Astrosphaeriella Sydow, a misunderstood genus of melanommataceous pyrenomycetes

The genus Astrosphaeriella Sydow has been regarded as a synonym of Microthelia Körber in recent surveys of bitunicate pyrenomycetes. The structure of the ascomata and the presence of trabeculate pseudoparaphyses show that it belongs to the series of melanommataceous pyrenomycetes and is unrelated to the pleosporaceous taxa commonly referred to Microthelia. All taxa which have been referred to Astrosphaeriella, Astrotheca , or Asterotheca are revised and four species accepted: A. aosimensis Hino & Katumoto, A. stellata (Pat.) Sacc., A. trochus (Penzig & Sacc.) D. Hawksw. and A. venezuelensis Barr & D. Hawksw. As circumscribed here, the genus is exclusively tropical, comprising species characteristically occurring on petioles of palms and bamboo culms. Notes on excluded taxa are provided and the new combination Mycomicrothelia inaequalis (Fabre) D. Hawksw. is made.     

Freshwater ascomycetes: Jahnula apiospora (Jahnulales, Dothideomycetes), a new species from Prince Edward Island, Canada

A new ascomycete species, Jahnula apiospora (Jahnulales, Dothideomycetes), collected from submerged wood in a freshwater creek on Prince Edward Island, Canada, is described and illustrated. The characteristic features of the new species are globose to subglobose, black, ostiolate, membranous ascomata with broad, brown, subtending hyphae; a peridial wall composed of an outer layer of thick-walled cells occluded by black, amorphous material along the upper two-thirds of the ascoma; trabeculate pseudoparaphyses; cylindrical to narrowly fusoid, fissitunicate asci; and brown, one-septate, apiosporous ascospores without a gelatinous sheath or appendages.     

CENTRUM DEVELOPMENT IN DIDYMELLA BRYONIAE

Early stages of pseudothecium development consist of small pseudoparenchymatous stromata in which ascogonia differentiate. Deeply staining cells in the apical region of the young pseudothecium elongate to form pseudoparaphyses, which grow down to fill the centrum. Ascogenous hyphae grow out from ascogenous cells, located in the basal plectenchyma, and croziers arise and proliferate from the ascogenous hyphae. Bitunicate asci grow up among the pseudoparaphyses and forcibly discharge two-celled hyaline ascospores at maturity. Because centrum development in Didymella bryoniae (Auersw.) Rehm is pseudoparaphysate, the causal agent of gummy stem blight in watermelon is properly placed in the order Pleosporales. The placement of this species in Didymella on the basis of the Ascochyta cucumis Fautr. et Roum. anamorph is supported by centrum structure.     

Bambusicolous fungi in Japan (6): Katumotoa, a new genus of phaeosphaeriaceous ascomycetes

A new genus, Katumotoa, is established for a single species, K. bambusicola, collected from culms of Sasa kurilensis. Morphological differences between Katumotoa and some related genera are noted. Katumotoa is characterized by perithecioid ascomata, thin ascomal wall composed of small pseudoparenchymatous cells, cellular pseudoparaphyses, fissitunicate asci, and apiosporous fusiform ascospores with bipolar mucilaginous sheath. From these features, it is considered that the genus belongs to Phaeosphaeriaceae in Pleosporales.     

Freshwater ascomycetes: Wicklowia aquatica, a new genus and species in the Pleosporales from Florida and Costa Rica

During a latitudinal survey of freshwater ascomycetes, an unidentified fungus with bitunicate asci was found on submerged wood and herbaceous material from Florida and Costa Rica. Based on morphological characteristics and 28S rDNA large subunit (LSU) sequence data, this fungus is described as a new genus and species, Wicklowia aquatica, and placed in the Pleosporales (Pleosporomycetidae, Dothideomycetes). Phylogenetic analyses based on LSU sequences did not resolve the familial placement of W. aquatica within the Pleosporales. The characteristic features of W. aquatica are subglobose, dorsiventrally flattened, ostiolate, immersed to erumpent, black ascomata; a peridial wall composed of 4–5 layers of darkened pseudoparenchymatic cells; cellular pseudoparaphyses immersed in a gel matrix; broadly clavate, bitunicate asci; and cylindrical, hyaline, one-septate ascospores with rounded apices and surrounded by a gelatinous sheath that expands in water; ascospore sheath attached at the ascospore base with a gelatinous curtain extending from the base that fragments into basal filamentous appendages which radiate from the base of the ascospore.     

Evaluation of the monophyly of Fomitopsis using parsimony and MCMC methods

To evaluate the monophyly of Fomitopsis and elucidate phylogenetic relationships of its members, partial nuclear large subunit (partial 28S) ribosomal RNA genes were sequenced from 10 species of Fomitopsis and 15 related species. Phylogenetic analyses indicated that Fomitopsis was phylogenetically heterogeneous and its members were divided into three subgroups. The constrained tree excluding F. palustris (the type species of Pilatoporus) from Fomitopsis core group was rejected, thus rejecting the taxonomic concept to segregate Pilatoporus from Fomitopsis. The monophyly of taxa belonging to F. rosea complex was rejected, thus rejecting the complex definition based on morphological similarities. The exclusion of Piptoporus betulinus (the type species of Piptoporus) from Fomitopsis core group was rejected and Piptoporus proved to be heterogeneous in both best MP and MAP trees. The monophyly of F. officinalis with Fomitopsis core group also was rejected. Fomitopsis officinalis was closely related to Antrodia xantha and formed an independent lineage from Fomitopsis core group at the basal position of brown rotting fungi comprising Antrodia, Daedalea, Fomitopsis, Piptoporus and Postia. The MAP tree topologyobtained from MCMC computation of Bayesian inference was similar to the one of the best MP tree based on the parsimony analysis but showed a higher likelihood score in the Kishino-Hasegawa test and reflected better evolutionary patterns for the phylogeny of Fomitopsis.     

Phylogeny of pteromalid parasitic wasps (Hymenoptera: Pteromalidae): initial evidence from four protein-coding nuclear genes

Chalcidoidea (approximately 22,000 described species) is the most ecologically diverse superfamily of parasitic Hymenoptera and plays a major role in the biological control of insect pests. However, phylogenetic relationships both within and between chalcidoid families have been poorly understood, particularly for the large family Pteromalidae and relatives. Forty-two taxa, broadly representing Chalcidoidea but concentrated in the 'pteromalid lineage,' were sequenced for 4620 bp of protein-coding sequence from four nuclear genes for which we present new primers. These are: CAD (1719 bp) DDC (708 bp), enolase (1149 bp), and PEPCK (1044 bp). The combined data set was analyzed using parsimony, maximum likelihood, and Bayesian methods. Statistical significance of the apparent non-monophyly of some taxonomic groups on our trees was evaluated using the approximately unbiased test of Shimodaira [Shimodaira, H. 2002. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 51(3), 492-508]. In accord with previous studies, we find moderate to strong support for monophyly of Chalcidoidea, a sister-group relationship of Mymaridae to the remainder of Chalcidoidea, and a relatively basal placement of Encarsia (Aphelinidae) within the latter. The 'pteromalid lineage' of families is generally recovered as monophyletic, but the hypothesis of monophyly for Pteromalidae, which appear paraphyletic with respect to all other families sampled in that lineage, is decisively rejected (P < 10(-14)). Within Pteromalidae, monophyly was strongly supported for nearly all tribes represented by multiple exemplars, and for two subfamilies. All other multiply-represented subfamilies appeared para- or polyphyletic in our trees, although monophyly was significantly rejected only for Miscogasterinae, Ormocerinae, and Colotrechninae. The limited resolution obtained in the analyses presented here reinforces the idea that reconstruction of pteromalid phylogeny is a difficult problem, possibly due to rapid radiation of many chalcidoid taxa. Initial phylogenetic comparisons of life history traits suggest that the ancestral chalcidoid was small-bodied and parasitized insect eggs.     

Variance of molecular datings, evolution of rodents and the phylogenetic affinities between Ctenodactylidae and Hystricognathi

The von Willebrand factor (vWF) gene has been used to understand the origin and timing of Rodentia evolution in the context of placental phylogeny vWF exon 28 sequences of 15 rodent families and eight non-rodent eutherian clades are analysed with two different molecular dating methods (uniform clock on a linearized tree; quartet dating). Three main conclusions are drawn from the study of this nuclear exon. First, Ctenodactylidae (gundis) and Hystricognathi (e.g. porcupines, guinea-pigs, chinchillas) robustly cluster together in a newly recognized clade, named 'Ctenohystrica'. The Sciurognathi monophyly is subsequently rejected. Pedetidae (springhares) is an independent and early diverging rodent lineage, suggesting a convergent evolution of the multiserial enamel of rodent incisors. Second, molecular date estimates are here more influenced by accuracy and choice of the palaeontological temporal references used to calibrate the molecular clock than by either characters analysed (nucleotides versus amino acids) or species sampling. The caviomorph radiation at 31 million years (Myr) and the pig porpoise split at 63 Myr appear to be reciprocally compatible dates. Third, during the radiation of Rodentia, at least three lineages (Gliridae, Sciuroidea and Ctenohystrica) emerged close to the Cretaceous-Tertiary boundary, and their common ancestor separated from other placental orders in the Late Cretaceous.     

ORIGINS AND AFFINITIES OF THE FILAMENTOUS GREEN ALGAL ORDERS CHAETOPHORALES AND OEDOGONIALES BASED ON 18S rRNA GENE SEQUENCES

The order Chaetophorales includes filamentous green algae whose taxonomic relationships to other chlorophycean orders is uncertain. Chaetophoralean taxa include filamentous species which are both branched and unbranched. Ultrastructural studies of zoospores have revealed similar flagellar apparatuses in a number of genera, including Uronema, Stigeoclonium, and Fritschiella, suggesting a close phylogenetic relationship among these taxa. The order Oedogoniales represents a second group of branched and unbranched filamentous green algae whose relationships to other chlorophycean orders also has been unclear. A possible close relationship between the Chaetophorales and Oedogoniales has been suggested. Using DNA sequences from the small-subunit ribosomal RNA gene (SSU rRNA) of several members of each order, we have examined the monophyly of the Chaetophorales and Oedogoniales, as well as the nature of their relationship to other chlorophycean orders. Our results show that chaetophoralean and oedogonialean taxa form separate monophyletic groups. Results also suggest that the two orders are not closely related to each other.     

Exploring population genetic structure in three species of Lesser Antillean bats

We explore population genetic structure in phyllostomid bats (Ardops nichollsi, Brachyphylla cavernarum and Artibeus jamaicensis) from the northern Lesser Antilles by investigating the degree to which island populations are genetically differentiated. Our hypothesis, that the island populations are genetically distinct because of a combination of founding events, limited migration and genetic drift exacerbated by catastrophe-induced fluctuations in population size, is derived from a priori hypotheses erected in the literature. The first prediction of this hypothesis, that within each species island populations are monophyletic, was tested using a parametric bootstrap approach. Island monophyly could not be rejected in Ardops nichollsi (P = 0.718), but could be rejected in B. cavernarum (P < 0.001) and Artibeus jamaicensis (P < 0.001). A second prediction, that molecular variance is partitioned among islands, was tested using an amova and was rejected in each species [Ardops nichollsi (P = 0.697); B. cavernarum (P = 0.598); Artibeus jamaicensis (P = 0.763)]. In B. cavernarum and Artibeus jamaicensis, the admixture in mitochondrial haplotypes from islands separated by > 100 km of ocean can be explained either by interisland migration or by incomplete lineage sorting of ancestral polymorphism in the source population. As an a posteriori test of lineage sorting, we used simulations of gene trees within a population tree to suggest that lineage sorting is an unlikely explanation for the observed pattern of nonmonophyly in Artibeus jamaicensis (PW < 0.01; PSE = 0.04), but cannot be rejected in B. cavernarum (PW = 0.81; PSE = 0.79). A conservative interpretation of the molecular data is that island populations of Artibeus jamaicensis, although isolated geographically, are not isolated genetically.     

Saccharicola, a new genus for two Leptosphaeria species on sugar cane

Leptosphaeria bicolor, causal agent of a leaf scorch disease of sugar cane, is referred to the new genus Saccharicola. The ascospores are 1-3 transseptate and hyaline at first but become melanized and rough after release, as is the case in some members of Massarina and Lophiostoma. SSU rDNA data indicate that it is closely related to M. eburnea but is biotrophic in leaves of sugar cane and not corticolous, the ascomata are less melanized, and it has Stagonospora- and Phoma-like synanamorphs, not a Ceratophoma-like anamorph. A second species, Leptosphaeria taiwanensis, is transferred to Saccharicola. It differs in slightly larger, normally 1-septate, hyaline spores with more attenuated ends. The family Massarinaceae is resurrected to accommodate Massarina s. str., Keissleriella, Saccharicola and Helminthosporium. These genera formed a clade with 100% bootstrap support in a parsimony analysis of SSU rDNA sequences from 38 ascomycetes, 30 of them members of Pleosporales (including Melanommatales).     

A multigene phylogeny of the Dothideomycetes using four nuclear loci

We present an expanded multigene phylogeny of the Dothideomycetes. The final data matrix consisted of four loci (nuc SSU rDNA, nuc LSU rDNA, TEF1, RPB2) for 96 taxa, representing five of the seven orders in the current classification of Dothideomycetes and several outgroup taxa representative of the major clades in the Pezizomycotina. The resulting phylogeny differentiated two main dothideomycete lineages comprising the pseudoparaphysate Pleosporales and aparaphysate Dothideales. We propose the subclasses Pleosporomycetidae (order Pleosporales) and Dothideomycetidae (orders Dothideales, Capnodiales and Myriangiales). Furthermore we provide strong molecular support for the placement of Mycosphaerellaceae and Piedraiaceae within the Capnodiales and introduce Davidiellaceae as a new family to accommodate species of Davidiella with Cladosporium anamorphs. Some taxa could not be placed with certainty (e.g. Hysteriales), but there was strong support for new groupings. The clade containing members of the genera Botryosphaeria and Guignardia resolved well but without support for any relationship to any other described orders and we hereby propose the new order Botryosphaeriales. These data also are consistent with the removal of Chaetothyriales and Coryneliales from the Dothideomycetes and strongly support their placement in the Eurotiomycetes.     

Phylogenetic relationships among insect orders based on three nuclear protein-coding gene sequences

Many attempts to resolve the phylogenetic relationships of higher groups of insects have been made based on both morphological and molecular evidence; nonetheless, most of the interordinal relationships of insects remain unclear or are controversial. As a new approach, in this study we sequenced three nuclear genes encoding the catalytic subunit of DNA polymerase delta and the two largest subunits of RNA polymerase II from all insect orders. The predicted amino acid sequences (In total, approx. 3500 amino acid sites) of these proteins were subjected to phylogenetic analyses based on the maximum likelihood and Bayesian analysis methods with various models. The resulting trees strongly support the monophyly of Palaeoptera, Neoptera, Polyneoptera, and Holometabola, while within Polyneoptera, the groupings of Isoptera/"Blattaria"/Mantodea (Superorder Dictyoptera), Dictyoptera/Zoraptera, Dermaptera/Plecoptera, Mantophasmatodea/Grylloblattodea, and Embioptera/Phasmatodea are supported. Although Paraneoptera is not supported as a monophyletic group, the grouping of Phthiraptera/Psocoptera is robustly supported. The interordinal relationships within Holometabola are well resolved and strongly supported that the order Hymenoptera is the sister lineage to all other holometabolous insects. The other orders of Holometabola are separated into two large groups, and the interordinal relationships of each group are (((Siphonaptera, Mecoptera), Diptera), (Trichoptera, Lepidoptera)) and ((Coleoptera, Strepsiptera), (Neuroptera, Raphidioptera, Megaloptera)). The sister relationship between Strepsiptera and Diptera are significantly rejected by all the statistical tests (AU, KH and wSH), while the affinity between Hymenoptera and Mecopterida are significantly rejected only by AU and KH tests. Our results show that the use of amino acid sequences of these three nuclear genes is an effective approach for resolving the relationships of higher groups of insects.     

The virtues of gaps: xenarthran (Edentate) monophyly supported by a unique deletion in alpha A-crystallin

Shared insertions or deletions (indels) in protein-coding DNA can be strong indicators of the monophyly of a taxon. A three-amino acid deletion had previously been noted in the eye lens protein alpha A-crystallin of two species of sloths and two species of anteaters, which represent the Pilosa, one of the two infraorders of Xenarthra (Edentata). This deletion has not been observed in 55 species from 16 other eutherian orders, or in 2 species of marsupials, or in 34 nonmammalian vertebrates, from birds to shark. At the genomic level, we have now detected this deletion in two species of armadillos of the second xenarthran infraorder, Cingulata, as well as in an additional species of anteater. Phylogenetic trees were constructed from a 145-bp sequence of the alpha A-crystallin gene of 39 tetrapod species, supporting xenarthran monophyly with values from 76% to 90%. To quantify the additional support for xenarthran monophyly, as given by the three-residue deletion, we computed the probabilities for the occurrence of this deletion per evolutionary time unit for alternative hypothetical tree topologies. In the estimates obtained, the six trees in which the xenarthran subgroups are unresolved or paraphyletic give an increasingly lower likelihood than do the two trees that assume xenarthran monophyly. For the monophyletic trees, the probability that the deletion observed in the xenarthrans is due to a single event is > 0.99. Thus, this deletion in alpha A-crystallin gives strong molecular support for the monophyly of this old and diverse order.     

The First Mitochondrial Genome for the Fishfly Subfamily Chauliodinae and Implications for the Higher Phylogeny of Megaloptera

Megaloptera are a basal holometabolous insect order with larvae exclusively predacious and aquatic. The evolutionary history of Megaloptera attracts great interest because of its antiquity and important systematic status in Holometabola. However, due to the difficulties identifying morphological apomorphies for the group, controversial hypotheses on the monophyly and higher phylogeny of Megaloptera have been proposed. Herein, we describe the complete mitochondrial (mt) genome of a fishfly species, Neochauliodes punctatolosus Liu & Yang, 2006, representing the first mt genome of the subfamily Chauliodinae. A phylogenomic analysis was carried out based on the mt genomic sequences of 13 mt protein-coding genes (PCGs) and two rRNA genes of nine Neuropterida species, comprising all three orders of Neuropterida and all families and subfamilies of Megaloptera. Both maximum likelihood and Bayesian inference analyses highly support the monophyly of Megaloptera, which was recovered as the sister of Neuroptera. Within Megaloptera, the sister relationship between Corydalinae and Chauliodinae was corroborated. The divergence time estimation suggests that stem lineage of Neuropterida and Coleoptera separated in the Early Permian. The interordinal divergence within Neuropterida might have occurred in the Late Permian.     

Probing the Monophyly of the Sphaeropleales (Chlorophyceae) Using Data From Five Genes

Molecular phylogenetic analyses have had a major impact on the classification of the green algal class Chlorophyceae, corroborating some previous evolutionary hypotheses, but primarily promoting new interpretations of morphological evolution. One set of morphological traits that feature prominently in green algal systematics is the absolute orientation of the flagellar apparatus in motile cells, which correlates strongly with taxonomic classes and orders. The order Sphaeropleales includes diverse green algae sharing the directly opposite (DO) flagellar apparatus orientation of their biflagellate motile cells. However, algae across sphaeroplealean families differ in specific components of the DO flagellar apparatus, and molecular phylogenetic studies often have failed to provide strong support for the monophyly of the order. To test the monophyly of Sphaeropleales and of taxa with the DO flagellar apparatus, we conducted a molecular phylogenetic study of 16 accessions representing all known families and diverse affiliated lineages within the order, with data from four plastid genes (psaA, psaB, psbC, rbcL) and one nuclear ribosomal gene (18S). Although single‐gene analyses varied in topology and support values, analysis of combined data strongly supported a monophyletic Sphaeropleales. Our results also corroborated previous phylogenetic hypotheses that were based on chloroplast genome data from relatively few taxa. Specifically, our data resolved Volvocales, algae possessing predominantly biflagellate motile cells with clockwise (CW) flagellar orientation, as the monophyletic sister lineage to Sphaeropleales, and an alliance of Chaetopeltidales, Chaetophorales, and Oedogoniales, orders having multiflagellate motile cells with distinct flagellar orientations involving the DO and CW forms.     

Evolutionary Phycology: Toward a Macroalgal Species Conceptual Framework

Species concepts formalize evolutionary and ecological processes, but often conflict with one another when considering the mechanisms that ultimately lead to species delimitation. Evolutionary biologists are, however, recognizing that the conceptualization of a species is separate and distinct from the delimitation of species. Indeed, if species are generally defined as separately evolving metapopulation lineages, then characteristics, such as reproductive isolation or monophyly, can be used as evidence of lineage separation and no longer conflict with the conceptualization of a species. However, little of this discussion has addressed the formalization of this evolutionary conceptual framework for macroalgal species. This may be due to the complexity and variation found in macroalgal life cycles. While macroalgal mating system variation and patterns of hybridization and introgression have been identified, complex algal life cycles generate unique eco-evolutionary consequences. Moreover, the discovery of frequent macroalgal cryptic speciation has not been accompanied by the study of the evolutionary ecology of those lineages, and, thus, an understanding of the mechanisms underlying such rampant speciation remain elusive. In this perspective, we aim to further the discussion and interest in species concepts and speciation processes in macroalgae. We propose a conceptual framework to enable phycological researchers and students alike to portray these processes in a manner consistent with dialogue at the forefront of evolutionary biology. We define a macroalgal species as an independently evolving metapopulation lineage, whereby we can test for reproductive isolation or the occupation of distinct adaptive zones, among other mechanisms, as secondary lines of supporting evidence.     

Actin gene family evolution and the phylogeny of coleoid cephalopods (Mollusca: Cephalopoda)

Phylogenetic analysis conducted on a 784-bp fragment of 82 actin gene sequences of 44 coleoid cephalopod taxa, along with results obtained from genomic Southern blot analysis, confirmed the presence of at least three distinct actin loci in coleoids. Actin isoforms were characteri zed through phylogenetic analysis of representative cephalopod sequences from each of the three isoforms, along with translated actin cDNA sequences from a diverse array of metazoan taxa downloaded from GenBank. One of the three isoforms found in cephalopods was closely related to actin sequences expressed in the muscular tissues of other molluscs. A second isoform was most similar to cytoplasmic-specific actin amino acid sequences. The muscle type actins of molluscs were found to be distinct from those of arthropods, suggesting at least two independent derivations of muscle actins in the protostome lineage, although statistical support for this conclusion was lacking. Parsimony and maximum-likelihood analyses of two of the isoforms from which >30 orthologous coleoid sequences had been obtained (one of the cytoplasmic actins and the muscle actin) supported the monophyly of several higher-level coleoid taxa. These included the superorders Octopodiformes and Decapodiformes, the order Octopoda, the octopod suborder Incirrata, and the teuthoid suborder Myopsida. The monophyly of several taxonomic groups within the Decapodiformes was not supported, including the orders Teuthoidea and Sepioidea and the teuthoid suborder Oegopsida. Parametric bootstrap analysis conducted on the simulated cytoplasmic actin data set provided statistical support to reject the monophyly of the Sepioidea. Although parametric bootstrap analysis of the muscle actin isoform did not reject sepioid monophyly at the 5% level, the results (rejection at P: = 0.068) were certainly suggestive of sepioid nonmonophyly.     

Molecular phylogenetics of the melyrid lineage (Coleoptera: Cleroidea)

The melyrid lineage of beetles form a distinct group of the superfamily Cleroidea with a high level of soft‐bodiedness. Here we present the first molecular phylogenetic analysis of this group. The data matrix included partial sequences of the small and large subunits of rRNA, the mitochondrial large subunit rRNA, and cytochrome oxidase subunit I of 67 melyrid and eight outgroup taxa. The concatenated sequences were analysed using maximum‐parsimony (MP), maximum‐likelihood (ML) and Bayesian analysis (BA) approach. The results strongly supported the monophyly of the melyrid lineage splitting into six major clades: Rhadalidae, Mauroniscidae, Prionoceridae, Melyridae sensu stricto, Dasytidae and Malachiidae. The rhadalids were placed in the most basal position, followed by mauroniscids and prionocerids. Three terminal lineages—the true melyrids, dasytids, and malachiids—are well supported by all analyses, but their mutual relationships remain uncertain as MP analysis proposed alternative topologies to that of the ML and BA trees, with often low node support in the latter two methods. The monophyly of the subfamily Danacaeinae (Dasytidae) with respect to the danacaeine genera of the southern hemisphere (Hylodanacaea, Listrocerus, Amecocerus) was challenged as they were found to be polyphyletic. Similarly, the monophyly of Attalus was rejected by our analyses and shown to be polyphyletic. Based on the preferred phylogenetic hypothesis, the subfamilies Rhadalinae, Dasytinae and Malachiinae are elevated to family rank. © The Willi Hennig Society 2011.