Molecular phylogeny of the Entomophthoromycota

The Entomophthoromycota is a ubiquitous group of fungi best known as pathogens of a wide variety of economically important insect pests, and other soil invertebrates. This group of fungi also includes a small number of parasites of reptiles, vertebrates (including humans), macromycetes, fern gametophytes, and desmid algae, as well as some saprobic species. Here we report on recent studies to resolve the phylogenetic relationships within the Entomophthoromycota and to reliably place this group among other basal fungal lineages. Bayesian Interference (BI) and Maximum Likelihood (ML) analyses of three genes (nuclear 18S and 28S rDNA, mitochondrial 16S, and the protein-coding RPB2) as well as non-molecular data consistently and unambiguously identify 31 taxa of Entomophthoromycota as a monophyletic group distinct from other Zygomycota and flagellated fungi. Using the constraints of our multi-gene dataset we constructed the most comprehensive rDNA phylogeny yet available for Entomophthoromycota. The taxa studied here belong to five distinct, well-supported lineages. The Basidiobolus clade is the earliest diverging lineage, comprised of saprobe species of Basidiobolus and the undescribed snake parasite Schizangiella serpentis nom. prov. The Conidiobolus lineage is represented by a paraphyletic grade of trophically diverse species that include saprobes, insect pathogens, and facultative human pathogens. Three well supported and exclusively entomopathogenic lineages in the Entomophthoraceae center around the genera Batkoa, Entomophthora and Zoophthora, although several genera within this crown clade are resolved as non-monophyletic. Ancestral state reconstruction suggests that the ancestor of all Entomophthoromycota was morphologically similar to species of Conidiobolus. Analyses using strict, relaxed, and local molecular clock models documented highly variable DNA substitution rates among lineages of Entomophthoromycota. Despite the complications caused by different rates of molecular evolution among lineages, our dating analysis indicates that the Entomophthoromycota originated 405±90million years ago. We suggest that entomopathogenic lineages in Entomophthoraceae probably evolved from saprobic or facultatively pathogenic ancestors during or shortly after the evolutionary radiation of the arthropods.     

Dracula ant phylogeny as inferred by nuclear 28S rDNA sequences and implications for ant systematics (Hymenoptera: Formicidae: Amblyoponinae)

Ants are one of the most ecologically and numerically dominant families of organisms in almost every terrestrial habitat throughout the world, though they include only about 1% of all described insect species. The development of eusociality is thought to have been a driving force in the striking diversification and dominance of this group, yet we know little about the evolution of the major lineages of ants and have been unable to clearly determine their primitive characteristics. Ants within the subfamily Amblyoponinae are specialized arthropod predators, possess many anatomically and behaviorally primitive characters and have been proposed as a possible basal lineage within the ants. We investigate the phylogenetic relationships among the members of the subfamily, using nuclear 28S rDNA sequence data. Outgroups for the analysis include members of the poneromorph and leptanillomorph (Apomyrma, Leptanilla) ant subfamilies, as well as three wasp families. Parsimony, maximum likelihood, and Bayesian analyses provide strong support for the monophyly of a clade containing the two genera Apomyrma+Mystrium (100% bpp; 97% ML bs; and 97% MP bs), and moderate support for the monophyly of the Amblyoponinae as long as Apomyrma (Apomyrminae) is included (87% bpp; 57% ML bs; and 76% MP bs). Analyses did not recover evidence of monophyly of the Amblyopone genus, while the monophyly of the other genera in the subfamily is supported. Based on these results we provide a morphological diagnosis of the Amblyoponinae that includes Apomyrma. Among the outgroup taxa, Typhlomyrmex grouped consistently with Ectatomma, supporting the recent placement of Typhlomyrmex in the Ectatomminae. The results of this present study place the included ant subfamilies into roughly two clades with the basal placement of Leptanilla unclear. One clade contains all the Amblyoponinae (including Apomyrma), Ponerinae, and Proceratiinae (Poneroid clade). The other clade contains members from subfamilies Cerapachyinae, Dolichoderinae, Ectatomminae, Formicinae, Myrmeciinae, and Myrmicinae (Formicoid clade).     

Molecular analysis of the biting midges (Diptera: Ceratopogonidae), based on mitochondrial cytochrome oxidase subunit 2

Sequences from the mitochondrial cytochrome oxidase subunit 2 gene (cox2) were determined for 14 species from the family Ceratopogonidae, representing 12 genera and all five subfamilies, along with six representatives of other nematoceran families. The purpose was to develop a molecular phylogeny of the Ceratopogonidae, and interpret the phylogenetic position of the family within the infraorder Culicomorpha. These taxa have been analysed using cladistic methodology which, in combination with an excellent fossil record, provides a well established morphological phylogeny. Sequence analysis of cox2 revealed a high degree of sequence divergence among the species, reflecting in part the antiquity of the family, but also a significant acceleration of sequence evolution in the ceratopogonids compared to other nematoceran Diptera. Phylogenetic reconstruction by neighbor-joining and maximum parsimony gave strong support for an early separation of an ancient lineage that includes the two genera, Austroconops and Leptoconops, from the remainder of the family. The results support the existence of a clade that includes two subfamilies, Dasyheleinae and Forcipomyiinae, and this clade appears as sister to the remaining subfamily, Ceratopogoninae. The molecular phylogeny also supports monophyly of the Ceratopogonidae, and either a sister or paraphyletic relationship of this family with the Chironomidae.     

Phylogeny and character evolution in the Empidonax group of tyrant flycatchers (Aves: Tyrannidae): a test of W. E. Lanyon's hypothesis using mtDNA sequences

We sequenced mitochondrial DNA from four protein-coding genes for 26 taxa to test W. E. Lanyon's hypothesis of intergeneric relationships and character evolution in the Empidonax group of tyrant flycatchers. Three genera in this group (Empidonax, Contopus, and Sayornis) successfully occupy north temperate habitats for breeding, while the remaining genera (Mitrephanes, Cnemotriccus, Aphanotriccus, Lathrotriccus, and Xenotriccus) are restricted to neotropical latitudes. Lanyon hypothesized two major clades in the group based on differences in syringeal morphology and proposed relationships among genera using a combination of morphologic, behavioral, and allozymic characters. The mtDNA data strongly support Lanyon's division of genera into two clades. In addition, the molecular and nonmolecular data sets agree in uniting Aphanotriccus and Lathrotriccus as sister taxa, with Cnemotriccus as basal to these genera. Species of Aphanotriccus, Lathrotriccus, and Cnemotriccus form a clade that exploits a distinctive nesting niche relative to other members of the Empidonax group. Within the second major clade, mtDNA sequences support a reconstruction based on allozymes that places Contopus and Empidonax as sister taxa. This hypothesis contradicts that of Lanyon, who allied Contopus with Mitrephanes on the basis of similarity in foraging mode. Genera in the Empidonax group are members of a larger assemblage that radiated in South America. Occupancy of temperate habitats by certain genera in this group is coincident with their evolution of migratory behavior and with independent diversification in foraging modes that reduces potential competition in sympatry.     

Angiosperm phylogeny inferred from sequences of four mitochondrial genes

An angiosperm phylogeny was reconstructed in a maximum likelihood analysis of sequences of four mitochondrial genes, atpl, matR, had5, and rps3, from 380 species that represent 376 genera and 296 families of seed plants. It is largely congruent with the phylogeny of angiosperms reconstructed from chloroplast genes atpB, matK, and rbcL, and nuclear 18S rDNA. The basalmost lineage consists of Amborella and Nymphaeales (including Hydatellaceae). Austrobaileyales follow this clade and are sister to the mesangiosperms, which include Chloranthaceae, Ceratophyllum, magnoliids, monocots, and eudicots. With the exception of Chloranthaceae being sister to Ceratophyllum, relationships among these five lineages are not well supported. In eudicots, Ranunculales, Sabiales, Proteales, Trochodendrales, Buxales, Gunnerales, Saxifragales, Vitales, Berberidopsidales, and Dilleniales form a basal grade of lines that diverged before the diversification of rosids and asterids. Within rosids, the COM (Celastrales-Oxalidales-Malpighiales) clade is sister to malvids (or rosid Ⅱ), instead of to the nitrogen-fixing clade as found in all previous large-scale molecular analyses of angiosperms. Santalales and Caryophyllales are members of an expanded asterid clade. This study shows that the mitochondrial genes are informative markers for resolving relationships among genera, families, or higher rank taxa across angiosperms. The low substitution rates and low homoplasy levels of the mitochondrial genes relative to the chloroplast genes, as found in this study, make them particularly useful for reconstructing ancient phylogenetic relationships. A mitochondrial gene-based angiosperm phylogeny provides an independent and essential reference for comparison with hypotheses of angiosperm phylogeny based on chloroplast genes, nuclear genes, and non-molecular data to reconstruct the underlying organismal phylogeny.     

Internal transcribed spacer sequence phylogeny of Crambe L. (Brassicaceae): molecular data reveal two Old World disjunctions

Crambe L. (Brassicaceae) is an Old World genus with a disjunct distribution among four major centers of species diversity. A phylogenetic analysis of nucleotide sequences of the internal transcribed spacers (ITS) of the nuclear ribosomal repeat was conducted with 27 species of Crambe and 18 related genera. Cladistic analyses using weighted and unweighted parsimony support Crambe as a monophyletic genus with three major lineages. The first comprises those taxa endemic to the Macaronesian archipelagos. Taxa with a predominant Mediterranean distribution form the second assemblage, and a disjunction between east Africa (C. abyssinica) and the Mediterranean (C. hispanica) occurs in this clade. The third lineage includes all Eurosiberian-Asian taxa and C. kilimandscharica, a species from the highlands of east Africa. A basal biogeographic split between east Africa and Eurasia is present in the third clade. The patterns of relationships in the ITS tree are concordant with known climatic events in northern Africa and southwestern Asia since the middle Miocene. The ITS trees are congruent with the current sectional classification except for a few members of sections Crambe, Leptocrambe, and Orientecrambe (C. cordifolia, C. endentula, C. kilimandscharica, and C. kotschyana). Low levels of support in the basal branches do not allow resolution of which genera of the subtribes Raphaniae or Brassicinae are sister to Crambe. Both subtribes appear to be highly polyphyletic in the ITS trees.     

A molecular phylogenetic analysis of the "true thrushes" (Aves: Turdinae)

The true thrushes (Passeriformes: Muscicapidae, subfamily Turdinae) are a speciose and widespread avian lineage presumed to be of Old World origin. Phylogenetic relationships within this assemblage were investigated using mitochondrial DNA (mtDNA) sequence data that included the cytochrome b and ND2 genes. Our ingroup sampling included 54 species representing 17 of 20 putative turdine genera. Phylogenetic trees derived via maximum parsimony and maximum likelihood were largely congruent. Most of the Turdine taxa sampled can be placed into one of six well supported clades. Our data indicate a polyphyletic Zoothera which can be divided into at least two (Afro-Asian and Austral-Asian) main clades. The genus Turdus, as presently recognized, is paraphyletic but forms a well supported clade with the addition of three mostly monotypic genera (Platycichla, Nesocichla, and Cichlherminia). We identify an exclusively New World clade that includes a monophyletic Catharus, Hylocichla, Cichlopsis, Entomodestes, Ridgwayia, and Ixoreus. Members of the morphologically and behaviorally distinct genera Sialia, Myadestes, and Neocossyphus unexpectedly form a basal clade. Using multiple outgroup choices, we show that this group is distantly related, but unequivocally the sister group to the remaining Turdines sampled. The Turdinae appear to be a relatively old songbird lineage, originating in the mid to late Miocene. If the Turdinae are indeed Old World in origin, our data indicate a minimum of three separate invasions of the New World.     

Three new genera representing novel lineages of Sordariomycetidae (Sordariomycetes, Ascomycota) from tropical freshwater habitats in Costa Rica

Three new genera are established in the Sordariomycetidae based on morphological and molecular data (SSU and LSU nrDNA) to accommodate five ascomycete species collected from submerged woody debris in freshwater habitats from Costa Rica. The genus Bullimyces contains three new species, B. communis, B. costaricensis and B. aurisporus. Bullimyces is characterized by globose to subglobose, membranous, black, ostiolate ascomata; deliquescent, hyaline, globose cells that fill the center of the centrum; unitunicate asci that deliquesce early in some species; and septate, thick-walled ascospores with or without gelatinous sheaths or appendages. Bullimyces species form a well supported clade with 100% bootstrap support, but the position of the genus in the Sordariomycetidae remains unclear. The second genus, Riomyces, is represented by a single species, R. rotundus. Riomyces is characterized by globose to subglobose, membranous, black, ostiolate ascomata, unitunicate, cylindrical asci, hyaline, globose cells that fill the hamathecium and septate, thick-walled ascospores with a gelatinous sheath. Although Riomyces is morphologically similar to Bullimyces, the two genera did not group together with support in any analysis. The third genus, Hydromelitis, is represented by a single species, H. pulchella. Hydromelitis is characterized by pyriform, membranous, black, ostiolate ascomata, unitunicate asci lacking an apical structure, simple, thin-walled, septate paraphyses and hyaline to golden yellow, multiseptate, thick-walled ascospores with a gelatinous sheath. Bullimyces, Riomyces and Hydromelitis were nested within an unsupported clade consisting of members of the Ophiostomatales, Magnaporthales and freshwater Annulatacaceae sensu lato and sensu stricto.     

Independent terrestrial origins of the Halosphaeriales (marine Ascomycota)

A phylogenetic study of marine ascomycetes was initiated to test and refine evolutionary hypotheses of marine-terrestrial transitions among ascomycetes. Taxon sampling focused on the Halosphaeriales, the largest order of marine ascomycetes. Approximately 1050 base pairs (bp) of the gene that codes for the nuclear small subunit (SSU) and 600 bp of the gene that codes for the nuclear large subunit (LSU) ribosomal RNAs (rDNA) were sequenced for 15 halosphaerialean taxa and integrated into a data set of homologous sequences from terrestrial ascomycetes. An initial set of phylogenetic analyses of the SSU rDNA from 38 taxa representing 15 major orders of the phylum Ascomycota confirmed a close phylogenetic relationship of the halosphaerialean species with several other orders of perithecial ascomycetes. A second set of analyses, which involved more intensive taxon sampling of perithecial ascomycetes, was performed using the SSU and LSU rDNA data in combined analyses. These second analyses included 15 halosphaerialean taxa, 26 terrestrial perithecial fungi from eight orders, and five outgroup taxa from the Pezizales. In these analyses the Halosphaeriales were polyphyletic and comprised two distinct lineages. One clade of Halosphaeriales comprised 12 taxa from 11 genera and was most closely related to terrestrial fungi of the Microascales. The second clade of halosphaerialean fungi comprised taxa from the genera Lulworthia and Lindra and was an isolated lineage among the perithecial fungi. Both the main clade of Halosphaeriales and the Lulworthia/Lindra clade are supported by the data as being independently derived from terrestrial ancestors.     

Testing morphology-based hypotheses of phylogenetic relationships in Parmeliaceae (Ascomycota) using three ribosomal markers and the nuclear RPB1 gene

Parmeliaceae is the largest family of lichen-forming fungi with more than 2000 species and includes taxa with different growth forms. Morphology was widely employed to distinguish groups within this large, cosmopolitan family. In this study we test these morphology-based groupings using DNA sequence data from three nuclear and one mitochondrial marker from 120 taxa that include 59 genera and represent the morphological and chemical diversity in this lineage. Parmeliaceae is strongly supported as monophyletic and six well-supported main clades can be distinguished within the family. The relationships among them remain unresolved. The clades largely agree with the morphology-based groupings and only the placement of four of the genera studied is rejected by molecular data, while four other genera belong to clades previously unrecognised. The classification of these previously misplaced genera, however, has already been questioned by some authors based on morphological evidence. These results support morphological characters as important for the identification of monophyletic clades within Parmeliaceae.     

Out of the blue: a novel, trans-Atlantic clade of geckos (Gekkota, Squamata)

Phylogenetic relationships among gekkotan lizards were estimated from five nuclear protein-coding genes in separate and combined analyses using maximum parsimony, maximum likelihood and Bayesian analyses. All analyses recovered a monophyletic trans-Atlantic gecko clade (Phyllodactylidae) consisting of the genera Asaccus, Haemodracon, Homonota, Phyllodactylus, Phyllopezus, Ptyodactylus, Tarentola and Thecadactylus . No other phylogenetic or taxonomic hypotheses have proposed linking these genera, which have been consistently grouped with other taxa outside of the clade. In this paper, we determine the relationships of this new clade to other major gekkotan groups, evaluate previous phylogenetic hypotheses regarding constituent members of this novel clade, and critically examine the use of historically important morphological characters in gekkotan systematics as they relate to this novel clade, specifically — phalangeal formulae, hyoid morphology and external structure of the toe-pads.     

A complete species-level molecular phylogeny for the "Eurasian" starlings (Sturnidae: Sturnus, Acridotheres, and allies): recent diversification in a highly social and dispersive avian group

We generated the first complete phylogeny of extant taxa in a well-defined clade of 26 starling species that is collectively distributed across Eurasia, and which has one species endemic to sub-Saharan Africa. Two species in this group-the European starling Sturnus vulgaris and the common Myna Acridotheres tristis-now occur on continents and islands around the world following human-mediated introductions, and the entire clade is generally notable for being highly social and dispersive, as most of its species breed colonially or move in large flocks as they track ephemeral insect or plant resources, and for associating with humans in urban or agricultural landscapes. Our reconstructions were based on substantial mtDNA (4 kb) and nuclear intron (4 loci, 3 kb total) sequences from 16 species, augmented by mtDNA NDII gene sequences (1 kb) for the remaining 10 taxa for which DNAs were available only from museum skin samples. The resulting mitochondrial gene tree embedded within a multilocus framework shows that the well-studied taxa S. vulgaris/unicolor are the sister lineage to the remaining members of the radiation, from which other relatively early lineages gave rise to forms that are now nomadic or locally migrant in Africa (Creatophora) and western Asia (Pastor). The remaining taxa form a clade with a complicated biogeographic history primarily in central and eastern Asia; this group contains a range of sedentary to highly migratory taxa, as well as widely distributed species and single-island endemics such as the highly endangered Bali myna (Leucopsar). Several groups of species in the genus Acridotheres have low magnitudes of within-group divergence and likely diversified via their respective colonization of islands. The taxonomy of this entire group has remained highly volatile over the past century; we propose dividing these 26 species among 11 reciprocally monophyletic genera (Acridotheres, Poliopsar, Temenuchus, Sturnornis, Leucopsar, Gracupica, Agropsar, Pastor, Creatophora, and Sturnus).     

A molecular systematic revision of two historically problematic songbird clades: Aimophila and Pipilo

The emberizid genera Aimophila and Pipilo represent longstanding taxonomic conundrums. Each is comprised of sub-clades whose members appear to share diagnostic morphological and behavioral characters; however, relationships among sub-clades within each of these genera remain unclear, and numerous authors have suggested that either one or both of these genera may be polyphyletic. We addressed this taxonomic problem by sequencing and analyzing complete mitochondrial cytochrome- b and NADH dehydrogenase subunit 2 genes for all members of Aimophila and Pipilo along with 33 species representing 17 additional emberizid genera. Our maximum likelihood and Bayesian analyses indicate that both Aimophila and Pipilo are polyphyletic. Aimophila is divided into a minimum of three distinct groups. The forms notosticta, ruficeps , and rufescens are part of a well-supported clade that includes all members of Melozone and some members of Pipilo . Aimophila quinquestriata is placed within Amphispiza , and the remaining members of Aimophila are placed within a clade that includes all members of Arremonops and some members of Ammodramus . Within Pipilo , the "rufous-sided" and "brown" towhee groups do not form sister groups. Rather, the former are most closely related to the tropical genus Atlapetes whereas the latter are placed nearest Melozone and some Aimophila . Our analyses reject traditional taxonomic arrangements for both genera, and we present suggestions for a revised taxonomy for all members of Aimophila and Pipilo . These results provide further evidence of discordance among phylogenetic hypotheses based on morphological and molecular characters for groups of birds with generally conserved morphology.     

A Molecular Study of Euglenoid Phylogeny using Small Subunit rDNA

The euglenoids are an ancient and extremely diverse lineage of eukaryotic flagellates with unclear relationships among taxa. Synapomorphies for the euglenoids include a surface pellicle and a closed mitosis with a series of separate sub-spindles. The taxonomy currently in use is inconsistent with the available data and needs revision. Most euglenoid phylogenies are largely intuitive reconstructions based on a limited number of morphological characters. Therefore, we have added molecular characters from the Small Subunit (SSU) rDNA to generate an overall phylogenetic framework for the euglenoids. SSU rDNA sequences from photosynthetic, osmotrophic, and phagotrophic euglenoids were aligned based on secondary structure. Phylogenetic analysis using the conserved areas of the sequence was performed using parsimony, maximum likelihood, and distance methods. Trees derived using different criteria are in agreement. The euglenoids form a distinct monophyletic clade with phagotrophic members diverging prior to the phototrophic and osmotrophic members. Among photosynthetic members, the biflagellate form diverged prior to the uniflagellate form. Additionally, the genus Euglena appears to be paraphyletic, with osmotrophic taxa, such as Astasia and Khawkinea, diverging independently within the clade containing the photosynthetic genus Euglena.