A molecular phylogenetic framework for the phylum Ctenophora using 18S rRNA genes.

This paper presents the first molecular phylogenetic analysis of the phylum Ctenophora, by use of 18S ribosomal RNA sequences from most of the major taxa. The ctenophores form a distinct monophyletic group that, based on this gene phylogeny, is most closely related to the cnidarians. Our results suggest that the ancestral ctenophore was tentaculate and cydippid-like and that the presently recognized order Cydippida forms a polyphyletic group. The other ctenophore orders that we studied (Lobata, Beroida, and Platyctenida) are secondarily derived from cydippid-like ancestors, a conclusion that is also supported by developmental and morphological data. The very short evolutionary distances between characterized ctenophore 18S rRNA gene sequences suggests that extant ctenophores are derived from a recent common ancestor. This has important consequences for future studies and for an understanding of the evolution of the metazoans.     

Haeckelia (= Euchlora) and Hydroctena and the phylogenetic interrelationships of Cnidaria and Ctenophora

A scrutiny of the literature shows that the ctenophore Haeckelia (= Euchlora) ruba has only kleptocnidae and that Hydroctena salenskii is a ctenophore without special cnidarian affinities. The “missing links” between cnidarians and ctenophores have thus turned out to be based on misinterpretations and must be excluded from future discussions on phylogeny.     

Reorganising the order Bacillales through phylogenomics

Bacterial classification at higher taxonomic ranks such as the order and family levels is currently reliant on phylogenetic analysis of 16S rRNA and the presence of shared phenotypic characteristics. However, these may not be reflective of the true genotypic and phenotypic relationships of taxa. This is evident in the order Bacillales, members of which are defined as aerobic, spore-forming and rod-shaped bacteria. However, some taxa are anaerobic, asporogenic and coccoid. 16S rRNA gene phylogeny is also unable to elucidate the taxonomic positions of several families incertae sedis within this order. Whole genome-based phylogenetic approaches may provide a more accurate means to resolve higher taxonomic levels. A suite of phylogenomic approaches were applied to re-evaluate the taxonomy of 80 representative taxa of eight families (and six family incertae sedis taxa) within the order Bacillales. This showed several anomalies in the current family and order level classifications including the existence of four Bacillaceae and two Paenibacillaceae “family” clades. Furthermore, the families Staphylococcaceae and Listeriaceae belong to the sister order Lactobacillales. Finally, we propose a consensus phylogenomic approach which may diminish algorithmic biases associated with single approaches and facilitate more accurate classification of a broad range of taxa at the higher taxonomic levels.     

Eoandromeda and the origin of Ctenophora

The Ediacaran fossil Eoandromeda octobrachiata had a high conical body with eight arms in helicospiral arrangement along the flanks. The arms carried transverse bands proposed to be homologous to ctenophore ctenes (comb plates). Eoandromeda is interpreted as an early stem‐group ctenophore, characterized by the synapomorphies ctenes, comb rows, and octoradial symmetry but lacking crown‐group synapomorphies such as tentacles, statoliths, polar fields, and biradial symmetry. It probably had a pelagic mode of life. The early appearance in the fossil record of octoradial ctenophores is most consistent with the Planulozoa hypothesis (Ctenophora is the sister group of Cnidaria + Bilateria) of metazoan phylogeny.     

Molecular phylogenetics of Vespoidea indicate paraphyly of the superfamily and novel relationships of its component families and subfamilies

The 24 000+ described species of Vespoidea include many well-known stinging wasps, such as paper wasps and hornets (Vespidae), velvet ants (Mutillidae), spider wasps (Pompilidae) and ants (Formicidae). The compelling behaviours of vespoids have been instrumental in developing theories of stepwise evolutionary transitions, which necessarily depend on an understanding of phylogeny, yet, existing morphological phylogenies for Vespoidea conflict. We collected molecular data from four nuclear genes (elongation factor-1α F2 copy, long-wavelength rhodopsin, wingless and the D2–D3 regions of 28S ribosomal RNA (2700 bp in total)) to produce the first molecular phylogeny of Vespoidea. We analysed molecular data alone and in combination with published morphological data from Brothers and Carpenter. Parsimony analyses left many deeper nodes unsupported, but suggested paraphyly of three families. Total-evidence Bayesian inference produced a more resolved tree, in which the monophyly of Vespoidea was nevertheless ambiguous. Bayesian inference of molecular data alone returned a well-resolved consensus with posterior probabilities of over 95% for most nodes. We used this topology as the best estimate of phylogeny at the family and subfamily levels. Notable departures from previous estimates include: (i) paraphyly of Vespoidea resulting from the nesting of Apoidea within a lineage comprising Formicidae, Scoliidae and two subfamilies of Bradynobaenidae; (ii) paraphyly of Bradynobaenidae, Mutillidae and Tiphiidae; (iii) a sister relationship between Rhopalosomatidae and Vespidae; and (iv) Rhopalosomatidae + Vespidae as sister to all other vespoids/apoids. We discuss character evidence in light of the new phylogeny, and propose a new classification of Aculeata that recognizes eight superfamilies: Apoidea, Chrysidoidea, Formicoidea, Pompiloidea, Scolioidea, Tiphioidea, Thynnoidea and Vespoidea.     

Bacterial communities associated with the ctenophores Mnemiopsis leidyi and Beroe ovata

Residing in a phylum of their own, ctenophores are gelatinous zooplankton that drift through the ocean's water column. Although ctenophores are known to be parasitized by a variety of eukaryotes, no studies have examined their bacterial associates. This study describes the bacterial communities associated with the lobate ctenophore Mnemiopsis leidyi and its natural predator Beroe ovata in Tampa Bay, Florida, USA. Investigations using terminal restriction fragment length polymorphism (T-RFLP) and cloning and sequencing of 16S rRNA genes demonstrated that ctenophore bacterial communities were distinct from the surrounding water. In addition, each ctenophore genus contained a unique microbiota. Ctenophore samples contained fewer bacterial operational taxonomic units (OTUs) by T-RFLP and lower diversity communities by 16S rRNA gene sequencing than the water column. Both ctenophore genera contained sequences related to bacteria previously described in marine invertebrates, and sequences similar to a sea anemone pathogen were abundant in B.?ovata. Temporal sampling revealed that the ctenophore-associated bacterial communities varied over time, with no single OTU detected at all time points. This is the first report of distinct and dynamic bacterial communities associated with ctenophores, suggesting that these microbial consortia may play important roles in ctenophore ecology. Future work needs to elucidate the functional roles and mode of acquisition of these bacteria.     

Molecular phylogenetics of Diseae (Orchidaceae): a contribution from nuclear ribosomal ITS sequences

We present here the first molecular phylogeny of tribe Diseae (Orchidoideae: Orchidaceae). Nuclear ribosomal ITS1, 5.8S rDNA, and ITS2 sequences were compared for 30 Diseae, 20 Orchideae, and four Cranichideae and Diurideae outgroups. ITS - rDNA sequences exhibited a transition:transversion ratio of 1.3 and extensive ITS length polymorphism. Phylogenetic analyses using maximum parsimony identified seven major core orchidoid groups. The branching order of the five Diseae and two Orchideae clades was weakly supported but indicated paraphyly of Diseae, with Disperis sister to the rest, followed by successive divergence of Brownleea, Disinae, Coryciinae sensu stricto (s.s.), Satyriinae, and terminated by Orchidinae plus Habenariinae. Within the monophyletic Disinae, Herschelia and Monadenia were nested within a paraphyletic Disa and clustered with D. sect. Micranthae. Within monophyletic Satyriinae, Satyridium rostratum plus Satyrium bicallosum was sister to the rest of Satyrium, and then Satyrium nepalense plus S. odorum was distinct from a cluster of six species. Coryciinae are paraphyletic because Disperis is sister to all other core orchidoids. Coryciinae s.s. are sister to Satyriinae plus Orchideae, with Pterygodium nested within Corycium. Maximum likelihood analysis supported possible affinities among Disinae, Brownleeinae, and Coryciinae but did not support monophyly of Diseae or an affinity between Disinae and Satyriinae. Morphological characters are fully congruent with the well-supported groups identified in the ITS phylogeny.     

Examination of subfamilial phylogeny in Bromeliaceae using comparative sequencing of the plastid locus ndhF

Parsimony analysis of 31 sequences of the chloroplast locus ndhF was used to address questions of subfamilial phylogeny in Bromeliaceae. Results presented here are congruent with those from chloroplast DNA restriction site analysis in recognizing a clade containing Bromelioideae and Pitcairnioideae, and in resolving Tillandsioideae near the base of the family. Placements of several taxonomically difficult genera (e.g., Glomeropitcairnia and Navia) corroborate those of traditional treatments; however, these data suggest that Brocchinia (Pitcairnioideae) is the sister group to the remainder of Bromeliaceae. Further evidence for the paraphyly of Pitcairnioideae includes the resolution of Puya as the sister group to Bromelioideae. Implications for taxonomic realignment at the subfamily level are considered.     

Phylogeny of amorpheae (fabaceae: papilionoideae)

The legume tribe Amorpheae comprises eight genera and 240 species with variable floral form. In this study, we inferred a phylogeny for Amorpheae using DNA sequence data from the plastid trnK intron, including matK, and the nuclear ribosomal ITS1, 5.8S, and ITS2. Our data resulted in a well-resolved phylogeny in which the tribe is divided into the daleoids (Dalea, Marina, and Psorothamnus), characterized by generally papilionaceous corollas, and the amorphoids (Amorpha, Apoplanesia, Errazurizia, Eysenhardtia, and Parryella), characterized by non-papilionaceous flowers. We found evidence for the paraphyly of Psorothamnus and for the monophyly of Dalea once D. filiciformis is transferred to monophyletic Marina. Errazurizia rotundata is more closely related to Amorpha than to the other errazurizias, and Eysenhardtia is supported to be monophyletic. The monotypic Parryella and Apoplanesia are placed within the amorphoids. Among Papilionoideae, trnK/matK sequence data provide strong evidence for the monophyly of Amorpheae and place Amorpheae as sister to the recently discovered dalbergioid clade.     

Phylogeny and systematic position of Opiliones: a combined analysis of chelicerate relationships using morphological and molecular data

The ordinal level phylogeny of the Arachnida and the suprafamilial level phylogeny of the Opiliones were studied on the basis of a combined analysis of 253 morphological characters, the complete sequence of the 18S rRNA gene, and the D3 region of the 28S rRNA gene. Molecular data were collected for 63 terminal taxa. Morphological data were collected for 35 exemplar taxa of Opiliones, but groundplans were applied to some of the remaining chelicerate groups. Six extinct terminals, including Paleozoic scorpions, are scored for morphological characters. The data were analyzed using strict parsimony for the morphological data matrix and via direct optimization for the molecular and combined data matrices. A sensitivity analysis of 15 parameter sets was undertaken, and character congruence was used as the optimality criterion to choose among competing hypotheses. The results obtained are unstable for the high-level chelicerate relationships (except for Tetrapulmonata, Pedipalpi, and Camarostomata), and the sister group of the Opiliones is not clearly established, although the monophyly of Dromopoda is supported under many parameter sets. However, the internal phylogeny of the Opiliones is robust to parameter choice and allows the discarding of previous hypotheses of opilionid phylogeny such as the "Cyphopalpatores" or "Palpatores." The topology obtained is congruent with the previous hypothesis of "Palpatores" paraphyly as follows: (Cyphophthalmi (Eupnoi (Dyspnoi + Laniatores))). Resolution within the Eupnoi, Dyspnoi, and Laniatores (the latter two united as Dyspnolaniatores nov.) is also stable to the superfamily level, permitting a new classification system for the Opiliones.     

First phylogenetic analysis of Dryophthorinae (Coleoptera,Curculionidae) based on structural alignment of ribosomal DNA reveals Cenozoic diversification

Dryophthorinae is an economically important, ecologically distinct, and ubiquitous monophyletic group of pantropical weevils with more than 1,200 species in 153 genera. This study provides the first comprehensive phylogeny of the group with the aim to provide insights into the process and timing of diversification of phytophagous insects, inform classification and facilitate predictions. The taxon sampling is the most extensive to date and includes representatives of all five dryophthorine tribes and all but one subtribe. The phylogeny is based on secondary structural alignment of 18S and 28S rRNA totaling 3,764 nucleotides analyzed under Bayesian and maximum likelihood inference. We used a fossil‐calibrated relaxed clock model with two approaches, node‐dating and fossilized birth‐death models, to estimate divergence times for the subfamily. All tribes except the species‐rich Rhynchophorini were found to be monophyletic, but higher support is required to ascertain the paraphyly of Rhynchophorini with more confidence. Nephius is closely related to Dryophthorini and Stromboscerini, and there is strong evidence for paraphyly of Sphenophorina. We find a large gap between the divergence of Dryophthorinae from their sister group Platypodinae in the Jurassic‐Cretaceous boundary and the diversification of extant species in the Cenozoic, highlighting the role of coevolution with angiosperms in this group.     

Vertebrate evolution reflected in the evolution of nuclear ribosomal internal transcribed spacer 2

In eukaryotes, mature rRNA sequences are produced from single large (45S) precursor (pre-rRNA) as the result of successive removal of spacers through a series of rapid and intricate actions of endo- and exonucleases. The excision of internal transcribed spacer (ITS2), a eukaryotic-specific insertion, remains the most elusive processing step. ITS2 is the element mandatory for all eukaryotic pre-rRNAs that contain at least three processing cleavage sites for precise 5.8S and 28S formation. Conserved core sequences (cis-elements) binding to trans-factors provide for precise rRNA processing, whereas rapidly diverging regions between the core sequences preserve internal complementarity, which guarantees the spatial integrity of ITS2. Characteristic differences in the formation of such insertions during evolution should reflect the relationships between taxa. The phylogeny of the reptiles and the relationships between taxa proposed by scientists are controversial. To delineate the structural and functional features preserved among reptilian ITS2s, we cloned and sequenced 58 ITS2s belonging to four reptile orders: Squamata, Crocodilians, Aves, and Testudines. We studied the subsequent alignment and folding of variable regions. The sizes and packing of the loop–stems between conserved consensus segments in reptiles vary considerably between taxa. Our phylogenetic trees constructed on the basis of the reptile ITS2s primary structural alignments revealed a split between Iguania clade and all other taxa. True lizards (suborder Scleroglossa) and snakes (suborder Serpentes) show sister relationships, as well as the two other reptilian orders, Crocodilia + Aves and Testudines. In summary, our phylogenetic trees exhibit a mix of specific features deduced or, to the contrary, rejected earlier by other authors.     

Phylogenetic relationships in the millipede family Julidae

A phylogenetic analysis of 40 species (22 genera) of the Palaearctic millipede family Julidae was made based on partial sequences of the mitochondrial 16S rRNA (16S) gene and the nuclear 28S rRNA (28S) gene, respectively. The two data sets (16S rDNA and 28S rDNA) were analysed individually and in combination using direct optimization as implemented in POY. The 16S rDNA and the 28S rDNA sequences vary from 410 to 449 bp and from 467 to 525 bp in length, respectively. All searches were performed under six different gap opening costs, an extension gap cost of 1, and a substitution cost of 2. Incongruence length difference values were used to select the preferred tree. The order Julida was recovered as monophyletic under all weight sets. The family Julidae was recovered as monophyletic except under one weight set where the genus Nepalmatoiulus is sister to all other Julida. Within Julidae, a clade of Paectophyllini + Calyptophyllini is sister to all others on the preferred tree but this relationship is not robust. A hitherto unrecognized clade of (South) east Asian genera (Anaulaciulus and Nepalmatoiulus) was recovered under five weight sets. Another “new” robust clade (Oncoiulini + Schizophyllini) is congruent with a hitherto unrecognized complex morphological character. Further clades recovered within the Julidae partly conflict with the accepted classification, which is only to a limited extent based on phylogenetic arguments.     

Identifying the sister group to the bees: a molecular phylogeny of Aculeata with an emphasis on the superfamily Apoidea

Debevec, AH., Cardinal, S & Danforth, BN. Identifying the sister group to the bees: a molecular phylogeny of Aculeata with an emphasis on the superfamily Apoidea. —Zoologica Scripta, 41, 527–535. The hymenopteran superfamily Apoidea includes the bees (Anthophila) as well as four predatory wasp families (Heterogynaidae, Ampulicidae, Sphecidae and Crabronidae) collectively referred to as the “sphecoid” or “apoid” wasps. The most widely cited studies suggest that bees are sister to the wasp family Crabronidae, but alternative hypotheses have been proposed based on both morphological and molecular data. We combined DNA sequence data from previously published studies and newly generated data for four nuclear genes (28S, long‐wavelength rhodopsin, elongation factor‐1α and wingless) to identify the likely sister group to the bees. Analysis of our four‐gene data set by maximum likelihood and Bayesian methods indicates that bees most likely arise from within a paraphyletic Crabronidae. Possible sister groups to the bees include Philanthinae, Pemphredoninae or Philanthinae + Pemphredoninae. We used Bayesian methods to explore the robustness of our results. Bayes Factor tests strongly rejected the hypotheses of crabronid monophyly as well as placement of Heterogynaidae within Crabronidae. Our results were also stable to alternative rootings of the bees. These findings provide additional support for the hypothesis that bees arise from within Crabronidae, rather than being sister to Crabronidae, thus altering our understanding of bee ancestry and evolutionary history.     

Cryptic speciation on the high seas; global phylogenetics of the copepod family Eucalanidae

Few genetic data are currently available to assess patterns of population differentiation and speciation in planktonic taxa that inhabit the open ocean. A phylogenetic study of the oceanic copepod family Eucalanidae was undertaken to develop a model zooplankton taxon in which speciation events can be confidently identified. A global survey of 20 described species (526 individuals) sampled from 88 locations worldwide found high levels of cryptic diversity at the species level. Mitochondrial (16S rRNA, CO1) and nuclear (ITS2) DNA sequence data support 12 new genetic lineages as highly distinct from other populations with which they are currently considered conspecific. Out of these 12, at least four are new species. The circumglobal, boundary current species Rhincalanus nasutus was found to be a cryptic species complex, with genetic divergence between populations unrelated to geographic distance. 'Conspecific' populations of seven species exhibited varying levels of genetic differentiation between Atlantic and Pacific basins, suggesting that continental landmasses form barriers to dispersal for a subset of circumglobal species. A molecular phylogeny of the family based on both mitochondrial (16S rRNA) and nuclear (ITS2, 18S rRNA) gene loci supports monophyly of the family Eucalanidae, all four eucalanid genera and the 'pileatus' and 'subtenuis' species groups.     

Phylogenetic relationships among superfamilies of Hymenoptera

The first comprehensive analysis of higher‐level phylogeny of the order Hymenoptera is presented. The analysis includes representatives of all extant superfamilies, scored for 392 morphological characters, and sequence data for four loci (18S, 28S, COI and EF‐1α). Including three outgroup taxa, 111 terminals were analyzed. Relationships within symphytans (sawflies) and Apocrita are mostly resolved. Well supported relationships include: Xyeloidea is monophyletic, Cephoidea is the sister group of Siricoidea + [Xiphydrioidea + (Orussoidea + Apocrita)]; Anaxyelidae is included in the Siricoidea, and together they are the sister group of Xiphydrioidea + (Orussoidea + Apocrita); Orussoidea is the sister group of Apocrita, Apocrita is monophyletic; Evanioidea is monophyletic; Aculeata is the sister group of Evanioidea; Proctotrupomorpha is monophyletic; Ichneumonoidea is the sister group of Proctotrupomorpha; Platygastroidea is sister group to Cynipoidea, and together they are sister group to the remaining Proctotrupomorpha; Proctotrupoidea s. str. is monophyletic; Mymarommatoidea is the sister group of Chalcidoidea; Mymarommatoidea + Chalcidoidea + Diaprioidea is monophyletic. Weakly supported relationships include: Stephanoidea is the sister group of the remaining Apocrita; Diaprioidea is monophyletic; Ceraphronoidea is the sister group of Megalyroidea, which together form the sister group of [Trigonaloidea (Aculeata + Evanioidea)]. Aside from paraphyly of Vespoidea within Aculeata, all currently recognized superfamilies are supported as monophyletic. The diapriid subfamily Ismarinae is raised to family status, Ismaridae stat. nov. © The Will Henning Society 2011.     

Phylogeny of harvestmen family Gonyleptidae inferred from a multilocus approach (Arachnida: Opiliones)

Gonyleptidae is the second most diverse harvestmen family and the most studied in terms of morphology, behaviour, and ecology. Despite this, few phylogenetic studies have focused on gonyleptids, and those are based on a very limited number of taxa. We addressed this gap by constructing a phylogenetic hypothesis of the family using 101 taxa from all 16 gonyleptid subfamilies and four mitochondrial and nuclear loci (COI, 28S rRNA, 12S rRNA, and 16S rRNA). These were analysed under parsimony and likelihood optimality criteria (and using direct optimization for the former). Relationships among Gonyleptoidea and within each subfamily of Gonyleptidae were largely congruent between parsimony and maximum‐likelihood approaches. Taxonomic actions from our phylogeny include the following: Tricommatidae, new status, is restored as a family; Metasarcidae, new status, is recognized as a family and considered sister to the Cosmetidae; and Cranainae and Manaosbiinae are suggested as members of Gonyleptidae, restoring Roewer's concept of the family. Within Gonyleptidae, the “K92” group—composed of Sodreaninae, Caelopyginae, Hernandariinae, Progonyleptoidellinae, and Gonyleptinae—forms a clade, although the latter two subfamilies are not monophyletic. The genus Parampheres is here transferred to Caelopyginae, and “Multumbo” dimorphicus to Gonyleptinae. Gonyleptidae is characterized by the presence of a ventral process on the penis glans and a bifid apophysis on the male coxa IV. The long‐legged Mitobatinae can be considered monophyletic only if some short‐legged pachylines are included, or if we assume that elongate legs arose twice independently (in the true mitobatine genera and in Longiperna). Pachylinae, the most diverse gonyleptid subfamily, represents several distinct lineages. We further conclude that the traditional use of a small set of morphological characters in the systematics of Gonyleptidae is unable to explain the complex evolution of the family.     

Deuterostome phylogeny and the sister group of the chordates: evidence from molecules and morphology

Complete coding regions of the 18S rRNA gene of an enteropneust hemichordate and an echinoid and ophiuroid echinoderm were obtained and aligned with 18S rRNA gene sequences of all major chordate clades and four outgroups. Gene sequences were analyzed to test morphological character phylogenies and to assess the strength of the signal. Maximum- parsimony analysis of the sequences fails to support a monophyletic Chordata; the urochordates form the sister taxon to the hemichordates, and together this clade plus the echinoderms forms the sister taxon to the cephalochordates plus craniates. Decay, bootstrap, and tree-length distribution analyses suggest that the signal for inference of dueterostome phylogeny is weak in this molecule. Parsimony analysis of morphological plus molecular characters supports both monophyly of echinoderms plus enteropneust hemichordates and a sister group relationship of this clade to chordates. Evolutionary parsimony does not support chordate monophyly. Neighbor-joining, Fitch-Margoliash, and maximum-likelihood analyses support a chordate lineage that is the sister group to an echinoderm-plus-hemichordate lineage. The results illustrate both the limitations of the 18S rRNA molecule alone for high- level phylogeny inference and the importance of considering both molecular and morphological data in phylogeny reconstruction.      

Contribution to the molecular phylogenetic analysis of extant holocephalan fishes (Holocephali, Chimaeriformes)

Much attention has been paid to the molecular phylogeny of holocephalan fishes during recent years, but sampling was very low and not all genera were examined. This study offers an extended sampling of species from all known genera to clarify their phylogeny and to provide an estimate of the time of origin of extant holocephalan taxa. Three mitochondrial genes (cytochrome b, 12S rRNA, and 16S rRNA) were sequenced and analysed using a variety of phylogenetic methods (Bayes, maximum likelihood, and maximum parsimony). Callorhinchidae diverged from Rhinochimaeridae and Chimaeridae about 187?Ma ago. Chimaeridae and Rhinochimaeridae diverged from each other about 159?Ma ago. Within Rhinochimaeridae, Neoharriotta is the sister genus to the closely related Harriotta and Rhinochimaera. Eight species of the family Chimaeridae, belonging to the genera Hydrolagus and Chimaera, were examined. They probably had a common ancestor about 107?Ma ago and appear paraphyletic. These results indicate that the traditional morphological generic definition of the families Rhinochimaeridae and Chimaeridae has to be reinvestigated.