Re-thinking the classification of corticioid fungi

Corticioid fungi are basidiomycetes with effused basidiomata, a smooth, merulioid or hydnoid hymenophore, and holobasidia. These fungi used to be classified as a single family, Corticiaceae, but molecular phylogenetic analyses have shown that corticioid fungi are distributed among all major clades within Agaricomycetes. There is a relative consensus concerning the higher order classification of basidiomycetes down to order. This paper presents a phylogenetic classification for corticioid fungi at the family level. Fifty putative families were identified from published phylogenies and preliminary analyses of unpublished sequence data. A dataset with 178 terminal taxa was compiled and subjected to phylogenetic analyses using MP and Bayesian inference. From the analyses, 41 strongly supported and three unsupported clades were identified. These clades are treated as families in a Linnean hierarchical classification and each family is briefly described. Three additional families not covered by the phylogenetic analyses are also included in the classification. All accepted corticioid genera are either referred to one of the families or listed as incertae sedis.     

Amphitremida (Poche, 1913) Is a New Major,Ubiquitous Labyrinthulomycete Clade

Micro-eukaryotic diversity is poorly documented at all taxonomic levels and the phylogenetic affiliation of many taxa – including many well-known and common organisms - remains unknown. Among these incertae sedis taxa are Archerella flavum (Loeblich and Tappan, 1961) and Amphitrema wrightianum (Archer, 1869) (Amphitremidae), two filose testate amoebae commonly found in Sphagnum peatlands. To clarify their phylogenetic position, we amplified and sequenced the SSU rRNA gene obtained from four independent DNA extractions of A. flavum and three independent DNA extractions of A. wrightianum. Our molecular data demonstrate that genera Archerella and Amphitrema form a fully supported deep-branching clade within the Labyrinthulomycetes (Stramenopiles), together with Diplophrys sp. (ATCC50360) and several environmental clones obtained from a wide range of environments. This newly described clade we named Amphitremida is diverse genetically, ecologically and physiologically. Our phylogenetic analysis suggests that osmotrophic species evolved most likely from phagotrophic ancestors and that the bothrosome, an organelle that produces cytoplasmic networks used for attachment to the substratum and to absorb nutrients from the environments, appeared lately in labyrithulomycete evolution.     

Genome-based taxonomic classification of the closest-to-Comamonadaceae group supports a new family Sphaerotilaceae fam. nov. and taxonomic revisions

Many genera closest to the family Comamonadaceae have not been classified into any family; moreover, some of them are not monophyletic groups beyond the genus level. To resolve the taxonomic uncertainty of the closest-to-Comamonadaceae (CTC) group, we performed 16S rRNA gene- and genome-based phylogenetic analyses combined with genome relatedness indices and phenotypic traits comparison. Phylogenies based on the 16S rRNA gene and genome sequences demonstrated that the CTC group formed a coherent and robust monophyletic lineage and was sister to the family Comamonadaceae, thereby proposing the CTC group as a novel family, Sphaerotilaceae fam. nov. The resolved genus- and species-level taxonomic relationships of this new family were then validated by the phylogenomic reconstruction and comparisons of genome relatedness indices including digital DNA-DNA hybridization and average nucleotide identity (ANI) as well as comprehensive phenotypic analysis for type strains. Finally, we reclassified all misidentified genera and species, resulting in 19 new combinations, and proposed Sphaerotilaceae-specific thresholds of ANI and average amino acid identity for genus delineation. Collectively, this study has established a sound taxonomic framework of the novel family Sphaerotilaceae and will help guide future taxonomic efforts and prevent the propagation of taxonomic errors.     

Multilocus analysis reveals diversity in the genus Tissierella: Description of Tissierella carlieri sp. nov. in the new class Tissierellia classis nov.

The genus Tissierella and its relatives Tepidimicrobium, Soehngenia and Sporanaerobacter comprise anaerobic Gram-positive bacilli classified along with Gram-positive cocci in a family with controversial placement designated as incertae sedis XI, in the phylum Firmicutes. We performed a top-down reappraisal of the taxonomy from the phylum to the species level within the genus Tissierella. Reconstruction of high-rank 16S rRNA gene-based phylogenies and their interpretation in a taxonomic purpose allowed defining Tissierellia classis nov. within the phylum Firmicutes while the frames of Tissierellales ord. nov. and Tissierellaceae fam. nov. have to be further strengthened. For species delineation in the genus Tissierella, we studied a population of clinical strains. Beside Tissierella praeacuta, a sub-population of five strains formed a clade in multilocus phylogenies (16S rRNA, cpn60, tpi, recA and spo0A genes). Data such as 16S rRNA gene similarity level, population structure, chromosome organization and murein type indicated that this clade corresponded to a novel species for which the name Tissierella carlieri sp. nov. is proposed, with type strain LBN 295^T = AIP 268.01^T = DSM 23816^T = CCUG 60010^T. Such an approach, associating a phylogenetic reappraisal of high-level taxonomic ranks with weak taxonomic structure and a population study for genus and species delineation is needed to strengthen the taxonomic frame of incertae sedis groups in the phylum Firmicutes.     

Reorganisation of the superfamily Lepocreadioidea Odhner, 1905 based on an inferred molecular phylogeny

Utilising phylogenetic estimates inferred from molecular sequences, the superfamily Lepocreadioidea Odhner, 1905 is re-organised, with the major family, the Lepocreadiidae, split into three separate families, the Lepocreadiidae Odhner, 1905, Aephnidiogenidae Yamaguti, 1934 and Lepidapedidae Yamaguti, 1958. These families have been widely recognised as subfamilies. Also recognised are the families Enenteridae Yamaguti, 1958, Gorgocephalidae Manter, 1966 and Gyliauchenidae Fukui, 1929. The constituent genera of these families are listed, some relying on molecular data and others on morphological similarity to molecularly-typed genera. Nine genera have not been placed in families and are considered incertae sedis.     

The evolution of the diatoms (Bacillariophyta). I. Origin of the group and assessment of the monophyly of its major divisions

The diatoms are one of the best characterised algal groups. Despite this, little is known of the evolution of the group from the earliest cell to the myriad of taxa known today. Relationships among taxa at the family or generic level have been recognised in some diatoms. However, relationships at higher taxonomic levels are poorly understood and have often been strongly influenced by the first appearances of key taxa in the fossil record. An independent assessment of relationships among the diatoms at these higher taxonomic levels has been made using rRNA sequence data to infer phylogenetic relationships. In this paper we present an analysis of 18S rRNA data from several chosen centric, araphid and raphid pennate taxa. The phylogenetic inferences from these 18S rRNA sequences are supported by evidence from the fossil record and evidence from ontogenetic data. Ribosomal RNA data indicate that both the centric and araphid pennate lineages may not be monophyletic.     

Phylogenetic relationships within the speciose family Characidae (Teleostei: Ostariophysi: Characiformes) based on multilocus analysis and extensive ingroup sampling

Background

With nearly 1,100 species, the fish family Characidae represents more than half of the species of Characiformes, and is a key component of Neotropical freshwater ecosystems. The composition, phylogeny, and classification of Characidae is currently uncertain, despite significant efforts based on analysis of morphological and molecular data. No consensus about the monophyly of this group or its position within the order Characiformes has been reached, challenged by the fact that many key studies to date have non-overlapping taxonomic representation and focus only on subsets of this diversity.

Results

In the present study we propose a new definition of the family Characidae and a hypothesis of relationships for the Characiformes based on phylogenetic analysis of DNA sequences of two mitochondrial and three nuclear genes (4,680 base pairs). The sequences were obtained from 211 samples representing 166 genera distributed among all 18 recognized families in the order Characiformes, all 14 recognized subfamilies in the Characidae, plus 56 of the genera so far considered incertae sedis in the Characidae. The phylogeny obtained is robust, with most lineages significantly supported by posterior probabilities in Bayesian analysis, and high bootstrap values from maximum likelihood and parsimony analyses.

Conclusion

A monophyletic assemblage strongly supported in all our phylogenetic analysis is herein defined as the Characidae and includes the characiform species lacking a supraorbital bone and with a derived position of the emergence of the hyoid artery from the anterior ceratohyal. To recognize this and several other monophyletic groups within characiforms we propose changes in the limits of several families to facilitate future studies in the Characiformes and particularly the Characidae. This work presents a new phylogenetic framework for a speciose and morphologically diverse group of freshwater fishes of significant ecological and evolutionary importance across the Neotropics and portions of Africa.     

Molecular phylogeny of the Astrophorida (Porifera, Demospongiae(p)) reveals an unexpected high level of spicule homoplasy

Background

The Astrophorida (Porifera, Demospongiae ^p) is geographically and bathymetrically widely distributed. Systema Porifera currently includes five families in this order: Ancorinidae, Calthropellidae, Geodiidae, Pachastrellidae and Thrombidae. To date, molecular phylogenetic studies including Astrophorida species are scarce and offer limited sampling. Phylogenetic relationships within this order are therefore for the most part unknown and hypotheses based on morphology largely untested. Astrophorida taxa have very diverse spicule sets that make them a model of choice to investigate spicule evolution.

Methodology/Principal Findings

With a sampling of 153 specimens (9 families, 29 genera, 89 species) covering the deep- and shallow-waters worldwide, this work presents the first comprehensive molecular phylogeny of the Astrophorida, using a cytochrome c oxidase subunit I (COI) gene partial sequence and the 5′ end terminal part of the 28S rDNA gene (C1-D2 domains). The resulting tree suggested that i) the Astrophorida included some lithistid families and some Alectonidae species, ii) the sub-orders Euastrophorida and Streptosclerophorida were both polyphyletic, iii) the Geodiidae, the Ancorinidae and the Pachastrellidae were not monophyletic, iv) the Calthropellidae was part of the Geodiidae clade (Calthropella at least), and finally that v) many genera were polyphyletic (Ecionemia, Erylus, Poecillastra, Penares, Rhabdastrella, Stelletta and Vulcanella).

Conclusion

The Astrophorida is a larger order than previously considered, comprising ca. 820 species. Based on these results, we propose new classifications for the Astrophorida using both the classical rank-based nomenclature (i.e., Linnaean classification) and the phylogenetic nomenclature following the PhyloCode, independent of taxonomic rank. A key to the Astrophorida families, sub-families and genera incertae sedis is also included. Incongruences between our molecular tree and the current classification can be explained by the banality of convergent evolution and secondary loss in spicule evolution. These processes have taken place many times, in all the major clades, for megascleres and microscleres.     

The Phylogenetic Affinities of the Enigmatic Mammalian Clade Gondwanatheria

Gondwanatheria is a group of extinct mammals known from the Cretaceous and Paleogene of Gondwana. Resolution of the phylogenetic affinities of gondwanatherians has proven problematical, with the group currently considered Mammalia incertae sedis. We briefly review the morphology of known gondwanatherians, and argue that isolated upper premolars and a partial dentary preserving a blade-like p4 originally referred to the ferugliotheriid gondwanatherian Ferugliotherium windhauseni but subsequently identified as Multituberculata incertae sedis do indeed belong to F. windhauseni. We also suggest that the recently described ?cimolodontan multituberculate Argentodites coloniensis, based on an isolated lower premolar, may in fact be an unworn p4 of Ferugliotherium or a closely related taxon. We present the first phylogenetic analyses to include gondwanatherians, using maximum parsimony and Bayesian methods. Both methods place Ferugliotherium and sudamericid gondwanatherians in a clade with cimolodontan and “plagiaulacidan” multituberculates, although relationships within this clade are largely unresolved. The Gondwanatheria + Multituberculata clade supported here may reflect the convergent evolution of similar dental features, but it is the best supported hypothesis based on currently available data. However, denser sampling of multituberculate taxa and the discovery of more complete gondwanatherian fossils will be required to clarify the precise relationship between gondwanatherians and multituberculates, specifically to determine whether or not gondwanatherians are members of Multituberculata. We hypothesize that the anterior molariforms of sudamericid gondwanatherians evolved from blade-like precursors similar to the p4 of Ferugliotherium, possibly in response to the appearance of grasses in Gondwana during the Cretaceous.     

Evolutionary relationships among scyphozoan jellyfish families based on complete taxon sampling and phylogenetic analyses of 18S and 28S ribosomal DNA

A stable phylogenetic hypothesis for families within jellyfish class Scyphozoa has been elusive. Reasons for the lack of resolution of scyphozoan familial relationships include a dearth of morphological characters that reliably distinguish taxa and incomplete taxonomic sampling in molecular studies. Here, we address the latter issue by using maximum likelihood and Bayesian methods to reconstruct the phylogenetic relationships among all 19 currently valid scyphozoan families, using sequence data from two nuclear genes: 18S and 28S rDNA. Consistent with prior morphological hypotheses, we find strong evidence for monophyly of subclass Discomedusae, order Coronatae, rhizostome suborder Kolpophorae and superfamilies Actinomyariae, Kampylomyariae, Krikomyariae, and Scapulatae. Eleven of the 19 currently recognized scyphozoan families are robustly monophyletic, and we suggest recognition of two new families pending further analyses. In contrast to long-standing morphological hypotheses, the phylogeny shows coronate family Nausithoidae, semaeostome family Cyaneidae, and rhizostome suborder Daktyliophorae to be nonmonophyletic. Our analyses neither strongly support nor strongly refute monophyly of order Rhizostomeae, superfamily Inscapulatae, and families Ulmaridae, Catostylidae, Lychnorhizidae, and Rhizostomatidae. These taxa, as well as familial relationships within Coronatae and within rhizostome superfamily Inscapulatae, remain unclear and may be resolved by additional genomic and taxonomic sampling. In addition to clarifying some historically difficult taxonomic questions and highlighting nodes in particular need of further attention, the molecular phylogeny presented here will facilitate more robust study of phenotypic evolution in the Scyphozoa, including the evolution characters associated with mass occurrences of jellyfish.     

Phylogenetic balance and ecological evenness

The frequency distribution of numbers of species in taxonomic groups, where many species belong to a few very diverse higher taxa, is mirrored by that of species in most communities, where many individuals belong to a few very abundant species. Various hypotheses mechanistically link a species' community abundance with the diversity of the higher level taxon (genus, family, order) to which it belongs, but empirical data are equivocal about general trends in the relation between rank-taxon diversity and mean abundance. One reason for this inconclusive result may be the effect of the semisubjective nature of rank-based classification. We assessed the relationship between clade diversity and mean species abundance for two diverse tropical tree communities, using both traditional rank-based analysis and two new phylogenetic analyses (based on the ratio of individuals to taxa at each node in the phylogeny). Both rank-based and phylogenetic analyses using taxonomic ranks above the species level as terminal taxa detected a trend associating common species with species-rich families. In contrast, phylogenetic analyses using species as terminal taxa could not distinguish the observed distribution of species abundances from a random distribution with respect to clade diversity. The difference between these results might be due to (1) the absence of a real phylogeny-wide relationship between clade abundance and diversity, (2) the influence of poor phylogenetic resolution within families in our phylogenies, or (3) insufficient sensitivity of our metrics to subtle tree-wide effects. Further development and application of phylogeny-based methods for testing abundance-diversity relationships is needed.     

Comparison of DNA and RNA, and Cultivation Approaches for the Recovery of Terrestrial and Aquatic Fungi from Environmental Samples

Estimates of fungal biodiversity from environmental samples are all subject to bias. Major issues are that the commonly adopted cultivation-based approaches are suitable for taxa which grow readily under laboratory conditions, while the DNA-based approaches provide more reliable estimates, but do not indicate whether taxa are metabolically active. In this study, we have evaluated these approaches to estimate the fungal diversity in soil and freshwater samples from a subtropical forest, and compared these to RNA-based culture-independent approach intended to indicate the metabolically active fungal assemblage. In both soil and freshwater samples, the dominant taxon recovered by all three approaches was the same (Anguillospora furtiva). This taxon was cultivable from all samples and comprised 85–86 % DNA libraries and 90–91 % RNA libraries. The remaining taxa were phylogenetically diverse and spanned the Ascomycota, Basidiomycota, and Fungi incertae sedis. Their recovery was not consistent among the three approaches used and suggests that less abundant members of the assemblage may be subjected to greater bias when diversity estimates employ a single approach.     

Phylogenetic classification of the Drosophilidae Rondani (Diptera): the role of morphology in the postgenomic era

Molecular sequences now overwhelm morphology in phylogenetic inference. Nonetheless, most molecular studies are conducted on a limited number of taxa, as DNA rarely can be analysed from old museum types or fossils. During the last 20 years, more than 150 molecular studies have challenged the current phylogenetic classification of the family Drosophilidae Rondani based on morphological characters. Most studies concerned a single genus, Drosophila Fallén, and included only few representative species from 17 out of the 78 genera of the family. Therefore, these molecular studies were unable to provide an alternative classification scheme. A supermatrix analysis of seven nuclear and one mitochondrial genes (8248 bp) for 33 genera was conducted using outgroups from one calyptrate and four ephydroid families. The Bayesian phylogeny was consistent with previous molecular studies including whole genome sequences and divided the Drosophilidae into four monophyletic clades. Morphological characters, mostly male genitalia, then were compared thoroughly between the four clades and homologous character states were identified. These states were then checked for 70 genera and a revised phylogenetic, family‐group classification for the Drosophilidae is proposed. Two genera –Cladochaeta Coquillett and Diathoneura Duda – of the tribe Cladochaetini Grimaldi are transferred to the family Ephydridae. The Drosophilidae is divided into two subfamilies: Steganinae Hendel (30 genera) and Drosophilinae Rondani (43 genera). A further two genera, Apacrochaeta Duda and Sphyrnoceps de Meijere, are incertae sedis, and Palmophila Grimaldi, is synonymized with Drosophila syn.n. The Drosophilinae is subdivided into two tribes: the re‐elevated Colocasiomyini Okada (nine genera) and Drosophilini Okada. The paraphyly of the genus Drosophila was not resolved to avoid affecting the binomina of important laboratory model species; however, its subgeneric classification was revised in light of molecular and morphological data. Three subgenera, namely Chusqueophila Brncic, Phloridosa Sturtevant and Psilodorha Okada, were synonymized with the subgenus Drosophila (Drosophila) Fallén syns.n. Among the 45 species groups and 5 species complexes of Drosophila (Drosophila), 22 groups and 1 complex were transferred to the subgenus Drosophila (Siphlodora) Patterson & Mainland and 6 groups, 2 species subgroups and 3 complexes are considered incertae sedis within the genus Drosophila. Different morphological characters provide different signals at different phylogenetic scales: thoracic characters (wing venation and presternal shape) discriminate families; grasping and erection‐related characters discriminate subfamilies to tribes; whereas phallic paraphyses, i.e. auxiliary intromittent organs, discriminate genera and Drosophila subgenera. The study shows the necessity of analysing morphological characters within a molecular phylogenetic framework to translate molecular phylogenies into taxonomically‐comprehensive classifications.     

Putting incertae sedis taxa in their place: a proposal for ten new families and three new genera in Sphaeropleales (Chlorophyceae,Chlorophyta)

Best known for aquatic colonial algae such as Hydrodictyon, Pediastrum, or Scenedesmus, the order Sphaeropleales also contains numerous coccoid taxa from aquatic and terrestrial habitats. Recent findings indicate that coccoid lineages in this order are very diverse genetically and may be the prevalent form, although their diversity is often hidden morphologically. This study characterizes coccoid algae recently discovered from desert soil crusts that share morphological and ecological features with the genera Bracteacoccus, Pseudomuriella, and Chromochloris. Analyses of a multi‐gene data set that includes members from all sphaeroplealean families are used to examine the monophyly of these morphologically similar taxa, which are shown instead to be phylogenetically distinct and very divergent. We propose new generic names for these lineages: Bracteamorpha, Rotundella, and Tumidella. In addition, we propose an updated family‐level taxonomy within Sphaeropleales that includes ten new families of coccoid algae to accommodate the newly presented genera and many incertae sedis taxa in the order: Bracteamorphaceae, Chromochloridaceae, Dictyococcaceae, Dictyochloridaceae, Mychonastaceae, Pseudomuriellaceae, Rotundellaceae, Schizochlamydaceae, Schroederiaceae, and Tumidellaceae.     

Whole genome-based assessment of the taxonomic position of the arthropod pathogenic bacterium Rickettsiella grylli

Rickettsiella grylli is an intracellular bacterial pathogen of aquatic and terrestrial arthropods. Previous determination of its 16S rRNA-encoding sequence has led to the taxonomic classification of the genus Rickettsiella in the class Gammaproteobacteria, order Legionellales, family Coxiellaceae, i.e. in close vicinity to vertebrate pathogenic bacteria of the genera Coxiella and Legionella. Here we use the additional information available from the recently published first whole genome sequence from this genus to evaluate critically the taxonomic classification of R. grylli beyond the 16S rRNA gene level. Using phylogenetic reconstruction, together with significance testing on a data basis defined by a core set of 211 previously identified families of protein-encoding genes, together with a reanalysis of 16S rRNA gene data, the present study firmly corroborates the assignment of this species to both the class Gammaproteobacteria and the order Legionellales. However, the results obtained from concatenated and single protein, single protein-encoding gene, and 16S rRNA gene data demonstrate a similar phylogenetic distance of R. grylli to both the Coxiellaceae and the Legionellaceae and are, therefore, inconsistent with its current family-level classification. Consequently, a respective reorganization of the order Legionellales is proposed.     

Patterns of taxonomic diversity among terrestrial isopods

The publication of the world catalog of terrestrial isopods some ten years ago by Schmalfuss has facilitated research on isopod diversity patterns at a global scale. Furthermore, even though we still lack a comprehensive and robust phylogeny of Oniscidea, we do have some useful approaches to phylogenetic relationships among major clades which can offer additional insights into isopod evolutionary dynamics. Taxonomic diversity is one of many approaches to biodiversity and, despite its sensitiveness to biases in taxonomic practice, has proved useful in exploring diversification dynamics of various taxa. In the present work, we attempt an analysis of taxonomic diversity patterns among Oniscidea based on an updated world list of species containing 3,710 species belonging to 527 genera and 37 families (data till April 2014). The analysis explores species diversity at the genus and family level, as well as the relationships between species per genera, species per families, and genera per families. In addition, we consider the structure of isopod taxonomic system under the fractal perspective that has been proposed as a measure of a taxon’s diversification. Finally, we check whether there is any phylogenetic signal behind taxonomic diversity patterns. The results can be useful in a more detailed elaboration of Oniscidea systematics.     

Whole genome sequencing reveals the genomic diversity,taxonomic classification,and evolutionary relationships of the genus Nocardia

Nocardia is a complex and diverse genus of aerobic actinomycetes that cause complex clinical presentations, which are difficult to diagnose due to being misunderstood. To date, the genetic diversity, evolution, and taxonomic structure of the genus Nocardia are still unclear. In this study, we investigated the pan-genome of 86 Nocardia type strains to clarify their genetic diversity. Our study revealed an open pan-genome for Nocardia containing 265,836 gene families, with about 99.7% of the pan-genome being variable. Horizontal gene transfer appears to have been an important evolutionary driver of genetic diversity shaping the Nocardia genome and may have caused historical taxonomic confusion from other taxa (primarily Rhodococcus, Skermania, Aldersonia, and Mycobacterium). Based on single-copy gene families, we established a high-accuracy phylogenomic approach for Nocardia using 229 genome sequences. Furthermore, we found 28 potentially new species and reclassified 16 strains. Finally, by comparing the topology between a phylogenomic tree and 384 phylogenetic trees (from 384 single-copy genes from the core genome), we identified a novel locus for inferring the phylogeny of this genus. The dapb1 gene, which encodes dipeptidyl aminopeptidase BI, was far superior to commonly used markers for Nocardia and yielded a topology almost identical to that of genome-based phylogeny. In conclusion, the present study provides insights into the genetic diversity, contributes a robust framework for the taxonomic classification, and elucidates the evolutionary relationships of Nocardia. This framework should facilitate the development of rapid tests for the species identification of highly variable species and has given new insight into the behavior of this genus.