The Archiborborinae is a diverse Neotropical subfamily of Sphaeroceridae, with many undescribed species. The existing generic classification includes three genera consisting of brachypterous species, with all other species placed in the genus Archiborborus. We present the first phylogenetic hypothesis for the subfamily based on morphological, molecular, and combined datasets. Morphological data include 53 characters and cover all valid described taxa (33 species in 4 genera) in the subfamily, as well as 83 undescribed species. Molecular data for five genes (mitochondrial 12S rDNA, cytochrome c oxidase subunit I, and cytochrome B, and nuclear alanyl-tRNA synthetase and 28S rDNA) were obtained for 21 ingroup taxa. Data support the separation of the Archiborborinae from the Copromyzinae, with which they were formerly combined. Analyses support consistent groups within the subfamily, but relationships between groups are poorly resolved. The validity of the brachypterous genera Penola Richards and Frutillaria Richards is supported. The former genus Archiborborus Duda is paraphyletic, and will be divided into monophyletic genera on the basis of this work. Aptery and brachyptery have evolved multiple times in the subfamily. Antrops Enderlein, previously including a single brachypterous species, is a senior synonym of Archiborborus.
Frequent convergent evolution in phylogenetically unrelated taxa points to the importance of ecological factors during evolution, whereas convergent evolution in closely related taxa indicates the importance of favourable pre-existing characters (pre-adaptations). We investigated the transitions to arboreal life in oribatid mites (Oribatida, Acari), a group of mostly soil-living arthropods. We evaluated which general force—ecological factors, historical constraints or chance—was dominant in the evolution of arboreal life in oribatid mites. A phylogenetic study of 51 oribatid mite species and four outgroup taxa, using the ribosomal 18S rDNA region, indicates that arboreal life evolved at least 15 times independently. Arboreal oribatid mite species are not randomly distributed in the phylogenetic tree, but are concentrated among strongly sclerotized, sexual and evolutionary younger taxa. They convergently evolved a capitate sensillus, an anemoreceptor that either precludes overstimulation in the exposed bark habitat or functions as a gravity receptor. Sexual reproduction and strong sclerotization were important pre-adaptations for colonizing the bark of trees that facilitated the exploitation of living resources (e.g. lichens) and served as predator defence, respectively. Overall, our results indicate that ecological factors are most important for the observed pattern of convergent evolution of arboreal life in oribatid mites, supporting an adaptationist view of evolution.
convergent evolution; adaptation; ecological niche; pre-adaptation; oribatid mites; constraints
Phylogenies were inferred from nearly complete small subunit (SSU) 18S rDNA sequences of 12 species of Meloidogyne and 4 outgroup taxa (Globodera pallida, Nacobbus abberans, Subanguina radicicola, and Zygotylenchus guevarai). Alignments were generated manually from a secondary structure model, and computationally using ClustalX and Treealign. Trees were constructed using distance, parsimony, and likelihood algorithms in PAUP* 4.0b4a. Obtained tree topologies were stable across algorithms and alignments, supporting 3 clades: clade I = [M. incognita (M. javanica, M. arenaria)]; clade II = M. duytsi and M. maritima in an unresolved trichotomy with (M. hapla, M. microtyla); and clade III = (M. exigua (M. graminicola, M. chitwoodi)). Monophyly of [(clade I, clade II) clade III] was given maximal bootstrap support (mbs). M. artiellia was always a sister taxon to this joint clade, while M. ichinohei was consistently placed with mbs as a basal taxon within the genus. Affinities with the outgroup taxa remain unclear, although G. pallida and S. radicicola were never placed as closest relatives of Meloidogyne. Our results show that SSU sequence data are useful in addressing deeper phylogeny within Meloidogyne, and that both M. ichinohei and M. artiellia are credible outgroups for phylogenetic analysis of speciations among the major species.
18S; Globodera; Meloidogyne spp.; Nacobbus; nematode; phylogeny; rDNA; root-knot nematode; SSU; Subanguina; Zygotylenchus
TrilineeIlus clathrocutis n.g., n.sp. is described and illustrated. It was found as an associate of corn (Zea mays) in Stockton, Georgia, USA, and is related to a group of Tylenchorhynchus sensu lato species having three lines in nonareolated lateral fields. This new species is closely related to Tylenehorhynehus divittatus Siddiqi 1961, T. sculptus Seinhorst 1963, and T. triglyphus Seinhorst 1963 (syn. T. chonai Sethi & Swarup 1968) Tarjan 1973. It differs from these species primarily by having longitudinal striae on the body. These four species are differentiated from Tylenchorhynchus sensu stricto by having three lateral lines instead of four. They differ from Uliginotylenchus Siddiqi 1971 by having nonareolated lateral fields, fewer than 25 annules on conoid rounded tails, differently shaped gubernacula, nonattenuated stylets, and other distinctive characters. They differ from Triversus Sher 1973 by having the male tail enclosed by the bursa and by having rounded female tails. SEM observations of T. clathrocutis reveal a cuticle deeply cut by longitudinal and horizontal striae and bearing wide (> 2.0 μm) annules. Trilineellus is proposed to accommodate the new species and the three-incisured species still within Tylenchorhynchus. Tylenchorhynchus is thereby the repository for species within Tylenchorhynchinae having four lines in the lateral field, no conspicuous labial disc, and bursa enclosing the male tail.
taxonomy; morphology; Tylenchorhynchus; Trilineellus; Uliginotylenchus; Quinisulcius; Triversus; stunt nematode; new species; new genus; ryegrass; corn; SEM ultrastructure; Lolium perenne; Zea mays
The phylogenetic relationships of a number of flightless and volant rails have been investigated using mtDNA sequence data. The third domain of the small ribosomal subunit (12S) has been sequenced for 22 taxa, and part of the 5' end of the cytochrome-b gene has been sequenced for 12 taxa. Additional sequences were obtained from outgroup taxa, two species of jacana, sarus crane, spur-winged plover and kagu. Extinct rails were investigated using DNA extracted from subfossil bones, and in cases where fresh material could not be obtained from other extant taxa, feathers and museum skins were used as sources of DNA. Phylogenetic trees produced from these data have topologies that are, in general, consistent with data from DNA-DNA hybridization studies and recent interpretations based on morphology. Gallinula chloropus moorhen) groups basally with Fulica (coots), Amaurornis (= Megacrex) ineptus falls within the Gallirallus/Rallus group, and Gallinula (= Porphyrula) martinica is basal to Porphyrio (swamphens) and should probably be placed in that genus. Subspecies of Porphyrio porphyrio are paraphyletic with respect to Porphyrio mantelli (takahe). The Northern Hemisphere Rallus aquaticus is basal to the south-western Pacific Rallus (or Gallirallus) group. The flightless Rallus philippensis dieffenbachii is close to Rallus modestus and distinct from the volant Rallus philippensis, and is evidently a separate species. Porzana (crakes) appears to be more closely associated with Porphyrio than Rallus. Deep relationships among the rails remain poorly resolved. Rhynochetus jubatus (kagu) is closer to the cranes than the rails in this analysis. Genetic distances between flightless rails and their volant counterparts varied considerably with observed 12S sequence distances, ranging from 0.3% (Porphyrio porphyrio melanotus and P. mantelli mantelli) to 7.6% (Rallus modestus and Rallus philippensis). This may be taken as an indication of the rapidity with which flightlessness can evolve, and of the persistence of flightless taxa. Genetic data supported the notion that flightless taxa were independently derived, sometimes from similar colonizing ancestors. The morphology of flightless rails is apparently frequently dominated by evolutionary parallelism although similarity of external appearance is not an indication of the extent of genetic divergence. In some cases taxa that are genetically close are morphologically distinct from one another (e.g. Rallus (philippensis) dieffenbachii and R. modestus), whilst some morphologically similar taxa are evidently independently derived (e.g. Porphyio mantelli hochstetteri and P.m. mantelli).
The superficial resemblance of phylogenetic trees to other branching structures allows searching for macroevolutionary patterns. However, such trees are just statistical inferences of particular historical events. Recent meta-analyses report finding regularities in the branching pattern of phylogenetic trees. But is this supported by evidence, or are such regularities just methodological artifacts? If so, is there any signal in a phylogeny?
In order to evaluate the impact of polytomies and imbalance on tree shape, the distribution of all binary and polytomic trees of up to 7 taxa was assessed in tree-shape space. The relationship between the proportion of outgroups and the amount of imbalance introduced with them was assessed applying four different tree-building methods to 100 combinations from a set of 10 ingroup and 9 outgroup species, and performing covariance analyses. The relevance of this analysis was explored taking 61 published phylogenies, based on nucleic acid sequences and involving various taxa, taxonomic levels, and tree-building methods.
All methods of phylogenetic inference are quite sensitive to the artifacts introduced by outgroups. However, published phylogenies appear to be subject to a rather effective, albeit rather intuitive control against such artifacts. The data and methods used to build phylogenetic trees are varied, so any meta-analysis is subject to pitfalls due to their uneven intrinsic merits, which translate into artifacts in tree shape. The binary branching pattern is an imposition of methods, and seldom reflects true relationships in intraspecific analyses, yielding artifactual polytomies in short trees. Above the species level, the departure of real trees from simplistic random models is caused at least by two natural factors –uneven speciation and extinction rates; and artifacts such as choice of taxa included in the analysis, and imbalance introduced by outgroups and basal paraphyletic taxa. This artifactual imbalance accounts for tree shape convergence of large trees.
There is no evidence for any universal scaling in the tree of life. Instead, there is a need for improved methods of tree analysis that can be used to discriminate the noise due to outgroups from the phylogenetic signal within the taxon of interest, and to evaluate realistic models of evolution, correcting the retrospective perspective and explicitly recognizing extinction as a driving force. Artifacts are pervasive, and can only be overcome through understanding the structure and biological meaning of phylogenetic trees.
Catalan Abstract in Translation S1.
Background and Aims
In the Mediterranean basin, the Italian peninsula has been suggested to be one of the most important glacial refugia for temperate tree species. The orchid genus Epipactis is widely represented in the Italian peninsula by widespread species and several endemic, localized taxa, including selfing and outcrossing taxa. Here the phylogenetic and phylogeographic relationships in a group of closely related taxa in Epipactis are investigated with the aim of understanding the role of this refugial area for cladogenesis and speciation in herbaceous species, such as terrestrial orchids.
Ribosomal DNA (rDNA) was employed to assess phylogenetic relationships, and plastid sequence variation in the rbcL–accD spacer was used to reveal phylogeographic patterns among plastid haplotypes using a parsimony network.
Low genetic variation and shared ribotypes were detected in rDNA, whereas high levels of sequence variation and a strong phylogeographic structure were found in the examined plastid region. The parsimony plastid haplotype network identified two main haplotype groups, one including E. atrorubens/microphylla/muelleri/leptochila and the other including all accessions of E. helleborine and several localized and endemic taxa, with a combination of widespread and rare haplotypes detected across the Italian peninsula. A greater genetic divergence separated the Italian and other European accessions of E. helleborine.
Phylogenetic and phylogeographic patterns support a working hypothesis in which the Italian peninsula has only recently been colonized by Epipactis, probably during the most recent phase of the Quaternary age and, nevertheless, it acted as a remarkable centre of diversification for this orchid lineage. Changes in pollination strategy and recurrent shifts in mating system (from allogamy to autogamy) could have represented the mechanism promoting this rapid diversification and the observed high taxonomic complexity detected in the E. helleborine species complex.
Epipactis; chloroplast DNA; genetic variation; plastid haplotype network; mating systems; orchids; plastid spacer; ribosomal spacer
Bombyliidae (5000 sp.), or bee flies, are a lower brachyceran family of flower-visiting flies that, as larvae, act as parasitoids of other insects. The evolutionary relationships are known from a morphological analysis that yielded minimal support for higher-level groupings. We use the protein-coding gene CAD and 28S rDNA to determine phylogeny and to test the monophyly of existing subfamilies, the divisions Tomophtalmae, and ‘the sand chamber subfamilies’. Additionally, we demonstrate that consensus networks can be used to identify rogue taxa in a Bayesian framework. Pruning rogue taxa post-analysis from the final tree distribution results in increased posterior probabilities. We find 8 subfamilies to be monophyletic and the subfamilies Heterotropinae and Mythicomyiinae to be the earliest diverging lineages. The large subfamily Bombyliinae is found to be polyphyletic and our data does not provide evidence for the monophyly of Tomophthalmae or the ‘sand chamber subfamilies’.
The high sequence divergence within the small subunit ribosomal RNA gene (SSU rDNA) of foraminifera makes it difficult to establish the homology of individual nucleotides across taxa. Alignment-based approaches so far relied on time-consuming manual alignments and discarded up to 50% of the sequenced nucleotides prior to phylogenetic inference. Here, we investigate the potential of the multiple analysis approach to infer a molecular phylogeny of all modern planktonic foraminiferal taxa by using a matrix of 146 new and 153 previously published SSU rDNA sequences. Our multiple analysis approach is based on eleven different automated alignments, analysed separately under the maximum likelihood criterion. The high degree of congruence between the phylogenies derived from our novel approach, traditional manually homologized culled alignments and the fossil record indicates that poorly resolved nucleotide homology does not represent the most significant obstacle when exploring the phylogenetic structure of the SSU rDNA in planktonic foraminifera. We show that approaches designed to extract phylogenetically valuable signals from complete sequences show more promise to resolve the backbone of the planktonic foraminifer tree than attempts to establish strictly homologous base calls in a manual alignment.
planktonic foraminifera; phylogeny; fossil record; automated alignment
Whiteflies (Hemiptera: Sternorrhyncha: Aleyrodidae) are plant sap-sucking insects that harbor prokaryotic primary endosymbionts (P-endosymbionts) within specialized cells located in their body cavity. Four-kilobase DNA fragments containing 16S-23S ribosomal DNA (rDNA) were amplified from the P-endosymbiont of 24 whiteflies from 22 different species of 2 whitefly subfamilies. In addition, 3-kb DNA fragments containing mitochondrial cytB, nd1, and large-subunit rDNA (LrDNA) were amplified from 17 whitefly species. Comparisons of the P-endosymbiont (16S-23S rDNA) and host (cytB-nd1-LrDNA) phylogenetic trees indicated overall congruence consistent with a single infection of a whitefly ancestor with a bacterium and subsequent cospeciation (cocladogenesis) of the host and the P-endosymbiont. On the basis of both the P-endosymbiont and host trees, the whiteflies could be subdivided into at least five clusters. The major subdivision was between the subfamilies Aleyrodinae and Aleurodicinae. Unlike the P-endosymbionts of may other insects, the P-endosymbionts of whiteflies were related to Pseudomonas and possibly to the P-endosymbionts of psyllids. The lineage consisting of the P-endosymbionts of whiteflies is given the designation “Candidatus Portiera” gen. nov., with a single species, “Candidatus Portiera aleyrodidarum” sp. nov.
The effects of temperature on population development of 11 species of stunt nematodes in the subfamily Tylenchorhynchinae were compared on red clover or Kentucky bluegrass in constant-temperature tanks at 5-degree intervals from 10 to 35 C. The optimum temperature for population increase on red clover in 90 days was 30 C for Tylenchorhynchus agri, T. nudus, T. martini, and T. clarus, 25 C for T. sylvaticus and T. dubius, and 20 C for T. canalis, Merlinius brevidens, and Quinisulcius capitatus. The optimum was 30 C for T. robustoides and 25 C for T. maximus on Kentucky bluegrass. The temperature range for population increase was 20-35 C for T. agri, T. nudus, T. martini, and T. clarus, 20-30 C for T. sylvaticus and T. robustoides, 15-25 C for T. maximus, 10-25 C for T. dubius, and 10-20 C for M. brevidens and Q. capitatus. T. canalis increased only at 20 C. All species were recovered in numbers near their inoculum level at 10 C. There was no survival of T. sylvaticus, T. dubius, T. canalis, T. robustoides, T. maximus, M. brevidens, and Q. capitatus at 35 C, or of the last three of these species at 30 C. Temperature had no effect on sex ratio in final populations. Population increase was greatest in T. martini and least in T. canalis.
stunt nematodes; Tylenchorhynchus; Merlinius; Quinisulcius; red clover; Kentucky bluegrass; population development
The small ermine moth genus Yponomeuta (Lepidoptera, Yponomeutidae) contains 76 species that are specialist feeders on hosts from Celastraceae, Rosaceae, Salicaceae, and several other plant families. The genus is a model for studies in the evolution of phytophagous insects and their host-plant associations. Here, we reconstruct the phylogeny to provide a solid framework for these studies, and to obtain insight into the history of host-plant use and the biogeography of the genus.
DNA sequences from an internal transcribed spacer region (ITS-1) and from the 16S rDNA (16S) and cytochrome oxidase (COII) mitochondrial genes were collected from 20–23 (depending on gene) species and two outgroup taxa to reconstruct the phylogeny of the Palaearctic members of this genus. Sequences were analysed using three different phylogenetic methods (parsimony, likelihood, and Bayesian inference).
Roughly the same patterns are retrieved irrespective of the method used, and they are similar among the three genes. Monophyly is well supported for a clade consisting of the Japanese (but not the Dutch) population of Yponomeuta sedellus and Y. yanagawanus, a Y. kanaiellus–polystictus clade, and a Rosaceae-feeding, western Palaearctic clade (Y. cagnagellus–irrorellus clade). Within these clades, relationships are less well supported, and the patterns between the different gene trees are not so similar. The position of the remaining taxa is also variable among the gene trees and rather weakly supported. The phylogenetic information was used to elucidate patterns of biogeography and resource use. In the Palaearctic, the genus most likely originated in the Far East, feeding on Celastraceae, dispersing to the West concomitant with a shift to Rosaceae and further to Salicaceae. The association of Y. cagnagellus with Euonymus europaeus (Celastraceae), however, is a reversal. The only oligophagous species, Y. padellus, belongs to the derived western Palaearctic clade, evidence that specialisation is reversible.
Cyphellophora and Phialophora (Chaetothyriales, Pezizomycota) comprise species known from skin infections of humans and animals and from a variety of environmental sources. These fungi were studied based on the comparison of cultural and morphological features and phylogenetic analyses of five nuclear loci, i.e., internal transcribed spacer rDNA operon (ITS), large and small subunit nuclear ribosomal DNA (nuc28S rDNA, nuc18S rDNA), β-tubulin, DNA replication licensing factor (mcm7) and second largest subunit of RNA polymerase II (rpb2). Phylogenetic results were supported by comparative analysis of ITS1 and ITS2 secondary structure of representatives of the Chaetothyriales and the identification of substitutions among the taxa analyzed. Base pairs with non-conserved, co-evolving nucleotides that maintain base pairing in the RNA transcript and unique evolutionary motifs in the ITS2 that characterize whole clades or individual taxa were mapped on predicted secondary structure models. Morphological characteristics, structural data and phylogenetic analyses of three datasets, i.e., ITS, ITS-β-tubulin and 28S-18S-rpb2-mcm7, define a robust clade containing eight species of Cyphellophora (including the type) and six species of Phialophora. These taxa are now accommodated in the Cyphellophoraceae, a novel evolutionary lineage within the Chaetothyriales. Cyphellophora is emended and expanded to encompass species with both septate and nonseptate conidia formed on discrete, intercalary, terminal or lateral phialides. Six new combinations in Cyphellophora are proposed and a dichotomous key to species accepted in the genus is provided. Cyphellophora eugeniae and C. hylomeconis, which grouped in the Chaetothyriaceae, represent another novel lineage and are introduced as the type species of separate genera.
Calcareous sponges (Phylum Porifera, Class Calcarea) are known to be taxonomically difficult. Previous molecular studies have revealed many discrepancies between classically recognized taxa and the observed relationships at the order, family and genus levels; these inconsistencies question underlying hypotheses regarding the evolution of certain morphological characters. Therefore, we extended the available taxa and character set by sequencing the complete small subunit (SSU) rDNA and the almost complete large subunit (LSU) rDNA of additional key species and complemented this dataset by substantially increasing the length of available LSU sequences. Phylogenetic analyses provided new hypotheses about the relationships of Calcarea and about the evolution of certain morphological characters. We tested our phylogeny against competing phylogenetic hypotheses presented by previous classification systems. Our data reject the current order-level classification by again finding non-monophyletic Leucosolenida, Clathrinida and Murrayonida. In the subclass Calcinea, we recovered a clade that includes all species with a cortex, which is largely consistent with the previously proposed order Leucettida. Other orders that had been rejected in the current system were not found, but could not be rejected in our tests either. We found several additional families and genera polyphyletic: the families Leucascidae and Leucaltidae and the genus Leucetta in Calcinea, and in Calcaronea the family Amphoriscidae and the genus Ute. Our phylogeny also provided support for the vaguely suspected close relationship of several members of Grantiidae with giantortical diactines to members of Heteropiidae. Similarly, our analyses revealed several unexpected affinities, such as a sister group relationship between Leucettusa (Leucaltidae) and Leucettidae and between Leucascandra (Jenkinidae) and Sycon carteri (Sycettidae). According to our results, the taxonomy of Calcarea is in desperate need of a thorough revision, which cannot be achieved by considering morphology alone or relying on a taxon sampling based on the current classification below the subclass level.
Neighbor-joining, maximum-parsimony, minimum-evolution, maximum-likelihood and Bayesian trees constructed based on 16S rDNA sequences of 181 type strains of Bacillus species and related taxa manifested nine phylogenetic groups. The phylogenetic analysis showed that Bacillus was not a monophyletic group. B. subtilis was in Group 1. Group 4, 6 and 8 respectively consisted of thermophiles, halophilic or halotolerant bacilli and alkaliphilic bacilli. Group 2, 4 and 8 consisting of Bacillus species and related genera demonstrated that the current taxonomic system did not agree well with the 16S rDNA evolutionary trees. The position of Caryophanaceae and Planococcaceae in Group 2 suggested that they might be transferred into Bacillaceae, and the heterogeneity of Group 2 implied that some Bacillus species in it might belong to several new genera. Group 9 was mainly comprised of the genera (excluding Bacillus) of Bacillaceae, so some Bacillus species in Group 9: B. salarius, B. qingdaonensis and B. thermcloacae might not belong to Bacillus. Four Bacillus species, B. schlegelii, B. tusciae, B. edaphicus and B. mucilaginosus were clearly placed outside the nine groups.
Bacillus phylogeny; Bayesian inference; Evolutionary trees; 16S rDNA
Seven species of plant parasitic nematodes were found to be associated with leatherleaf fern (Rumohra adiantiformis) in central Florida. Of these, Pratylenchus penetrans, Tylenchorhynchus claytoni, and Criconemoides curvatum were commonly encountered. Nematode communities generally included two or three species of plant parasitic nematodes, with greatest diversity in nematode species occurring in ferneries shaded by oak trees. Species diversity was not correlated with fernery age. Leatherleaf fern was tolerant of P. penetrans and T. claytoni in microplot tests.
species diversity; tolerance; survey; pathogenicity
A phylogenetic analysis by parsimony of 16S rRNA gene sequences (16S rDNA) revealed that species and subspecies of Clavibacter and Rathayibacter form a discrete monophyletic clade, paraphyletic to Corynebacterium species. Within the Clavibacter-Rathayibacter clade, four major phylogenetic groups (subclades) with a total of 10 distinct taxa were recognized: (I) species C. michiganensis; (II) species C. xyli; (III) species R. iranicus and R. tritici; and (IV) species R. rathayi. The first three groups form a monophyletic cluster, paraphyletic to R. rathayi. On the basis of the phylogeny inferred, reclassification of members of Clavibacter-Rathayibacter group is proposed. A system for classification of taxa in Clavibacter and Rathayibacter was developed based on restriction fragment length polymorphism (RFLP) analysis of the PCR-amplified 16S rDNA sequences. The groups delineated on the basis of RFLP patterns of 16S rDNA coincided well with the subclades delineated on the basis of phylogeny. In contrast to previous classification systems, which are based primarily on phenotypic properties and are laborious, the RFLP analyses allow for rapid differentiation among species and subspecies in the two genera.
Previous phylogenetics studies of Asparagales, although extensive and generally well supported, have left several sets of taxa unclearly placed and have not addressed all relationships within certain clades thoroughly (some clades were relatively sparsely sampled). One of the most important of these is sampling within and placement of Nolinoideae (Ruscaceae s.l.) of Asparagaceae sensu Angiosperm Phylogeny Group (APG) III, which subfamily includes taxa previously referred to Convallariaceae, Dracaenaaceae, Eriospermaceae, Nolinaceae and Ruscaceae.
A phylogenetic analysis of a combined data set for 126 taxa of Ruscaceae s.l. and related groups in Asparagales based on three nuclear and plastid DNA coding genes, 18S rDNA (1796 bp), rbcL (1338 bp) and matK (1668 bp), representing a total of approx. 4·8 kb is presented. Parsimony and Bayesian inference analyses were conducted to elucidate relationships of Ruscaceae s.l. and related groups, and parsimony bootstrap analysis was performed to assess support of clades.
The combination of the three genes results in the most highly resolved and strongly supported topology yet obtained for Asparagales including Ruscaceae s.l. Asparagales relationships are nearly congruent with previous combined gene analyses, which were reflected in the APG III classification. Parsimony and Bayesian analyses yield identical relationships except for some slight variation among the core asparagoid families, which nevertheless form a strongly supported group in both types of analyses. In core asparagoids, five major clades are identified: (1) Alliaceae s.l. (sensu APG III, Amarylidaceae–Agapanthaceae–Alliaceae); (2) Asparagaceae–Laxmanniaceae–Ruscaceae s.l.; (3) Themidaceae; (4) Hyacinthaceae; (5) Anemarrhenaceae–Behniaceae–Herreriaceae–Agavaceae (clades 2–5 collectively Asparagaceae s.l. sensu APG III). The position of Aphyllanthes is labile, but it is sister to Themidaceae in the combined maximum-parsimony tree and sister to Anemarrhenaceae in the Bayesian analysis. The highly supported clade of Xanthorrhoeaceae s.l. (sensu APG III, including Asphodelaceae and Hemerocallidaceae) is sister to the core asparagoids. Ruscaceae s.l. are a well-supported group. Asparagaceae s.s. are sister to Ruscaceae s.l., even though the clade of the two families is weakly supported; Laxmanniaceae are strongly supported as sister to Ruscaceae s.l. and Asparagaceae. Ruscaceae s.l. include six principal clades that often reflect previously named groups: (1) tribe Polygonateae (excluding Disporopsis); (2) tribe Ophiopogoneae; (3) tribe Convallarieae (excluding Theropogon); (4) Ruscaceae s.s. + Dracaenaceae + Theropogon + Disporopsis + Comospermum; (5) Nolinaceae, (6) Eriospermum.
The analyses here were largely conducted with new data collected for the same loci as in previous studies, but in this case from different species/DNA accessions and greater sampling in many cases than in previously published analyses; nonetheless, the results largely mirror those of previously conducted studies. This demonstrates the robustness of these results and answers questions often raised about reproducibility of DNA results, given the often sparse sampling of taxa in some studies, particularly the earliest ones. The results also provide a clear set of patterns on which to base a new classification of the subfamilies of Asparagaceae s.l., particularly Ruscaceae s.l. (= Nolinoideae of Asparagaceae s.l.), and examine other putatively important characters of Asparagales.
Aphyllanthes; Asparagaceae; Convallariaceae; Dracaenaceae; Eriospermum; monocot phylogenetics; Nolinaceae; Nolinoideae
We isolated over 650 yeasts over a three year period from the gut of a variety of beetles and characterized them on the basis of LSU rDNA sequences and morphological and metabolic traits. Of these, at least 200 were undescribed taxa, a number equivalent to almost 30% of all currently recognized yeast species. A Bayesian analysis of species discovery rates predicts further sampling of previously sampled habitats could easily produce another 100 species. The sampled habitat is, thereby, estimated to contain well over half as many more species as are currently known worldwide. The beetle gut yeasts occur in 45 independent lineages scattered across the yeast phylogenetic tree, often in clusters. The distribution suggests that the some of the yeasts diversified by a process of horizontal transmission in the habitats and subsequent specialization in association with insect hosts. Evidence of specialization comes from consistent associations over time and broad geographical ranges of certain yeast and beetle species. The discovery of high yeast diversity in a previously unexplored habitat is a first step toward investigating the basis of the interactions and their impact in relation to ecology and evolution.
Brachiopod and phoronid phylogeny is inferred from SSU rDNA sequences of 28 articulate and nine inarticulate brachiopods, three phoronids, two ectoprocts and various outgroups, using gene trees reconstructed by weighted parsimony, distance and maximum likelihood methods. Of these sequences, 33 from brachiopods, two from phoronids and one each from an ectoproct and a priapulan are newly determined. The brachiopod sequences belong to 31 different genera and thus survey about 10% of extant genus-level diversity. Sequences determined in different laboratories and those from closely related taxa agree well, but evidence is presented suggesting that one published phoronid sequence (GenBank accession UO12648) is a brachiopod-phoronid chimaera, and this sequence is excluded from the analyses. The chiton, Acanthopleura, is identified as the phenetically proximal outgroup; other selected outgroups were chosen to allow comparison with recent, non-molecular analyses of brachiopod phylogeny. The different outgroups and methods of phylogenetic reconstruction lead to similar results, with differences mainly in the resolution of weakly supported ancient and recent nodes, including the divergence of inarticulate brachiopod sub-phyla, the position of the rhynchonellids in relation to long- and short-looped articulate brachiopod clades and the relationships of some articulate brachiopod genera and species. Attention is drawn to the problem presented by nodes that are strongly supported by non-molecular evidence but receive only low bootstrap resampling support. Overall, the gene trees agree with morphology-based brachiopod taxonomy, but novel relationships are tentatively suggested for thecideidine and megathyrid brachiopods. Articulate brachiopods are found to be monophyletic in all reconstructions, but monophyly of inarticulate brachiopods and the possible inclusion of phoronids in the inarticulate brachiopod clade are less strongly established. Phoronids are clearly excluded from a sister-group relationship with articulate brachiopods, this proposed relationship being due to the rejected, chimaeric sequence (GenBank UO12648). Lineage relative rate tests show no heterogeneity of evolutionary rate among articulate brachiopod sequences, but indicate that inarticulate brachiopod plus phoronid sequences evolve somewhat more slowly. Both brachiopods and phoronids evolve slowly by comparison with other invertebrates. A number of palaeontologically dated times of earliest appearance are used to make upper and lower estimates of the global rate of brachiopod SSU rDNA evolution, and these estimates are used to infer the likely divergence times of other nodes in the gene tree. There is reasonable agreement between most inferred molecular and palaeontological ages. The estimated rates of SSU rDNA sequence evolution suggest that the last common ancestor of brachiopods, chitons and other protostome invertebrates (Lophotrochozoa and Ecdysozoa) lived deep in Precambrian time. Results of this first DNA-based, taxonomically representative analysis of brachiopod phylogeny are in broad agreement with current morphology-based classification and systematics and are largely consistent with the hypothesis that brachiopod shell ontogeny and morphology are a good guide to phylogeny.
Psyllids are plant sap-feeding insects that harbor prokaryotic endosymbionts in specialized cells within the body cavity. Four-kilobase DNA fragments containing 16S and 23S ribosomal DNA (rDNA) were amplified from the primary (P) endosymbiont of 32 species of psyllids representing three psyllid families and eight subfamilies. In addition, 0.54-kb fragments of the psyllid nuclear gene wingless were also amplified from 26 species. Phylogenetic trees derived from 16S-23S rDNA and from the host wingless gene are very similar, and tests of compatibility of the data sets show no significant conflict between host and endosymbiont phylogenies. This result is consistent with a single infection of a shared psyllid ancestor and subsequent cospeciation of the host and the endosymbiont. In addition, the phylogenies based on DNA sequences generally agreed with psyllid taxonomy based on morphology. The 3′ end of the 16S rDNA of the P endosymbionts differs from that of other members of the domain Bacteria in the lack of a sequence complementary to the mRNA ribosome binding site. The rate of sequence change in the 16S-23S rDNA of the psyllid P endosymbiont was considerably higher than that of other bacteria, including other fast-evolving insect endosymbionts. The lineage consisting of the P endosymbionts of psyllids was given the designation Candidatus Carsonella (gen. nov.) with a single species, Candidatus Carsonella ruddii (sp. nov.).
Emergence from an aquatic environment to the land is one of the major evolutionary transitions within the arthropods. It is often considered that the first hexapods, and in particular the first springtails, were semi-aquatic and this assumption drives evolutionary models towards particular conclusions. To address the question of the ecological origin of the springtails, phylogenetic analyses by optimization alignment were performed on D1 and D2 regions of the 28S rDNA for 55 collembolan exemplars and eight outgroups. Relationships among the orders Symphypleona, Entomobryomorpha and Poduromorpha are inferred. More specifically, a robust hypothesis is provided for the subfamilial relationships within the order Poduromorpha. Contrary to previous statements, the semi-aquatic species Podura aquatica is not basal or 'primitive', but well nested in the Poduromorpha. The analyses performed for the 24 different weighting schemes yielded the same conclusion: semi-aquatic ecology is not ancestral for the springtails. It is a derived condition that evolved independently several times. The adaptation for semi-aquatic life is better interpreted as a step towards independence from land, rather than indication of an aquatic origin.
The host-parasite relationships of 13 species of plant parasitic nematodes and five species of hardwoods native to the southeastern United States were tested on greenhouse-grown tree seedlings for 6-10 months. Criteria for parasitism were completion o f life cycle and population increase of nematodes. Belonolaimus longicaudatus, Helicotylenchus dihystera, Scutellonema brachyurum and Tylenchorhynchus claytoni parasitized and reproduced on three or more of the species tested. Hoplolaimus galeatus and Pratylenchus brachyurus parasitized two species, Trichodorus christiei and Criconemoides xenoplax parasitized only red maple. Meloidogyne javanica/Liriodendron tulipifera combination was the only positive root-knot nematode/hardwood host-parasite relationship. Hemicycliophora silvestris, Meloidogyne arenaria, M. incognita, and M. hapla were not parasites of the tree species tested.
Host-parasite relations; Liquidambar styraciflua; Acer rubrum; Liriodendron tulipifera; Platanus occidentalis; Populus heterophylla
Physarales represents the largest taxonomic order among the plasmodial slime molds (myxomycetes). Physarales is of particular interest since the two best-studied myxomycete species, Physarum polycephalum and Didymium iridis, belong to this order and are currently subjected to whole genome and transcriptome analyses. Here we report molecular phylogeny based on ribosomal DNA (rDNA) sequences that includes 57 Physarales isolates.
The Physarales nuclear rDNA sequences were found to be loaded with 222 autocatalytic group I introns, which may complicate correct alignments and subsequent phylogenetic tree constructions. Phylogenetic analysis of rDNA sequences depleted of introns confirmed monophyly of the Physarales families Didymiaceae and Physaraceae. Whereas good correlation was noted between phylogeny and taxonomy among the Didymiaceae isolates, significant deviations were seen in Physaraceae. The largest genus, Physarum, was found to be polyphyletic consisting of at least three well supported clades. A synapomorphy, located at the highly conserved G-binding site of L2449 group I intron ribozymes further supported the Physarum clades.
Our results provide molecular relationship of Physarales genera, species, and isolates. This information is important in further interpretations of comparative genomics nd transcriptomics. In addition, the result supports a polyphyletic origin of the genus Physarum and calls for a reevaluation of current taxonomy.
Background and Aims
The orchid genus Dichaea, with over 100 species found throughout the neotropics, is easily recognized by distichous leaves on long stems without pseudobulbs and flowers with infrastigmatic ligules. The genus has previously been divided into four sections based primarily on presence of ovary bristles and a foliar abscission layer. The aim of this work is to use DNA sequence data to estimate phylogenetic relationships within Dichaea and map the distribution of major morphological characters that have been used to delimit subgenera/sections.
Sequence data for the nuclear ribosomal internal transcribed spacers and plastid matK, trnL intron, trnL-F spacer and ycf1 for 67 ingroup and seven outgroup operational taxonomic units were used to estimate phylogenetic relationships within Dichaea. Taxa from each of the four sections were sampled, with the greatest representation from section Dichaea, the most diverse and taxonomically puzzling group.
Molecular data and morphology support monophyly of Dichaea. Results indicate that section Dichaeopsis is polyphyletic and based on symplesiomorphies, including deciduous leaves and smooth ovaries that are widespread in Zygopetalinae. There are at least three well-supported clades within section Dichaeopsis. Section Pseudodichaea is monophyletic and defined by setose ovaries and leaves with an abscission layer. Sections Dichaea and Dichaeastrum are monophyletic and defined by pendent habit and persistent leaves. Section Dichaeastrum, distinguished from section Dichaea primarily by a glabrous ovary, is potentially polyphyletic.
The leaf abscission layer was lost once, occurring only in the derived sections Dichaea and Dichaeastrum. The setose fruit is a more homoplasious character with several losses and gains within the genus. We propose an informal division of the genus based upon five well-supported clades.
Dichaea; matK; nrITS; Orchidaceae; trnL intron; trnL-F spacer; ycf1; Zygopetalinae