Plastome phylogenomics of Cephalotaxus (Cephalotaxaceae) and allied genera

Background and Aims Cephalotaxus is a paleo-endemic genus in East Asia that consists of about 7–9 conifer species. Despite its great economic and ecological importance, the relationships between Cephalotaxus and related genera, as well as the interspecific relationships within Cephalotaxus, have long been controversial, resulting in contrasting taxonomic proposals in delimitation of Cephalotaxaceae and Taxaceae. Based on plastome data, this study aims to reconstruct a robust phylogeny to infer the systematic placement and the evolutionary history of Cephalotaxus.MethodsA total of 11 plastomes, representing all species currently recognized in Cephalotaxus and two Torreya species, were sequenced and assembled. Combining these with previously published plastomes, we reconstructed a phylogeny of Cephalotaxaceae and Taxaceae with nearly full taxonomic sampling. Under a phylogenetic framework and molecular dating, the diversification history of Cephalotaxus and allied genera was explored.Key ResultsPhylogenetic analyses of 81 plastid protein-coding genes recovered robust relationships between Cephalotaxus and related genera, as well as providing a well-supported resolution of interspecific relationships within Cephalotaxus, Taxus, Torreya and Amentotaxus. Divergence time estimation indicated that most extant species of these genera are relatively young, although fossil and other molecular evidence consistently show that these genera are ancient plant lineages.ConclusionsOur results justify the taxonomic proposal that recognizes Cephalotaxaceae as a monotypic family, and contribute to a clear-cut delineation between Cephalotaxaceae and Taxaceae. Given that extant species of Cephalotaxus are derived from recent divergence events associated with the establishment of monsoonal climates in East Asia and Pleistocene climatic fluctuations, they are not evolutionary relics.     

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.     

Phylogenetic relationships among families of Gadiformes (Teleostei, Paracanthopterygii) based on nuclear and mitochondrial data

Phylogenetic hypotheses among Gadiformes fishes at the suborder, family, and subfamily levels are controversial. To address this problem, we analyze nuclear and mitochondrial DNA (mtDNA) sequences for the most extensive taxonomic sampling compiled to date, representing all of the recognized families and subfamilies in the order (except the monotypic family Lyconidae). Our study sampled 117 species from 46 genera, comprising around 20% of the species described for the order (more than 60% of all genera in the order) and produced 2740 bp of DNA sequence data for each species. Our analysis was successful in confirming the monophyly of Gadiformes and most of the proposed families for the order, but alternative hypotheses of sister-group relationships among families were poorly resolved. Our results are consistent with dividing Gadiformes into 12 families in three suborders, Muraenolepidoidei, Macrouroidei, and Gadoidei. Muraenolepidoidei contains the single family Muraenolepididae. The suborder Macrouroidei includes at least three families: Macrouridae, Macruronidae and Steindachneriidae. Macrouridae is deeply divided into two well-supported subfamilies: Macrourinae and Bathygadinae, suggesting that Bathygadinae may be ranked at the family level. The suborder Gadoidei includes the families: Merlucciidae, Melanonidae, Euclichthyidae, Gadidae, Ranicipitidae, and Bregmacerotidae. Additionally, Trachyrincinae could be ranked at family level including two subfamilies: Trachyrincinae and Macrouroidinae within Gadoidei. Further taxonomic sampling and sequencing efforts are needed in order to corroborate these relationships.     

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.     

Plumage evolution in relation to light environment in a novel clade of Neotropical tanagers

Molecular phylogenetic analyses have greatly changed Neotropical avian systematics in the past couple of decades. These new phylogenies provide the necessary framework to study the ecology and natural history of species in the region in an evolutionary context. This study addresses the systematics of Poospiza, Compsospiza, Hemispingus, Thlypopsis, and eight monotypic genera, which form a strongly supported and novel clade within the tanagers. We find Poospiza, Hemispingus, and Thlypopsis to be polyphyletic, confirm or reject relationships proposed based on morphology and life history, and describe novel relationships among these and the monotypic genera. The diversity of plumage, habitat, and geography throughout the clade allows us to test hypotheses of plumage evolution in relation to light environment. We find that overall plumage brightness best fits a model that includes selective regimes based on open versus closed habitats and foraging strata, while plumage measures describing color diversity and chroma best fit a model that only includes selective regimes based on open and closed habitats.     

Taxonomic study of the tetrahedral, pentagonal and hexagonal spongy spumellarian Radiolaria from the middle Carnian (Late Triassic) of the Köseyahya nappe (Elbistan, SE Turkey) and other Triassic localities

This article is a taxonomic study of all spongy radiolarian taxa with five to six coplanar and four tetrahedrally disposed spines or spongy arms occurring in the middle Carnian from the Köseyahya section, near the town of Elbistan, SE Turkey. This fauna is characteristic of the Tetraporobrachia haeckeli radiolarian Zone, and comes from an 8 m thick succession of clayey–cherty limestones occurring at the lower part of the section. In addition, a few species from the Middle and Upper Triassic from other areas have been also included in this study to improve some generic diagnoses and to better understand the diversity and evolutionary trends of some genera, subfamilies and families. The taxonomy at the generic and suprageneric levels is based primarily on the types of microsphere. This new approach allowed new taxonomic arrangements of genera and suprageneric units, and suggested new and unexpected phylogenetic relationships among these radiolarians and between them and younger radiolarians. The authors discuss and describe 42 species, of which 36 are new, and 12 genera of which three are new (Charlottalum, Pentaspongodisculus, and Trimiducaella). The genera Pseudohagiastrum Pessagno, Natraglia Pessagno, Cantalum Pessagno and others are reinterpreted. All the genera studied, except Charlottalum, are assigned to three subfamilies, of which two (Pseudohagiastrinae and Trimiducinae) are new, and to two families (Angulobracchiidae and Relindellidae). The genus Charlottalum is described to replace the genus Cantalum, which has been erroneously used until present for Late Triassic pantanelliids with four tetrahedrally disposed three-bladed spines.     

Taxonomic study of spongy spumellarian Radiolaria with three and four coplanar spines or arms from the middle Carnian (Late Triassic) of the Köseyahya nappe (Elbistan, SE Turkey) and other Triassic localities

The present article is a taxonomic study of all spongy spumellarian radiolarian taxa with three and four coplanar spines or spongy arms occurring in the middle Carnian from the Köseyahya section, near the town of Elbistan, SE Turkey. This fauna is characteristic of the Tetraporobrachia haeckeli radiolarian Zone, and comes from an 8 m thick succession of clayey-cherty limestones occurring at the lower part of the section. In addition, a few species from the Middle and Upper Triassic from other areas have been also included in this study to improve some generic diagnoses, and to better comprehend the diversity and evolutionary trends of some genera, subfamilies and families. The taxonomy at the generic and suprageneric levels is based primarily on the types of microsphere. This new approach allowed new taxonomic arrangements of genera and suprageneric units, and suggested new phylogenetic relationships among these radiolarians and between them and younger radiolarians. The authors discuss and describe 69 species, of which 37 are new, and 14 genera, of which three are new (Paraparonaella, Pseudangulobracchia, and Ropanaella). The genus Triassoastrum and others are reinterpreted. All genera studied are assigned to five subfamilies, of which two are new (Tetrapaurinellinae and Triassocrucellinae), and two families (Tritrabidae and Veghicycliidae). Nine species in open nomenclature are also illustrated.     

Phylogeny and classification of Ranunculales: Evidence from four molecular loci and morphological data

Previous phylogenetic analyses of Ranunculales, which have mostly been focused on an individual family and were based on molecular data alone, have recovered three main clades within the order. However, support for relationships among these three clades was weak. Earlier hypotheses were often hampered by limited taxon sampling; to date less than one-tenth of the genera in the order have been sampled. In this study, we used a greatly enlarged taxon sampling (105 species, representing 99 genera of all seven families in the order). Our study is, furthermore, the first to employ morphology (65 characters) in combination with sequence data from four genomic regions, including plastid rbcL, matK and trnL-F, and nuclear ribosomal 26S rDNA to reconstruct phylogenetic relationships within Ranunculales. Maximum parsimony and Bayesian inference were performed on the individual and combined data sets. Our analyses concur with those of previous studies, but in most cases provide stronger support and better resolution for relationships among the three main clades retrieved. The first, comprised solely of the monogeneric family Eupteleaceae, is the earliest-diverging lineage. The second clade is composed exclusively of taxa of Papaveraceae, which is sister to the third clade, the core Ranunculales, comprising the other five families of the order. Circaeasteraceae and Lardizabalaceae form a strongly supported clade. Pteridophyllum is supported as sister to Hypecoum, contradicting the viewpoint that the former is the earliest-diverging genus in Papaveraceae. Glaucidium is basalmost in Ranunculaceae. Within this phylogenetic framework, the evolution of selected characters is inferred and diagnostic morphological characters at different taxonomic levels are identified and discussed. Based on both morphological and molecular evidence, a classification outline for Ranunculales is presented, including the proposal of two new subfamilies, Menispermoideae and Tinosporoideae in Menispermaceae and a new tribe, Callianthemeae, for the genus Callianthemum (Ranunculaceae).     

SEED MORPHOLOGY AND SYSTEMATICS OF MENYANTHACEAE

Scanning electron microscopic investigations of seed morphology of the five genera of Menyanthaceae illustrate a remarkable diversity of seed characteristics for a small family. Seeds of the monotypic northern hemisphere Menyanthes and Fauria are unomamented and similar, and those of the monotypic Liparophyllum of New Zealand and Tasmania are similar to some Australian species of Villarsia. Seed characteristics within the larger genera Villarsia and Nymphoides are variable and mostly species specific, but do not lend support to taxonomic separation of these genera. Interspecific affinities postulated on other grounds are, in many instances, supported by seed morphology. Various seed-coat features are believed to aid in water or animal dispersal of the seeds of several species. Ant dispersal appears to be important for Villarsia and Nymphoides in Australia, but does not seem to occur in these genera or in other members of the family outside of Australia.     

Evolutionary relationships among species of Puccinia and Uromyces (Pucciniaceae,Uredinales) inferred from partial protein coding gene phylogenies

The two rust genera with the largest number of species are Puccinia Pers. ex Pers. and Uromyces (Link) Unger in the family Pucciniaceae (Uredinales). The hosts of these pathogens include representatives from almost all major angiosperm orders. Despite their ecological and economic importance, the status of Puccinia and Uromyces as distinct genera has been disputed, and little is known about relationships within and among these groups. Here we present phylogenetic analyses based on sequence data from the translation elongation factor 1α gene for over 60 species in the family Pucciniaceae. In particular, we investigate evolutionary relationships between Puccinia and Uromyces. A relatively smaller phylogeny using the beta-tubulin 1 gene was generated to test support for this phylogeny. Two main phylogenetic clades were identified and indicate at least two radiations within the Pucciniaceae. As expected neither Puccinia s. lat. nor Uromyces s. lat. are supported as monophyletic groups by either of the protein coding genes. However, both Puccinia sensu stricto (type P. graminis), and Uromyces sensu stricto (type U. appendiculatus) constitute distinct clades. In general, members of Uromyces spp. occurred scattered throughout the phylogeny suggesting that they represent more recent radiations. Several host families are found in both of the two main clades while two families, Poaceae and Cyperaceae, are separated, with one in each of the two main clades.     

A new genus and species of arboreal toad with phytotelmonous larvae,from the Andaman Islands,India (Lissamphibia,Anura, Bufonidae)

A new bufonid amphibian, belonging to a new monotypic genus, is described from the Andaman Islands, in the Bay of Bengal, Republic of India, based on unique external morphological and skeletal characters which are compared with those of known Oriental and other relevant bufonid genera. Blythophryne gen. n. is distinguished from other bufonid genera by its small adult size (mean SVL 24.02 mm), the presence of six presacral vertebrae, an absence of coccygeal expansions, presence of an elongated pair of parotoid glands, expanded discs at digit tips and phytotelmonous tadpoles that lack oral denticles. The taxonomic and phylogenetic position of the new taxon (that we named as Blythophryne beryet gen. et sp. n.) was ascertained by comparing its 12S and 16S partial genes with those of Oriental and other relevant bufonid lineages. Resulting molecular phylogeny supports the erection of a novel monotypic genus for this lineage from the Andaman Islands of India.     

Hidden Mediterranean diversity: Assessing species taxa by molecular phylogeny within the opilionid family Trogulidae (Arachnida,Opiliones)

This is the first comprehensive study to evaluate the relationships between the western palearctic harvestman families Dicranolasmatidae, Trogulidae and Nemastomatidae with focus on the phylogeny and systematics of Trogulidae, using combined sequence data of the nuclear 28S rRNA and the mitochondrial cytochrome b gene. Bayesian analysis and Maximum parsimony do not reliably resolve Dicranolasma as distinct family but place it on a similar phylogenetic level as several lineages of Trogulidae. Nemastomatidae and Trogulidae turned out to be monophyletic, as did genera Anelasmocephalus and Trogulus within the Trogulidae. The genera Calathocratus, Platybessobius and Trogulocratus each appeared para or polyphyletic, respectively and are synonymized with Calathocratus. The monotypic genus Kofiniotis is well supported. We show molecular data to be in general concordance with taxa characterized by morphology. Molecular data are especially useful to calibrate morphological characters for systematic purposes within homogeneous taxa. In the majority of closely related valid species we show the lowest level of genetic distance to be not lower than 5%. By this threshold in terms of traditionally accepted species the estimated number of species turns out to be 1.5–2.4 times higher than previously believed. With respect to European fauna cryptic diversity in Trogulidae is obviously extraordinarily high and hitherto largely underestimated.     

Multigene Molecular Phylogeny and Biogeographic Diversification of the Earth Tongue Fungi in the Genera Cudonia and Spathularia (Rhytismatales,Ascomycota)

The family Cudoniaceae (Rhytismatales, Ascomycota) was erected to accommodate the “earth tongue fungi” in the genera Cudonia and Spathularia. There have been no recent taxonomic studies of these genera, and the evolutionary relationships within and among these fungi are largely unknown. Here we explore the molecular phylogenetic relationships within Cudonia and Spathularia using maximum likelihood and Bayesian inference analyses based on 111 collections from across the Northern Hemisphere. Phylogenies based on the combined data from ITS, nrLSU, rpb2 and tef-1α sequences support the monophyly of three main clades, the /flavida, /velutipes, and /cudonia clades. The genus Cudonia and the family Cudoniaceae are supported as monophyletic groups, while the genus Spathularia is not monophyletic. Although Cudoniaceae is monophyletic, our analyses agree with previous studies that this family is nested within the Rhytismataceae. Our phylogenetic analyses circumscribes 32 species-level clades, including the putative recognition of 23 undescribed phylogenetic species. Our molecular phylogeny also revealed an unexpectedly high species diversity of Cudonia and Spathularia in eastern Asia, with 16 (out of 21) species-level clades of Cudonia and 8 (out of 11) species-level clades of Spathularia. We estimate that the divergence time of the Cudoniaceae was in the Paleogene approximately 28 Million years ago (Mya) and that the ancestral area for this group of fungi was in Eastern Asia based on the current data. We hypothesize that the large-scale geological and climatic events in Oligocene (e.g. the global cooling and the uplift of the Tibetan plateau) may have triggered evolutionary radiations in this group of fungi in East Asia. This work provides a foundation for future studies on the phylogeny, diversity, and evolution of Cudonia and Spathularia and highlights the need for more molecular studies on collections from Europe and North America.     

Phylogenetic relationships of the Clavelinidae and Pycnoclavellidae (Ascidiacea) inferred from mtDNA data

Abstract. The phylogenetic relationships within the Order Aplousobranchiata (Ascidiacea) are largely unexplored. In this work, we study the phylogenetic status of the genera Clavelina and Pycnoclavella. Traditionally, both genera had been included in the family Clavelinidae, until the new family Pycnoclavellidae was defined, removing the genus Pycnoclavella from Clavelinidae. Not all authors accept the validity of Clavelina and Pycnoclavella as distinct genera, let alone their belonging to different families. In addition, the assignment of species to these genera, as well as to the genus Archidistoma , has been controversial. We analyzed sequences of the mitochondrial gene cytochrome c oxidase subunit I belonging to ten species of Pycnoclavella (including several formerly assigned to Archidistoma and Clavelina ), 11 species of Clavelinidae, and ten species of other aplousobranch genera belonging to seven families, plus two outgroups. Two different tree construction methods (maximum likelihood and Bayesian inference) showed similar results. Pycnoclavella and Clavelina appeared in distinct clades but formed a monophyletic group relative to representatives of the main families of the order Aplousobranchiata. Our phylogenetic results indicate that both genera are valid but should be included within a single family, with the name Clavelinidae having precedence. The monotypic clavelinid genus Nephtheis branches in our trees within the clade of the genus Clavelina. Our results also confirm that some forms assigned to Archidistoma and Clavelina have been misplaced and belong to the genus Pycnoclavella. Pycnoclavella martae n.sp. is described.     

Floristic summary ofManual of Vascular Plants of Northeastern United States and Adjacent Canada,second edition

The second edition of theManual of Vascular Plants of Northeastern United States and Adjacent Canada by Gleason and Cronquist (1991) is the most recent and up-to-date taxonomic treatment of the flora of that region. Since no floristic summary of theManual was included in the publication, a computer analysis of the taxonomic data of theManual was performed in order to generate a floristic summary. Totals of 4285 species, 1091 genera, and 191 families were tabulated. The largest genus wasCarex, with 230 species; the largest family was the Asteraceae, with 528 species. Comparisons made with earlier floras of the same region indicated small declines on the order of 10% for these taxonomic groups.     

A molecular phylogenetic assessment of the advanced Asiatic and Malesian didymocarpoid Gesneriaceae with focus on non-monophyletic and monotypic genera

Based on a considerably enlarged sampling, a phylogenetic analysis of the largest group of didymocarpoid Gesneriaceae, the ??advanced Asiatic and Malesian genera??, was performed, covering all but 3 of the 60 genera presently recognised in this group (20 of these, mostly from China, are monotypic). The results suggest that no fewer than 17 out of the 57 genera examined are poly- (or rarely para-)phyletic. Highly polyphyletic are Briggsia, Chirita, Henckelia and Raphiocarpus. Only a dozen of the non-monotypic genera (including the three species-richest genera, Cyrtandra, Aeschynanthus and Agalmyla) are confirmed as monophyletic entities, though some exhibit considerable genetic variation. For eight genera, no statement can be made, as only one (of two or several) species was included in the analysis. For a dozen of the (particularly Chinese) monotypic genera a close relationship (or possible congenerity) with other genera was found. In China, only Allostigma, Cathayanthe, Conandron and Metapetrocosmea seem to have no strong affinities to other genera, indicating that they represent phylogenetically isolated lineages or represent remnants of previously larger and earlier diversified groups. The present study forms the foundation for targeted molecular, morphological and phytogeographic studies of the polyphyletic and monotypic genera and particular of clades of genera with interrelations uncovered here for the first time.     

Pollen morphology of the dichapetalaceae with special reference to evolutionary trends and mutual relationships of pollen types

Pollen grains of all three genera of Dichapetalaceae (Dichapetalum, Stephanopodium and Tapura) comprising about 150 species have been studied. Twenty-nine pollen types were recognized and the family has to be considered eurypalynous. A key to the pollen types is added. Based on evolutionary trends it was possible to give a scheme to the mutual relationships of the pollen types. It is concluded that the centre of origin of the family may be Africa. It was pot possible to point to distinct relationships with other families on pollenmorphological data alone.