A genome-scale phylogeny of the kingdom Fungi

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Deep phylogeny and character evolution in thecostraca (crustacea: maxillopoda)

The thecostracans include the Facetotecta, Ascothoracida, and Cirripedia and show great diversity in both morphology and biology. This makes them ideal models for studying evolutionary adaptations of the larval and adult body-plan, lifestyle, and reproduction. Surprisingly, despite all the work published since Darwin's seminal monographs, few studies have tested evolutionary hypotheses about Thecostraca within a phylogenetic context. In this review, we combine a Bayesian phylogenetic method and multilocus sequence data to reconstruct the evolutionary history of 12 key thecostracan phenotypic traits associated with their lifecycle, larval biology, reproduction, and adult morphology. Our analyses show that thecostracan biological diversity resulted both from unique innovations and from events of convergence. This provides an opportunity to reevaluate previous classifications of the Thecostraca and the theories relating to the origin and diversification of this taxon.     

Molecular phylogeny of the Blastocladiomycota (Fungi) based on nuclear ribosomal DNA

The Blastocladiomycota is a recently described phylum of ecologically diverse zoosporic fungi whose species have not been thoroughly sampled and placed within a molecular phylogeny. In this study, we investigated the phylogeny of the Blastocladiomycota based on ribosomal DNA sequences from strains identified by traditional morphological and ultrastructural characters. Our results support the monophyly of the Coelomomycetaceae and Physodermataceae but the Blastocladiaceae and Catenariaceae are paraphyletic or polyphyletic. The data support two clades within Allomyces with strains identified as Allomyces arbusculus in both clades, suggesting that species concepts in Allomyces are in need of revision. A clade of Catenaria species isolated from midge larvae group separately from other Catenaria species, suggesting that this genus may need revision. In the Physodermataceae, Urophlyctis species cluster with a clade of Physoderma species. The algal parasite Paraphysoderma sedebokerensis nom. prov. clusters sister to other taxa in the Physodermataceae. Catenomyces persicinus, which has been classified in the Catenariaceae, groups with the Chytridiomycota rather than Blastocladiomycota. The rDNA operon seems to be suitable for classification within the Blastocladiomycota and distinguishes among genera; however, this region alone is not suitable to determine the position of the Blastocladiomycota among other basal fungal phyla with statistical support. A focused effort to find and isolate, or directly amplify DNA from additional taxa will be necessary to evaluate diversity in this phylum. We provide this rDNA phylogeny as a preliminary framework to guide further taxon and gene sampling and to facilitate future ecological, morphological, and systematic studies.     

Testing the new animal phylogeny: a phylum level molecular analysis of the animal kingdom

The new animal phylogeny inferred from ribosomal genes some years ago has prompted a number of radical rearrangements of the traditional, morphology based metazoan tree. The two main bilaterian clades, Deuterostomia and Protostomia, find strong support, but the protostomes consist of two sister groups, Ecdysozoa and Lophotrochozoa, not seen in morphology based trees. Although widely accepted, not all recent molecular phylogenetic analyses have supported the tripartite structure of the new animal phylogeny. Furthermore, even if the small ribosomal subunit (SSU) based phylogeny is correct, there is a frustrating lack of resolution of relationships between the phyla that make up the three clades of this tree. To address this issue, we have assembled a dataset including a large number of aligned sequence positions as well as a broad sampling of metazoan phyla. Our dataset consists of sequence data from ribosomal and mitochondrial genes combined with new data from protein coding genes (5139 amino acid and 3524 nucleotide positions in total) from 37 representative taxa sampled across the Metazoa. Our data show strong support for the basic structure of the new animal phylogeny as well as for the Mandibulata including Myriapoda. We also provide some resolution within the Lophotrochozoa, where we confirm support for a monophyletic clade of Echiura, Sipuncula and Annelida and surprising evidence of a close relationship between Brachiopoda and Nemertea.     

A multi-gene phylogeny of Clavicipitaceae (Ascomycota, Fungi): identification of localized incongruence using a combinational bootstrap approach

Multi-gene phylogenetic analyses were conducted to address the evolution of Clavicipitaceae (Ascomycota). Data are presented here for approximately 5900 base pairs from portions of seven loci: the nuclear ribosomal small and large subunit DNA (nrSSU and nrLSU), beta-tubulin, elongation factor 1alpha (EF-1alpha), the largest and second largest subunits of RNA polymerase II (RPB1 and RPB2), and mitochondrial ATP Synthase subunit 6 (mtATP6). These data were analyzed in a complete 66-taxon matrix and 91-taxon supermatrix that included some missing data. Separate phylogenetic analyses, with data partitioned according to genes, produced some conflicting results. The results of separate analyses from RPB1 and RPB2 are in agreement with the combined analyses that resolve a paraphyletic Clavicipitaceae comprising three well-supported clades (i.e., Clavicipitaceae clade A, B, and C), whereas the tree obtained from mtATP6 is in strong conflict with the monophyly of Clavicipitaceae clade B and the sister-group relationship of Hypocreaceae and Clavicipitaceae clade C. The distribution of relative contribution of nodal support for each gene partition was assessed using both partitioned Bremer support (PBS) values and combinational bootstrap (CB) analyses, the latter of which analyzed bootstrap proportions from all possible combinations of the seven gene partitions. These results suggest that CB analyses provide a more consistent estimate of nodal support than PBS and that combining heterogeneous gene partitions, which individually support a limited number of nodes, results in increased support for overall tree topology. Analyses of the 91-taxa supermatrix data sets revealed that some nodes were more strongly supported by increased taxon sampling. Identifying the localized incongruence of mtATP6 and analyses of complete and supermatrix data sets strengthen the evidence for rejecting the monophyly of Clavicipitaceae and much of the current subfamilial classification of the family. Although the monophyly of the grass-associated subfamily Clavicipitoideae (e.g., Claviceps, Balansia, and Epichlo?) is strongly supported, the subfamily Cordycipitoideae (e.g., Cordyceps and Torrubiella) is not monophyletic. In particular, species of the genus Cordyceps, which are pathogens of arthropods and truffles, are found in all three clavicipitaceous clades. These results imply that most characters used in the current familial classification of Clavicipitaceae are not diagnostic of monophyly.     

Molecular phylogeny of Juglans (Juglandaceae): a biogeographic perspective

The eastern Asian and eastern North American disjunction in Juglans offers an opportunity to estimate the time since divergence of the Eurasian and American lineages and to compare it with paleobotanical evidence. Five chloroplast DNA noncoding spacer (NCS) sequences: trnT−trnF, psbA−trnH, atpB−rbcL, trnV-16S rRNA, and trnS-trnfM and data from earlier studies (matK, ITS, and nuclear RFLP) were used to reconstruct phylogeny and to estimate the divergence time of major lineages. Seventeen taxa from four sections of Juglans and two outgroup taxa, Pterocarya stenoptera and Carya illinoiensis were included. NCS data was congruent only with matK data. Both maximum parsimony (MP) and maximum likelihood (ML) cladograms were concordant at the sectional level and revealed three well-supported monophyletic clades corresponding to sections Juglans, Cardiocaryon, and Rhysocaryon in both NCS and combined analyses. The single extant American butternut, Juglans cinerea was placed within the poorly resolved, but well-supported Rhysocaryon. Placement of taxa within Rhysocaryon and Cardiocaryon were inconsistent between NCS and combined analyses. Overall, the results suggest that: (1) the NCS sequence divergence observed within and between sections of Juglans is low and the addition of matK data only marginally improved resolution within Rhysocaryon; (2) the early divergence of section Juglans in both MP and ML analyses of NCS and combined data implies its ancient origin in contrast to fossil evidence, which suggests the earliest divergence of sections Rhysocaryon and Cardiocaryon; and (3) the extant taxa may not hold the footprints to unravel the evolutionary history of the genus.     

Fungal evolution: diversity,taxonomy and phylogeny of the Fungi

The fungal kingdom comprises a hyperdiverse clade of heterotrophic eukaryotes characterized by the presence of a chitinous cell wall, the loss of phagotrophic capabilities and cell organizations that range from completely unicellular monopolar organisms to highly complex syncitial filaments that may form macroscopic structures. Fungi emerged as a ‘Third Kingdom’, embracing organisms that were outside the classical dichotomy of animals versus vegetals. The taxonomy of this group has a turbulent history that is only now starting to be settled with the advent of genomics and phylogenomics. We here review the current status of the phylogeny and taxonomy of fungi, providing an overview of the main defined groups. Based on current knowledge, nine phylum‐level clades can be defined: Opisthosporidia, Chytridiomycota, Neocallimastigomycota, Blastocladiomycota, Zoopagomycota, Mucoromycota, Glomeromycota, Basidiomycota and Ascomycota. For each group, we discuss their main traits and their diversity, focusing on the evolutionary relationships among the main fungal clades. We also explore the diversity and phylogeny of several groups of uncertain affinities and the main phylogenetic and taxonomical controversies and hypotheses in the field.     

Plant power: converting a kingdom

This month, Genome Watch looks at the potential for bacterially derived enzymes to degrade lignocellulose from plant biomass and thus provide an efficient way of producing biofuels.     

Virulence of entomopathogenic Fungi (Fungi imperfecti) for the adults of Acanthoscelides obtectus (Coleoptera: Bruchidae)

Tests with the bean weevil, Acanthoscelides obtectus, in which the hosts were exposed indirectly to various dilutions of conidia of four entomopathogenic fungi showed that mortality was a function of the concentration of the inoculum. In these tests a given spore suspension was sprayed on the internal surfaces of a Petri dish. Adult weevils of a known age were placed in the dish, held there for 24 hr, then removed and kept at 20°C. After 20 days, the host mortality was determined. From the data obtained, it was possible to trace a probit regression line of the mortality in relation to the increasing spore concentration. Infection was observed in hosts exposed to a concentration of approximately 5 × 10⁶ spores/ml up to a maximum of about 1 × 10⁹ spores/ml. The A. obtectus was susceptible to infection by spores of Beauveria bassiana, B. tenella, Metarrhizium anisopliae, and Paecilomyces fumoso-roseus.     

Hemerodromiinae (Diptera: Empididae): a tentative phylogeny and biogeographical discussion

A cladistic analysis of adult morphological characters was used to hypothesize phylogenetic and zoogeographical relationships in Hemerodromiinae (Diptera: Empididae). Afrodromia Smith, Drymodromia Becker and an undescribed Chilean genus subtended a sister‐group relationship between the tribes Chelipodini and Hemerodromiini. Chelipodozus Smith and an undescribed Australian genus were supported only weakly in Hemerodromiini, and are regarded as incertae sedis within Hemerodromiinae. In Chelipodini, Anaclastoctedon Plant and an undescribed Australian genus subtended all others that form two sister‐group clades. (i) A widespread Chelipoda‐like group comprising Achelipoda Yang, Zhang & Zhang, Ptilophyllodromia Bezzi, Chelipoda Macquarts.s. and Phyllodromia Zetterstedt s.s. has a worldwide distribution, excepting the Afrotropical, considered to date from before or during the early phase of Gondwanan fragmentation. Phyllodromia s.s. is an exclusively Palaearctic genus of doubtful validity, to which Southern Hemisphere forms have been assigned incorrectly. Ptilophyllodromia Bezzi syn.n . is regarded as a junior synonym of Chelipoda, with the included species relegated to a species group. (ii) An austral Chelipoda‐like group confined to New Zealand, New Caledonia, Lord Howe Island and Vanuatu, includes Monodromia Collin and species currently incorrectly assigned to Chelipoda and Phyllodromia. The group is hypothesized as a relictual Gondwanan element that has survived Oligocene drowning as metapopulations persisting in situ on ephemeral islands along arcs, ridges and buoyant crustal blocks overlying hot spots in New Zealand and the Southwest Pacific. In the tribe Hemerodromiini, many Southern Hemisphere species assigned currently to Hemerodromia Meigen, Cladodromia Bezzi and Neoplasta Coquillett require reassignment. The sister‐group relationship between the southern African endemic Afrodromia and other Hemerodromiinae is viewed as evidence of early divergence of Hemerodromiinae and Empidinae by the early Cretaceous, pre‐dating major Gondwanan fragmentation. An assessment of fossil forms indicated that Chelifera detestata (Meunier) from Eocene/Oligocene Baltic amber is the only genuine described fossil representative of Hemerodromiinae.     

Comprehensive molecular sampling yields a robust phylogeny for geometrid moths (Lepidoptera: Geometridae)

Background

The moth family Geometridae (inchworms or loopers), with approximately 23 000 described species, is the second most diverse family of the Lepidoptera. Apart from a few recent attempts based on morphology and molecular studies, the phylogeny of these moths has remained largely uninvestigated.

Methodology/Principal Findings

We performed a rigorous and extensive molecular analysis of eight genes to examine the geometrid affinities in a global context, including a search for its potential sister-taxa. Our maximum likelihood analyses included 164 taxa distributed worldwide, of which 150 belong to the Geometridae. The selected taxa represent all previously recognized subfamilies and nearly 90% of recognized tribes, and originate from all over world. We found the Geometridae to be monophyletic with the Sematuridae+Epicopeiidae clade potentially being its sister-taxon. We found all previously recognized subfamilies to be monophyletic, with a few taxa misplaced, except the Oenochrominae+Desmobathrinae complex that is a polyphyletic assemblage of taxa and the Orthostixinae, which was positioned within the Ennominae. The Sterrhinae and Larentiinae were found to be sister to the remaining taxa, followed by Archiearinae, the polyphyletic assemblage of Oenochrominae+Desmobathrinae moths, Geometrinae and Ennominae.

Conclusions/Significance

Our study provides the first comprehensive phylogeny of the Geometridae in a global context. Our results generally agree with the other, more restricted studies, suggesting that the general phylogenetic patterns of the Geometridae are now well-established. Generally the subfamilies, many tribes, and assemblages of tribes were well supported but their interrelationships were often weakly supported by our data. The Eumeleini were particularly difficult to place in the current system, and several tribes were found to be para- or polyphyletic.     

Toward a phylogeny and biogeography of Diaphanosoma (Crustacea: Cladocera)

Aquatic Ecology - Diaphanosoma s.l., with 40+? described species, is the largest genus of the Sididae and the Ctenopoda, similar in many ways to the anomopod genus Daphnia. Here, we offer a c...     

Reticulate evolution on a global scale: a nuclear phylogeny for New World Dryopteris (Dryopteridaceae)

Reticulate, or non-bifurcating, evolution is now recognized as an important phenomenon shaping the histories of many organisms. It appears to be particularly common in plants, especially in ferns, which have relatively few barriers to intra- and interspecific hybridization. Reticulate evolutionary patterns have been recognized in many fern groups, though very few have been studied rigorously using modern molecular phylogenetic techniques in order to determine the causes of the reticulate patterns. In the current study, we examine patterns of branching and reticulate evolution in the genus Dryopteris, the woodferns. The North American members of this group have long been recognized as a classic example of reticulate evolution in plants, and we extend analysis of the genus to all 30 species in the New World, as well as numerous taxa from other regions. We employ sequence data from the plastid and nuclear genomes and use maximum parsimony (MP), maximum likelihood (ML), Bayesian inference (BI), and divergence time analyses to explore the relationships of New World Dryopteris to other regions and to reconstruct the timing and events which may have led to taxa displaying reticulate rather than strictly branching histories. We find evidence for reticulation among both the North and Central/South American groups of species, and our data support a classic hypothesis for reticulate evolution via allopolyploid speciation in the North America taxa, including an extinct diploid progenitor in this group. In the Central and South American species, we find evidence of extensive reticulation involving unknown ancestors from Asia, and we reject deep coalescent processes such as incomplete lineage sorting in favor of more recent intercontinental hybridization and chloroplast capture as an explanation for the origin of the Latin American reticulate taxa.     

Gonadotrophin-releasing hormone (GnRH) in the animal kingdom

As a major actor of the brain-pituitary-gonad axis, GnRH has received considerable attention, mainly in vertebrates. Biochemical, molecular, neuroanatomical, pharmacological and physiological studies have mainly focused on the role of GnRH as a gonadotrophin-releasing factor and have led to a detailed knowledge of the hypophysiotrophic GnRH system, primarily in mammals, but also in fish. It is now admitted that the corresponding neurons develop from the olfactory epithelium and migrate into the forebrain during embryogenesis to establish connections with the median eminence in tetrapods or the pituitary in teleost fish. However, all vertebrates possess a second GnRH system, expressing a variant known as chicken GnRH-II in neurons of the synencephalon, whose functions are still under debate. In addition, many fish species express a third form, salmon GnRH, whose expression is restricted to neurons of the olfactory systems and the ventral telencephalon, with extensive projections in the brain and a minor contribution to the pituitary. In vertebrates, GnRHs are also expressed in the gonads where they act on cell proliferation and steroidogenesis in males, and apoptosis of granulosa cells and reinititaion of meiosis in females. These functions could possibly represent the primitive roles of GnRH-like peptides, as an increasing number of studies in invertebrate classes point to a more or less direct connection between GnRH-producing sensory neurons and the gonads. According to recent studies, GnRHs appear as very ancient peptides that emerged at least in the cnidarians, the first animals with a nervous system. GnRH-like peptides have been partially characterized in several classes of invertebrates notably in molluscs, echinoderms and prochordates in which effects on the reproductive functions, notably gamete release and steroidogeneis, have been evidenced. It is possible that, with the increasing complexity of metozoa, GnRH neurons have lost their direct connection with the gonad to specialize in the control of additional regulatory centers such as the hypophysis in vertebrates or the optic gland in cephalopods. However, reminiscent effects of GnRH functions at the gonadal level would have persisted due to local production of GnRHs in the gonad itself. Altogether, these data indicate that GnRHs were involved in the control of reproduction long before the appearance of pituitary gonadotrophs.     

Deep molluscan phylogeny: synthesis of palaeontological and neontological data

The position of the earliest-derived living molluscs, the Polyplacophora (chitons) and shell-less vermiform Aplacophora, remains highly contentious despite many morphological, developmental and molecular studies of extant organisms. These two groups are thought to represent either a basal molluscan grade or a clade (Aculifera) sister to the 'higher' molluscs (Conchifera). These incompatible hypotheses result in very different predictions about the earliest molluscs. A new cladistic analysis incorporating both Palaeozoic and extant molluscs is presented here. Our results support the monophyly of Aculifera and suggest that extant aplacophorans and polyplacophorans both derive from a disparate group of multivalved molluscs in two major clades. Reanalysis of the critical Ordovician taxon 'Helminthochiton' thraivensis shows that this animal lacks a true foot despite bearing polyplacophoran-like valves. Its position within our phylogenetic reconstruction indicates that many fossil 'polyplacophorans' in the order Palaeoloricata are likely to represent footless stem-group aplacophorans. 'H.' thraivensis and similar forms such as Acaenoplax may be morphological stepping stones between chitons and the shell-less aplacophorans. Our results imply that crown-group molluscan synapomorphies include serial repetition, the presence of a foot, a mineralized scleritome and a creeping rather than worm-like mode of life.     

Coordination on Networks: Does Topology Matter?

Effective coordination is key to many situations that affect the well-being of two or more humans. Social coordination can be studied in coordination games between individuals located on networks of contacts. We study the behavior of humans in the laboratory when they play the Stag Hunt game – a game that has a risky but socially efficient equilibrium and an inefficient but safe equilibrium. We contrast behavior on a cliquish network to behavior on a random network. The cliquish network is highly clustered and resembles more closely to actual social networks than the random network. In contrast to simulations, we find that human players dynamics do not converge to the efficient outcome more often in the cliquish network than in the random network. Subjects do not use pure myopic best-reply as an individual update rule. Numerical simulations agree with laboratory results once we implement the actual individual updating rule that human subjects use in our laboratory experiments.     

Towards a phylogeny and evolution of Acochlidia (Mollusca: Gastropoda: Opisthobranchia)

The Acochlidia are unique among opisthobranch gastropods in combining extremely high morphological and ecological diversity with modest species diversity. The phylogeny of acochlidians has never been addressed by cladistic means, as their evolution has remained unknown. This study gives a first overview on more than 150 biological and morphological characters that are potentially useful for phylogenetic analysis. Based on 107 characters, a parsimony analysis (PAUP) was performed for all 27 valid acochlidian species together with 11 (plus two) outgroup taxa. The resulting strict consensus tree shows a moderate overall resolution, with at least some bootstrap support for most resolved nodes. The Acochlidia are clearly monophyletic, and originate from an unresolved basal opisthobranch level. The Acochlidia split into the Hedylopsacea (Tantulum (Hedylopsis (Pseudunela (Strubellia (‘Acochlidium’, ‘Palliohedyle’))))) and Microhedylacea (Asperspina (Pontohedyle, ‘Parhedyle’, ‘Microhedyle’, (Ganitus, Paraganitus))). The formerly enigmatic Ganitidae, resembling sacoglossan opisthobranchs by having dagger‐like rachidian radular teeth, are likely to be highly derived microhedylids. The paraphyly of some of the traditionally recognized family level taxa induced a preliminary reclassification. From the phylogenetic hypothesis obtained, we conclude that the acochlidian ancestor was marine mesopsammic. The colonization of limnic systems occurred twice, independently: first in the Caribbean (with the development of the small interstitial Tantulum elegans), and second in the Indo‐Pacific, with a radiation of large‐sized benthic acochlidian species. The evolution of extraordinary reproductive features, such as hypodermic impregnation by a complex copulative aparatus in hedylopsaceans, cutaneous insemination via spermatophores in microhedylaceans, and gonochorism in Microhedylidae s.l. (including Ganitidae), is discussed. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 158 , 124–154.     

Pachecoa prismatica (Fabaceae): Taxonomy and phylogeny

Pachecoa Standley & Steyerm., a monotypic legume genus of Mexico, Guatemala, and Venezuela, is described and illustrated with accompanying notes on its habitat, distribution, reproductive biology, phylogeny, cytology, and relationship (with key) to allied genera.