a total of 35 Achelatan species to test conflicting hypotheses of evolutionary relationships within the Achelata infraorder and solve the taxonomic disagreements in the group. The combined molecular dataset strongly supports the hypothesis that Achelata is a monophyletic group composed of two main families: Palinuridae and Scyllaridae. Synaxidae is found to be a polyphyletic group, which should be included within Palinuridae. Consequently, our results indicate that the origin of the stridulating organ occurred only once during Achelata evolution. Finally, the two main clades found within the Scyllaridae are in agreement with previous inferences based on adult morphological data. The dating of divergence of Achelata obtained with a relaxed-clock model is compatible with previous hypotheses of a Triassic origin of the Achelata.     

Sequence alignment of 18S ribosomal RNA and the basal relationships of Adephagan beetles: evidence for monophyly of aquatic families and the placement of Trachypachidae

Current hypotheses regarding family relationships in the suborder Adephaga (Coleoptera) are conflicting. Here we report full-length 18S ribosomal RNA sequences of 39 adephagans and 13 outgroup taxa. Data analysis focused on the impact of sequence alignment on tree topology, using two principally different approaches. Tree alignments, which seek to minimize indels and substitutions on the tree in a single step, as implemented in an approximate procedure by the computer program POY, were contrasted with a more traditional procedure based on alignments followed by phylogenetic inference based on parsimony, likelihood, and distance analyses. Despite substantial differences between the procedures, phylogenetic conclusions regarding basal relationships within Adephaga and relationships between the four suborders of Coleoptera were broadly similar. The analysis weakly supports monophyly of Adephaga, with Polyphaga usually as its sister, and the two small suborders Myxophaga and Archostemata basal to them. In some analyses, however, Polyphaga was reconstructed as having arisen from within Hydradephaga. Adephaga generally split into two monophyletic groups, corresponding to the terrestrial Geadephaga and the aquatic Hydradephaga, as initially proposed by Crowson in 1955, consistent with a single colonization of the aquatic environment by adephagan ancestors and contradicting the recent proposition of three independent invasions. A monophyletic Hydradephaga is consistently, though not strongly, supported under most analyses, and a parametric bootstrapping test significantly rejects an hypothesis of nonmonophyly. The enigmatic Trachypachidae, which exhibit many similarities to aquatic forms but whose species are entirely terrestrial, were usually recovered as a basal lineage within Geadephaga. Strong evidence opposes the view that terrestrial trachypachids are related to the dytiscoid water beetles.     

The origins and evolutionary expansion of the Strongylida (Nematoda)

The Strongylida are thought to have arisen from free-living rhabditoid nematodes, but the relationships between the major groupings within the Strongylida, the Strongylina, the Metastrongylina, Trichostrongylina and the Ancylostomatina are far from clear in spite of the abundance of morphological data now available for analysis. Evolutionary mechanisms including co-evolution, host switching, host dispersal, use of intermediate hosts, various sites of localisation within the definitive host and modifications of life-cycle strategies appear to have been utilised in the expansion of the Strongylida, with different mechanisms predominating in different families or superfamilies. Co-evolution appears to have been a major mode of evolution in the Strongylina, in contrast to the Trichostrongylina, which have used host dispersal and host-switching to great advantage. The phylogeny of the Ancylostomatina shows little association with host evolution, but does match the feeding preferences of the hosts. The Metastrongylina have utilised intermediate hosts and life cycle modifications including a shift to extra-intestinal sites as major means of diversification, in contrast to the other sub-orders. The review, while indicating much progress in our understanding of the phylogeny of the Strongylida, also reveals that enormous gaps still exist, and emphasises the tentative nature of many of the phylogenetic hypotheses tendered to date.     

The tempo and mode of barnacle evolution

Previous phylogenetic attempts at resolving barnacle evolutionary relationships are few and have relied on limited taxon sampling. Here we combine DNA sequences from three nuclear genes (18S, 28S and H3) and 44 morphological characters collected from 76 thoracican (ingroup) and 15 rhizocephalan (outgroup) species representing almost all the Thoracica families to assess the tempo and mode of barnacle evolution. Using phylogenetic methods of maximum parsimony, maximum likelihood, and Bayesian inference and 14 fossil calibrations, we found that: (1) Iblomorpha form a monophyletic group; (2) pedunculated barnacles without shell plates (Heteralepadomorpha) are not ancestral, but have evolved, at least twice, from plated forms; (3) the ontogenetic pattern with 5-->6-->8-->12+ plates does not reflect Thoracica shell evolution; (4) the traditional asymmetric barnacles (Verrucidae) and the Balanomorpha are each monophyletic and together they form a monophyletic group; (5) asymmetry and loss of a peduncle have evolved twice in the Thoracica, resulting in neither the Verrucomorpha nor the Sessilia forming monophyletic groups in their present definitions; (6) the Scalpellomorpha are not monophyletic; (7) the Thoracica suborders evolved since the Early Carboniferous (340mya) with the final radiation of the Sessilia in the Upper Jurassic (147mya). These results, therefore, reject many of the underlying hypotheses about character evolution in the Cirripedia Thoracica, stimulate a variety of new thoughts on thoracican radiation, and suggest the need for a major rearrangement in thoracican classification based on estimated phylogenetic relationships.     

Phylogenetic relationships of annelids,molluscs, and arthropods evidenced from molecules and morphology

Annelids and arthropods have long been considered each other's closest relatives, as evidenced by similarities in their segmented body plans. An alternative view, more recently advocated by investigators who have examined partial 18S ribosomal RNA data, proposes that annelids, molluscs, and certain other minor phyla with trochophore larva stages share a more recent common ancestor with one another than any do with arthropods. The two hypotheses are mutually exclusive in explaining spiralian relationships. Cladistic analysis of morphological data does not reveal phylogentic relationships among major spiralian taxa but does suggest monophyly for both the annelids and molluscs. Distance and maximum-likelihood analyses of 18S rRNA gene sequences from major spiralian taxa suggest a sister relationship between annelids and molluscs and provide a clear resolution within the major groups of the spiralians. The parsimonious tree based on molecular data, however, indicates a sister relationship of the Annelida and Bivalvia, and an earlier divergence of the Gastropoda than the Annelida–Bivalvia clade. To test further hypotheses on the phylogenetic relationships among annelids, molluscs, and arthropods, and the ingroup relationships within the major spiralian taxa, we combine the molecular and morphological data sets and subject the combined data matrix to parsimony analysis. The resulting tree suggests that the molluscs and annelids form a monophyletic lineage and unites the molluscan taxa to a monophyletic group. Therefore, the result supports the Eutrochozoa hypothesis and the monophyly of molluscs, and indicates early acquisition of segmented body plans in arthropods. Received: 25 September 1995 / Accepted: 15 March 1996     

300 million years of diversification: elucidating the patterns of orthopteran evolution based on comprehensive taxon and gene sampling

Orthoptera is the most diverse order among the polyneopteran groups and includes familiar insects, such as grasshoppers, crickets, katydids, and their kin. Due to a long history of conflicting classification schemes based on different interpretations of morphological characters, the phylogenetic relationships within Orthoptera are poorly understood and its higher classification has remained unstable. In this study, we establish a robust phylogeny of Orthoptera including 36 of 40 families representing all 15 currently recognized superfamilies and based on complete mitochondrial genomes and four nuclear loci, in order to test previous phylogenetic hypotheses and to provide a framework for a natural classification and a reference for studying the pattern of divergence and diversification. We find strong support for monophyletic suborders (Ensifera and Caelifera) as well as major superfamilies. Our results corroborate most of the higher‐level relationships previously proposed for Caelifera, but suggest some novel relationships for Ensifera. Using fossil calibrations, we provide divergence time estimates for major orthopteran lineages and show that the current diversity has been shaped by dynamic shifts of diversification rates at different geological times across different lineages. We also show that mitochondrial tRNA gene orders have been relatively stable throughout the evolutionary history of Orthoptera, but a major tRNA gene rearrangement occurred in the common ancestor of Tetrigoidea and Acridomorpha, thereby representing a robust molecular synapomorphy, which has persisted for 250 Myr.     

速足目主要类群系统发育的分子证据

文章基于速足目现生主要类群18S rDNA、28S rDNA和COI基因序列,采用贝叶斯法、邻接法和最大简约法,尝试构建速足目的分子系统树;结合形态特征和化石记录,主要对速足目各超科级分类阶元的系统发育关系进行探讨。结果表明,速足目现生超科Bairdiacea、Darwinulacea、Cypridacea和Cytheracea均为单系群,支持形态学上关于上述4个超科的的界定;3种基因均支持形态学上Darwinulacea和Cypridacea具有较近的亲缘关系的观点。18S rDNA序列分析在较显著水平上支持Darwinulacea和Bairdiacea为姐妹群,Darwinulacea可能从Bairdia-cea中的一支演化而来;Bairdiacea和Darwinulacea组成的分支是Cypridacea的姐妹群,支持将三者合并为Bairdio-copina亚目的观点;Cytheracea是Cypridacea(Darwinulacea Bairdiacea)的姐妹群,可提升为Cytheracopina亚目。     

Phylogenetic relationships within the leaf-mining flies (Diptera: Agromyzidae) inferred from sequence data from multiple genes

The leaf-mining flies (Diptera: Agromyzidae) are a diverse group whose larvae feed internally in leaves, stems, flowers, seeds, and roots of a wide variety of plant hosts. The systematics of agromyzids has remained poorly known due to their small size and morphological homogeneity. We investigated the phylogenetic relationships among genera within the Agromyzidae using parsimony and Bayesian analyses of 2965 bp of DNA sequence data from the mitochondrial COI gene, the nuclear ribosomal 28S gene, and the single copy nuclear CAD gene. We included 86 species in 21 genera, including all but a few small genera, and spanning the diversity within the family. The results from parsimony and Bayesian analyses were largely similar, with major groupings of genera in common. Specifically, both analyses recovered a monophyletic Phytomyzinae and a monophyletic Agromyzinae. Within the subfamilies, genera found to be monophyletic given our sampling include Agromyza, Amauromyza, Calycomyza, Cerodontha, Liriomyza, Melanagromyza, Metopomyza, Nemorimyza, Phytobia, and Pseudonapomyza. Several genera were found to be polyphyletic or paraphyletic including Aulagromyza, Chromatomyia, Phytoliriomyza, Phytomyza, and Ophiomyia. We evaluate our findings and discuss host-use evolution in light of current agromyzid taxonomy and two recent hypotheses of relationships based on morphological data.     

Molecular phylogenetics of Thysanoptera

Analyses of morphological data on the higher-level phylogenetics of Thysanoptera have suggested two alternative hypotheses: (1) sister-taxon status of the monophyletic suborders Terebrantia and Tubulifera. and (2) paraphyly of Terebrantia with respect to Tubulifera. Analyses of nucleotide sequence data from the mitochondrial gene cytochrome oxidase I and the nuclear gene I8S rONA using maximum parsimony. neighbour joining. and maximum likelihood provide strong support for the hypothesis of a sister-taxon relationship between the Terebrantia and Tubulifera. These data resolve this long-standing controversy in thysanopteran phylogenetics and provide a framework for further studies of higher-level relationships in this order.     

Molecular phylogeny of sea snakes reveals a rapidly diverged adaptive radiation

Evolutionary relationships within and between the marine hydrophiine sea snake groups have been inferred primarily using morphological characters, and two major groups traditionally are recognized. The Aipysurus group comprises nine species in two genera, and the taxonomically chaotic Hydrophis group comprises as many as 40 species, of which 27 are generally allocated to the genus Hydrophis and 13 to ten additional genera. In addition to these two major groups are three putatively ‘primitive’ monotypic genera, Hydrelaps darwiniensis, Ephalophis greyi and Parahydrophis mertoni. The present study investigated the evolutionary relationships of 23 representative species of marine hydrophiines, comprising 15 species from the Hydrophis group, six species from the Aipysurus group, and H. darwiniensis and P. mertoni, to address two broad aims. First, the aim was to provide a robust phylogeny for sea snakes to test previous phylogenetic hypotheses based on morphology, and thus provide some taxonomic stability to the group. Second, there was interest in evaluating the hypothesis that the Hydrophis group might represent a rapidly diverged adaptive radiation. A large mitochondrial DNA data set based on the cytochrome b gene (1080 bp, 401 parsimony informative) and the 16S rRNA gene (510 bp, 57 parsimony informative) was assembled and these data were analysed using parsimony, maximum‐likelihood and Bayesian approaches. All analyses yielded virtually the same optimal tree, confirming that hydrophiine sea snakes comprise at least three lineages. The Aipysurus group formed a strongly supported and well‐resolved monophyletic clade. The Hydrophis group also formed a strongly supported clade; however, resolution among the genera and species was very poor. Hydrelaps darwiniensis and P. mertoni formed a sister clade to the Hydrophis lineage. Our phylogeny was used to test the validity of previous taxonomic and phylogenetic hypotheses, and to demonstrate that the genus Hydrophis is not monophyletic. Genetic diversity relative to phenotypic diversity is four to seven times greater in the Hydrophis lineage compared with the Aipysurus lineage. The topology of our phylogenetic hypothesis, combined with the levels of genetic divergence relative to morphological diversity, demonstrate that the Hydrophis lineage represents a rapidly diverged adaptive radiation. The data are consistent with the hypothesis that this adaptive radiation may be due to historical sea level fluctuations that have isolated populations and promoted speciation. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 89 , 523–539.     

Urochordates are monophyletic within the deuterostomes

Understanding the phylogenetic relationships of the three major urochordate groups within the deuterostomes is central to understanding the evolution of the chordates. We have prepared a detailed phylogenetic analysis of urochordates based on comparisons of 10 new urochordate 18S ribosomal DNA sequences with other urochordate sequences in GenBank. Maximum parsimony, neighbor-joining, minimum evolution, and maximum likelihood analyses of this large urochordate data set are consistent with a topology in which the urochordates are monophyletic within the deuterostomes and there are four separate clades of urochordates. These four distinct clades--styelid + pyurid ascidians, molgulid ascidians, phlebobranch ascidians + thaliaceans, and larvaceans--are mostly consistent with traditional morphological hypotheses and classifications. However, we find that the ascidians may not be a monophyletic group (as they have been considered traditionally) but instead appear paraphyletic. Another disparity with traditional classification is that the thaliaceans do not form a separate urochordate clade but rather cluster with the phlebobranch ascidians. Larvaceans have long branch lengths, which can be problematic for molecular phylogenetic methods, and their position within the urochordates cannot be unequivocally determined with 18S rDNA. This is important because the tadpole morphology of larvacean and ascidian larvae is the key trait of interest that distinguishes urochordates as chordates. Nevertheless, the present data set resolves at least three clades of urochordates and suggests strongly that urochordates form a monophyletic clade within the deuterostomes.     

Phylogenetic position of the adeleorinid coccidia (Myzozoa, Apicomplexa, Coccidia, Eucoccidiorida, Adeleorina) inferred using 18S rDNA sequences

Investigating the evolutionary relationships of the major groups of Apicomplexa remains an important area of study. Morphological features and host-parasite relationships continue to be important in the systematics of the adeleorinid coccidia (suborder Adeleorina), but the systematics of these parasites have not been well-supported or have been constrained by data that were lacking or difficult to interpret. Previous phylogenetic studies of the Adeleorina have been based on morphological and developmental characters of several well-described species or based on nuclear 18S ribosomal DNA (rDNA) sequences from taxa of limited taxonomic diversity. Twelve new 18S rDNA sequences from adeleorinid coccidia were combined with published sequences to study the molecular phylogeny of taxa within the Adeleorina and to investigate the evolutionary relationships of adeleorinid parasites within the Apicomplexa. Three phylogenetic methods supported strongly that the suborder Adeleorina formed a monophyletic clade within the Apicomplexa. Most widely recognized families within the Adeleorina were hypothesized to be monophyletic in all analyses, although the single Hemolivia species included in the analyses was the sister taxon to a Hepatozoon sp. within a larger clade that contained all other Hepatozoon spp. making the family Hepatozoidae paraphyletic. There was an apparent relationship between the various clades generated by the analyses and the definitive (invertebrate) host parasitized and, to lesser extent, the type of intermediate (vertebrate) host exploited by the adeleorinid parasites. We conclude that additional taxon sampling and use of other genetic markers apart from 18S rDNA will be required to better resolve relationships among these parasites.     

Phylogeny of the Trichostrongylina (Nematoda) inferred from 28S rDNA sequences

We produced a molecular phylogeny of species within the order Strongylida (bursate nematodes) using the D1 and D2 domains of 28S rDNA, with 23 new sequences for each domain. A first analysis using Caenorhabditis elegans as an outgroup produced a tree with low resolution in which three taxa (Dictyocaulus filaria, Dictyocaulus noerneri, and Metastrongylus pudendotectus) showed highly divergent sequences. In a second analysis, these three species and C. elegans were removed and an Ancylostomatina, Bunostomum trigonocephalum, was chosen (on the basis of previous morphological analyses) as the outgroup for an analysis of the phylogenetic relationships between and within the Strongylina (strongyles) and Trichostrongylina (trichostrongyles). A very robust tree was obtained. The Trichostrongylina were monophyletic, but the Strongylina were paraphyletic, though this requires confirmation. Within the Trichostrongylina, the three superfamilies defined from morphological characters are confirmed, with the Trichostrongyloidea sister group to a clade including the Molineoidea and Heligmosomoidea. Within the Trichostrongyloidea, the Cooperiidae, Trichostrongylidae, and Haemonchidae were polytomous, the Haemonchinae were monophyletic, but the Ostertagiinae were paraphyletic. The sister-group relationships between Molineoidea and Heligmosomoidea were unsuspected from previous morphological analysis. No unequivocal morphological synapomorphy could be found for the grouping Molineoidea + Heligmosomoidea, but none was found which contradicted it.     

Phylogenetic relationships in Nuphar (Nymphaeaceae): evidence from morphology,chloroplast DNA,and nuclear ribosomal DNA

The genus Nuphar consists of yellow-flowered waterlilies and is widely distributed in north-temperate bodies of water. Despite regular taxonomic evaluation of these plants, no explicit phylogenetic hypotheses have been proposed for the genus. We investigated phylogenetic relationships in Nuphar using morphology and sequences of the chloroplast gene matK and of the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA. Two major lineages within Nuphar are consistently resolved with the morphological and molecular data sets. One lineage comprises New World taxa and the other represents a primarily Old World lineage. Relationships within the major lineages were poorly resolved by morphology and ITS, yet certain relationships were elucidated by all analyses. Most notable is the strong support for a monophyletic lineage of dwarf taxa and the alliance of the North American N. microphylla with the Eurasian taxa. Minor discordance between the independent cladograms is accounted for by hybridization. The common taxonomic practice of uniting all North American and Eurasian taxa under one species is not supported phylogenetically.     

Evolutionary relationships of trichostrongyloid nematodes (Strongylida) inferred from ribosomal DNA sequence data

The evolutionary relationships of 21 species of trichostrongyloid nematodes were determined by use of sequence data of the second internal transcribed spacer of the ribosomal DNA aligned according to secondary structure information. Irrespective of the method of analysis used, the topologies of the phylogenetic trees derived from the molecular data differed with respect to all four hypotheses proposed previously for the evolutionary relationships of the different subfamilies within the Trichostrongylidae based on morphological data. Thus, the molecular data set did not resolve the conflict between the four previous proposals for the subfamilial relationships. Nonetheless, all trees derived from the molecular data showed strong support for the exclusion of the genera Filarinema and Amidostomum from the clade containing the species within the family Trichostrongylidae. This represents a major difference from the most recent proposal of the systematics of the Trichostrongyloidea in which these two genera were included within the Trichostrongylidae. Therefore, the molecular data support an earlier systematic framework in which Filarinema and Amidostomum were considered to be sister groups of the Trichostrongyloidea.     

A molecular analysis of the interrelationships of tetraodontiform fishes (Acanthomorpha: Tetraodontiformes)

Tetraodontiform fishes (e.g., triggerfishes, boxfishes, pufferfishes, and giant ocean sunfishes) have long been recognized as a monophyletic group. Morphological analyses have resulted in conflicting hypotheses of relationships among the tetraodontiform families. Molecular data from the single-copy nuclear gene RAG1 and from two mitochondrial ribosomal genes, 12S and 16S, were used to test these morphology-based hypotheses. Total evidence (RAG1+12S+16S), RAG1-only, and mitochondrial-only analyses were performed using both maximum parsimony and Bayesian criteria. Total evidence and RAG1-only analyses recover a monophyletic Tetraodontiformes. However, the relationships recovered within the order differ, and none completely conform to previous hypotheses. Analysis of mitochondrial data alone fails to recover a monophyletic Tetraodontiformes and therefore does not support any of the morphology-based topologies. The RAG1 data appear to give the best estimate of tetraodontiform phylogeny, resulting in many strongly supported nodes and showing a high degree of congruence between both parsimony and Bayesian analyses. All analyses recover every tetraodontiform family for which more than one representative is included as a strongly supported monophyletic group. Balistidae and Monacanthidae are recovered as sister groups with robust support in every analysis, and all analyses except the Bayesian analyses of the mitochondrial data alone recover a strongly supported sister-group relationship between Tetraodontidae and Diodontidae. Many of the intrafamilial relationships recovered from the molecular data presented here corroborate previous morphological hypotheses.