Rhizomarasmius epidryas (Physalacriaceae): phylogenetic placement of an arctic-alpine fungus with obligate saprobic affinity to Dryas spp

As a part of a large-scale biogeographical study we examined the evolutionary relationships and taxonomic position of Marasmius epidryas, one of the most typical circumpolar arctic-alpine fungi, characterized by a specific, saprobic affinity to dead tissues of Dryas spp. A phylogenetic analysis based on nLSU and RPB2 DNA regions unequivocally indicated the phylogenetic placement of this species within the Physalacriaceae. The Bayesian MCMCMC analysis as well as other inference methods tested (ML, NJ) revealed a well supported affinity of M. epidryas to Rhizomarasmius pyrrhocephalus, type species of a recently circumscribed genus, Rhizomarasmius. As a consequence, based on these results, we introduce a new combination, Rhizomarasmius epidryas (Kühner ex A. Ronikier) A. Ronikier and M. Ronikier. Thus our results demonstrate that neither the traditional taxonomic placement of the fungus in genus Marasmius nor the recent transfer into genus Mycetinis are phylogenetically correct. In contrast they support the importance of the third lineage of the polyphyletic Marasmius s. l., having evolutionary links with taxa forming the Physalacriaceae clade of agaricoid fungi. In addition the lineage of Rhizomarasmius was confirmed to be closely related to the representatives of Gloiocephala, comprising small, often narrowly specialized saprobic species previously also classified within Marasmius s. l.     

A new genus to accommodate Gymnopus acervatus (Agaricales)

Phylogenies based on ITS and LSU nrDNA sequences show Agaricus (Gymnopus) acervatus as unique within the Gymnopus/Rhodocollybia complex. These phylogenies imply that a separate genus is necessary, and Connopus is proposed. Infraspecific morphological and DNA-based variation within C. acervatus suggests that a western North American clade might be reproductively isolated from the eastern North American/Scandinavian clade and that in this species complex the European and eastern North American clade might be conspecific. A Scandinavian exemplar is selected for bar-coding. Two GenBank sequences with name-phylogenetic placement inconsistencies are identified.     

Cladistic analysis and a revised classification of fossil and recent mysticetes

A cladistic analysis that includes representatives of all recent genera of mysticetes and several fossil species that were previously referred to the family Cetotheriidae, with tooth-bearing mysticetes and an archaeocete as an outgroup, is presented here. The result of this analysis forms the base of a revised classification of Mysticeti. Cetotheriidae is redefined as a monophyletic family, which includes the genera Cetotherium , Piscobalaena , and a new subfamily Herpetocetinae, including Herpetocetus , Nannocetus , Metopocetus , and Cephalotropis . Eschrichtiidae is the closest sister taxon to Cetotheriidae. A few species are referred to Eomysticetoidea, whereas the remaining species that were previously referred to Cetotheriidae appear in four clades that branch off from the lineage leading to Balaenopteridae. These are a Mauicetus clade and three clades that are named as new families Aglaocetidae, Pelocetidae, and Diorocetidae.  © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 150 , 875–894.     

Mating studies, new species, and new reports of Marasmius from northern Thailand

The mating systems operating in seven species of Marasmius collected recently in northern Thailand were determined. Marasmius cremeus belonging to sect. Sicci subsect. Siccini ser. Leonini, and Marasmius straminiceps belonging to sect. Marasmius subsect. Sicciformes are described as new species. Five members of sect. Marasmius were tetrapolar (bifactorial), viz. M. apatelius, M. guyanensis, M. nigrobrunneus, M. ruforotula, and M. straminiceps. Two members of sect. Sicci were bipolar (unifactorial), viz., M. corneri (syn. M. incarnatus) and M. cremeus. Our data support the hypothesis that the mating system is consistent within infrageneric taxa. The seven species that are herein described, illustrated, and compared with phenetically similar species represent the first reports for this genus in Thailand.     

The Ajellomycetaceae, a new family of vertebrate-associated Onygenales

Phylogenies inferred from the analysis of DNA sequence data have shown that the Onygenales contains clades that do not correspond with previously described families. One lineage identified in recent molecular phylogenetic studies includes the dimorphic pathogens belonging to the genera Ajellomyces, Emmonsia and Paracoccidioides. To evaluate the degree of support for this lineage and determine whether it includes additional taxa, we examined relationships among the members of this clade and selected saprobic onygenalean taxa based on maximum-parsimony analyses of partial nuclear large RNA subunit (LSU) and internal transcribed spacer (ITS) sequences. A clade distinct from the Onygenaceae was found to encompass Ajellomyces (including the anamorph genera Blastomyces, Emmonsia and Histoplasma) and Paracoccidioides brasiliensis. The members of this lineage are saprobic and pathogenic vertebrate-associated taxa distinguished by their globose ascomata with coiled appendages, muricate globose or oblate ascospores, and lack of keratinolytic activity. Anamorphs are solitary aleurioconidia or irregular alternate arthroconidia. Based on molecular data and on morphological and physiological similarities among these taxa, we propose the new family, Ajellomycetaceae.     

Cryptic goldfields: a molecular phylogenetic reinvestigation of Lasthenia californica sensu lato and close relatives (Compositae: Heliantheae sensu lato)

Maximum parsimony analysis of DNA sequence data from the internal and external transcribed spacer (ITS and ETS) regions of 18S-26S nuclear ribosomal DNA and the 3' trnK intron of chloroplast DNA from over 60 populations of Lasthenia sect. Amphiachaenia yielded a well-supported tree showing that the most common species of Lasthenia, L. californica sensu lato (s.l.), is not monophyletic. Members of Lasthenia californica s.l. belong to two well-supported but morphologically cryptic clades. One clade includes members of L. macrantha; the other represents a basally divergent lineage in L. sect. Amphiachaenia. Members of each clade can be diagnosed by pappus morphology and by geographic distribution, except for epappose plants that occur in a broad region of sympatry in central California. Overall diversification in the clade corresponding to L. sect. Amphiachaenia has been accompanied by minimal morphological divergence, which has resulted in previously underappreciated cryptic diversity.     

Phylogeny of the Pluteaceae (Agaricales, Basidiomycota): taxonomy and character evolution

The phylogeny of the genera traditionally classified in the family Pluteaceae (Agaricales, Basidiomycota) was investigated using molecular data from nuclear ribosomal genes (nSSU, ITS, nLSU) and consequences for taxonomy and character evolution were evaluated. The genus Volvariella is polyphyletic, as most of its representatives fall outside the Pluteoid clade and shows affinities to some hygrophoroid genera (Camarophyllus, Cantharocybe). Volvariella gloiocephala and allies are placed in a different clade, which represents the sister group of Pluteus, and a new generic name, Volvopluteus, is proposed to accommodate these taxa. Characters such as basidiospore size and pileipellis structure can be used to separate Pluteus, Volvariella and Volvopluteus. The genus Pluteus is monophyletic and includes species with partial veil traditionally classified in the genus Chamaeota. The evolution of morphological features used in the infrageneric taxonomy of the genus, such as metuloid cystidia and pileipellis structure, was analyzed. Agreement between the molecular phylogeny and morphological subdivision of Pluteus is, generally speaking, good, though some rearrangements are necessary: (i) species with non-metuloid pleurocystidia and pileipellis as a cutis are placed either in sect. Celluloderma, together with the species characterized by a hymenidermal pipeipellis, or in sect. Pluteus, with the metuloid bearing species; (ii) subdivision of sect. Celluloderma according to the presence/absence of cystidioid elements in the pileipellis is not supported by molecular data.     

16S rDNA studies on members of Arthrobacter and Micrococcus: An aid for their future taxonomic restructing

Abstract 16S rDNA sequence data was obtained for 11 species of Arthrobacter and 4 species of Micrococcus and compared with that from other members of the arthrobacterial lineage within the order Actinomycetales . The intermixing of members of these two genera and the placement of Renibacterium salmoninarum within the radiation of these two genera, as previously suggested by 16S rRNA cataloguing, is confirmed. The branching pattern reveals several closely related organisms that cluster around the type species of Arthrobacter and Micrococcus ; these species are considered 'core organisms'. A few species, however, branch outside the radiation of core organisms; these include Micrococcus kristinae, Micrococcus halophilus , and, as previously indicated, Micrococcus sedentarius and M. nishinomiyaensis . As phenotypic data that would support the exclusion of these four species from the genus Micrococcus are still lacking taxonomic conclusions should await more thorough comparative studies.     

Hypocrea/Trichoderma species with pachybasium-like conidiophores: teleomorphs for T. minutisporum and T. polysporum and their newly discovered relatives

We describe or redescribe species of Hypocrea/Trichoderma (Ascomycetes, Hypocreales) having hyaline ascospores and pachybasium-like conidiophores. Teleomorphs are reported for Trichoderma minutisporum (Hypocrea minutispora sp. nov.) and T. polysporum (H. pachybasioides). Hypocrea pilulifera/T. piluliferum is redescribed. Trichoderma croceum is synonymized with T. polysporum. The new species H. parapilulifera, H. stellata and H. lacuwombatensis are described. All of these species fall within the morphological concept of Trichoderma sect. Pachybasium and within the phylogenetic group pachybasium B5 of Kullnig-Gradinger et al (2002). Parsimony analysis of nucleotide sequences from three unlinked loci-ITS1 and 2, endochitinase (ech42) and translation elongation factor 1-alpha (tef1)-detects two distinct phylogenetic lineages within the group pachybasium B5. One comprises H. pachybasioides/T. polysporum, H. pilulifera/T. piluliferum, H. parapilulifera and H. stellata; this group, the "polysporum" lineage, is characterized by having conidia that are white in mass and is the only lineage within Hypocrea characterized by such conidia. The second group includes the green conidial T. minutisporum and H. lacuwombatensis. The partition homogeneity test reveals significant recombination within the "polysporum" lineage but not within the "minutisporum" lineage.     

<Emphasis Type="Italic">Rhodocollybia</Emphasis> in neotropical montane forests

Traditional concepts of Collybia (Agaricales) have included a variety of morphologically disparate taxa. Reapplication of some characters used in circumscribing Collybia s.l. suggests realignment of well-known North American and European species into three genera, viz. Collybia s.s, Rhodocollybia, and Gymnopus. Rhodocollybia is recognized here at generic rank based on morphological characteristics and phylogenetic signaling. Seven new species epithets under Rhodocollybia, and a new combination under Gymnopus, are proposed. A key to species of Rhodocollybia found in neotropical montane forests is provided.     

Synonymy of Boophilus Curtice, 1891 with Rhipicephalus Koch, 1844 (Acari: Ixodidae)

Recent molecular and morphological studies of the genera Rhipicephalus Koch, 1844 and Boophilus Curtice, 1891 revealed that the five species of Boophilus make the genus Rhipicephalus paraphyletic. Thus, Rhipicephalus Koch, 1844 is not a monophyletic (natural) lineage and some species of Rhipicephalus are more closely related to the species of Boophilus than to other species of Rhipicephalus. Here, we revise these genera: Boophilus is synonymised with Rhipicephalus, and Rhipicephalus (sensu lato) (including Boophilus) is redefined. By synonymising Boophilus with Rhipicephalus, we have changed the nomenclature so that it reflects our understanding of the phylogeny of these ticks. Boophilus is retained as a subgenus of Rhipicephalus, so the synonymy of Boophilus with Rhipicephalus does not result in the loss of the name Boophilus. In addition, Rhipicephalus is a well-known genus and the change proposed is simple -- all five species of Boophilus become members of Rhipicephalus (Boophilus).     

MOLECULAR PHYLOGENY AND TAXONOMY OF THE AEGAGROPILA CLADE (CLADOPHORALES,ULVOPHYCEAE), INCLUDING THE DESCRIPTION OF AEGAGROPILOPSIS GEN. NOV. AND PSEUDOCLADOPHORA GEN. NOV.1

The Aegagropila clade represents a unique group of cladophoralean green algae occurring mainly in brackish and freshwater environments. The clade is sister to the species‐rich and primarily marine Cladophora and Siphonocladus lineages. Phylogenetic analyses of partial LSU and SSU nrDNA sequences reveal four main lineages within the Aegagropila clade, and allow a taxonomic reassessment. One lineage consists of two marine ‘Cladophora’ species, for which the new genus Pseudocladophora and the new family Pseudocladophoraceae are proposed. For the other lineages, the family name Pithophoraceae is reinstated. Within the Pithophoraceae, the earliest diverging lineage includes Wittrockiella and Cladophorella calcicola, occurring mainly in brackish and subaerial habitats. The two other lineages are restricted to freshwater. One of them shows a strong tendency for epizoism, and consists of Basicladia species and Arnoldiella conchophila. The other lineage includes Aegagropila, Pithophora and a small number of tropical ‘Cladophora’ species. The latter are transferred to the new genus Aegagropilopsis. Previously, polypyramidal pyrenoids had been suggested to be apomorphous for this clade, but we report the finding of both polypyramidal and bilenticular pyrenoids in members of the Pithophoraceae, and thus show that this character has no diagnostic value.     

Molecular phylogeny of the Southeast Asian freshwater fish family Botiidae (Teleostei: Cobitoidea) and the origin of polyploidy in their evolution

The freshwater fish family Botiidae is represented by seven genera on the Indian subcontinent and in East and Southeast Asia and includes diploid as well as evolutionary tetraploid species. We present a phylogeny of Botiidae including 33 species representing all described genera using the mitochondrial cytochrome b and 12s rRNA genes to reconstruct the phylogenetic relationships among the genera and to estimate the number of polyploidisation events during their evolution. Our results show two major lineages, the subfamilies Leptobotiinae with the genera Leptobotia and Parabotia and Botiinae with the genera Botia, Chromobotia, Sinibotia, Syncrossus, and Yasuhikotakia. Our results suggest that two species that were traditionally placed into the genus Yasuhikotakia form a monophyletic lineage with the species of Sinibotia. A review of the data on the ploidy level of the included species shows all diploid species to belong to Leptobotiinae and all tetraploid species to Botiinae. A single polyploidisation event can therefore be hypothesised to have occurred in the ancestral lineage leading to the Botiinae.     

The causal agents of witches' broom and frosty pod rot of cacao (chocolate, Theobroma cacao) form a new lineage of Marasmiaceae

The two most devastating diseases of cacao (Theobroma cacao)--the source of chocolate--in tropical America are caused by the fungi Crinipellis perniciosa (witches' broom disease) and Moniliophthora roreri (frosty pod rot or moniliasis disease). Despite the agricultural, socio-economic and environmental impact of these fungi, most aspects of their life cycles are unknown, and the phylogenetic relationships of M. roreri have yet to be conclusively established. In this paper, extensive phylogenetic analyses of five nuclear gene regions (28S rDNA, 18S rDNA, ITS, RPB1, and EF1-alpha) confirm that C. perniciosa and M. roreri are sister taxa that belong in the Marasmiaceae (euagarics). Furthermore, these taxa form part of a separate and distinct lineage within the family. This lineage includes the biotrophic fungi Moniliophthora perniciosa comb. nov. and M. roreri, as well as one undescribed endophytic species. The sister genera to Moniliophthora are Marasmius, Crinipellis and Chaetocalathus, which consist mainly of saprotrophic litter fungi.     

A revision of the genera Sipunculus and Xenosiphon (Sipuncula)

A critical analysis of historically used characters, based on a large series of specimens, is presented. Based on a comparative morphological analysis of type specimens, the 19 species of Sipunculus and four of Xenosiphon are reviewed. The genera and subgenera are redefined so that, after appropriate revisions arc made, Sipunculus (Sipunculus) has eight, Sipunculus (Contraporus) new subgenus has two, and Xenosiphon has only one remaining valid species. A zoogeographical note and a key to the species are included.     

Phylogeny and taxonomy of Afrocayratia,a new genus of Vitaceae from continental Africa and Madagascar

The genus Cayratia Juss. in the traditional sense (i.e., Cayratia s.l.) of the grape family has been shown to be non‐monophyletic. Previous studies supported the splitting of Cayratia s.l. into three genera, that is, Cayratia s.s., Causonis Raf., and a new genus representing the African Cayratia clade. However, the morphology of the African Cayratia clade has not been studied carefully and its phylogenetic position within Vitaceae remains unclear. Our study integrates molecular, distributional, and morphological data and supports the recognition of the new genus Afrocayratia from continental Africa and Madagascar. Phylogenetic analyses strongly support the monophyly of Afrocayratia and resolve it as a sister of Cayratia s.s. based on the chloroplast data, but it is placed sister to Cyphostemma based on the internal transcribed spacer dataset. Molecular dating suggests that Afrocayratia split with Cayratia s.s. during the Paleocene, but that the extant species of Afrocayratia did not diversify until the early Miocene. Afrocayratia differs from its allied genera in having short stigmas and seeds with subcircular ventral infold cavities in cross‐section. Three clades are detected within Afrocayratia, with A. debilis (Baker) J.Wen & L.M.Lu as the first diverged lineage. The second diverged lineage includes A. delicatula (Willems) J.Wen & Z.D.Chen and A. gracilis (Guill. & Perr.) J.Wen & Z.D.Chen. The third diverged lineage includes A. imerinensis (Baker) J.Wen & L.M.Lu, A. longiflora (Desc.) J.Wen & Rabarijaona, and A. triternata (Baker) J.Wen & Rabarijaona from Madagascar, which form a monophyletic group that diverged from the second lineage in the middle Miocene. Combining the morphological and molecular evidence, we formally describe the new genus Afrocayratia, make seven new combinations, and provide a key to species of the genus.     

Defining a monophyletic Cardinalini: a molecular perspective

Within the New World nine-primaried oscine assemblage, feeding morphology and behavior have long been used as a guideline for assigning membership to subgroups. For example, birds with stout, conical bills capable of crushing heavy seeds have generally been placed within the tribe Cardinalini (cardinal-grosbeaks). Many workers have tried to characterize this group more definitively, using a variety of morphological characters; however, the characters used often conflicted with one another. Previous molecular studies addressing the monophyly of Cardinalini have had only limited sampling within the group. In this study, we analyze mtDNA sequence data from all genera and 34 of the 42 Cardinalini species (sensu [Sibley, C.G., Monroe, B.L., 1990. Distribution and Taxonomy of the Birds of the World, Yale University Press, New Haven, CT]) to address the monophyly of the group and to reconstruct the most complete phylogeny of this tribe published to date. We found strong support for a redefined Cardinalini that now includes some members previously placed within Thraupini (tanagers; the genera Piranga, Habia, Chlorothraupis, and Amaurospiza) and some members previously placed within the Parulini (wood-warblers; the genus Granatellus). In addition, some genera traditionally considered members of the Cardinalini are shown to have affinities with other groups (the genera Porphyrospiza, Parkerthraustes, and Saltator). Our redefined Cardinalini contains 48 species, six more than are listed in Sibley and Monroe's (1990) taxonomy of the group. Within the nine-primaried oscine assemblage, the Cardinalini are more closely related to the Thraupini (tanagers) than they are to the Emberizini (sparrows), Parulini (wood-warblers), or Icterini (blackbirds), consistently forming a monophyletic group with Thraupini across all analyses. The reconfigured Cardinalini is comprised of five well-supported, major clades: (1) a "masked" clade (Piranga, Cardinalis, Caryothraustes, Periporphyrus, and Rhodothraupis), (2) a "blue" clade (Amaurospiza, Cyanocompsa, Cyanoloxia, Passerina, and Spiza), (3) a clade containing the genera Habia and Chlorothraupis, (4) a clade containing all species of Granatellus, and (5) a clade containing only species of Pheucticus. Diversification of these five lineages from one another occurred relatively rapidly during the mid-Pliocene, around 5 or 8 million years ago. Each of these major clades includes both North and South American species; thus, a complex biogeographic history is inferred for the group.     

Monophyletic subgroups of the tribe Millettieae (Leguminosae) as revealed by phytochrome nucleotide sequence data

Phylogenetic analysis of phytochrome (PHY) genes reveals the identity and relationships of four PHY loci among papilionoid Leguminosae. A phylogenetic analysis of loci combined according to species suggests that most of the tribe Millettieae belongs to one of two monophyletic clades: the Derris–Lonchocarpus or the Tephrosia clade. Together these two form a monophyletic group that is sister to a lineage represented by Millettia grandis of Millettia sect. Compresso-gemmatae. Collectively, this large monophyletic group is referred to as the Millettieae-core group, which based on our sampling, includes species of Millettieae that do not accumulate the nonprotein amino acid canavanine and that mostly have pseudoracemose or pseudopaniculate inflorescences. This new phylogenetic framework assists in targeting additional taxa for future sampling. For example, the “American Derris” (Deguelia), which accumulate canavanine, might not be members of the Millettieae core group. Afgekia is also predicted not to be a member because it accumulates canavanine and has an inflorescence of terminal racemes. PHY gene analysis specifically reveals that certain genera traditionally classified in Millettieae are actually distantly related to the Millettieae core group, such as Austrosteensia, Callerya, Craibia, Cyclolobium, Fordia, Platycyamus, Poecilanthe, and Wisteria.