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Lianas constitute a diverse polyphyletic plant group that is advancing our understanding of ecological theory. Specifically, lianas are providing newinsights into the mechanisms that control plant distribution and diversity maintenance. For example, there is now evidence that a single, scalable mechanism may explain local, regional, and pan-tropical distribution of lianas, as well as the maintenance of liana species diversity. The ability to outcompete trees under dry, stressful conditions in seasonal forests provides lianas a growth advantage that, over time, results in relatively high abundance in seasonal forests and low abundance in aseasonal forests. Lianas may also gain a similar growth advantage following disturbance, thus explaining why liana density and diversity peak following disturbance at the local, forest scale. The study of ecology, however, is more than the effect of the environment on organisms; it also includes the effects of organisms on the environment. Considerable empirical evidence now indicates that lianas substantially alter their environment by consuming resources, suppressing tree performance, and influencing emergent properties of forests, such as ecosystem functioning, plant and animal diversity, and community composition. These recent studies using lianas are transcending classical tropical ecology research and are now providing novel insights into fundamental ecological theory.

Knowledge of the relationships and thus the classification of fungi, has developed rapidly with increasingly widespread use of molecular techniques, over the past 10–15 years, and continues to accelerate. Several genera have been found to be polyphyletic, and their generic concepts have subsequently been emended. New names have thus been introduced for species which are phylogenetically distinct from the type species of particular genera. The ending of the separate naming of morphs of the same species in 2011, has also caused changes in fungal generic names. In order to facilitate access to all important changes, it was desirable to compile these in a single document. The present article provides a list of generic names of Ascomycota (approximately 6500 accepted names published to the end of 2016), including those which are lichen-forming. Notes and summaries of the changes since the last edition of ‘Ainsworth & Bisby’s Dictionary of the Fungi’ in 2008 are provided. The notes include the number of accepted species, classification, type species (with location of the type material), culture availability, life-styles, distribution, and selected publications that have appeared since 2008. This work is intended to provide the foundation for updating the ascomycete component of the “Without prejudice list of generic names of Fungi ” published in 2013, which will be developed into a list of protected generic names. This will be subjected to the XIXth International Botanical Congress in Shenzhen in July 2017 agreeing to a modification in the rules relating to protected lists, and scrutiny by procedures determined by the Nomenclature Committee for Fungi (NCF). The previously invalidly published generic names Barriopsis , Collophora (as Collophorina ), Cryomyces , Dematiopleospora , Heterospora (as Heterosporicola ), Lithophila , Palmomyces (as Palmaria ) and Saxomyces are validated, as are two previously invalid family names, Bartaliniaceae and Wiesneriomycetaceae . Four species of Lalaria , which were invalidly published are transferred to Taphrina and validated as new combinations. Catenomycopsis Tibell & Constant. is reduced under Chaenothecopsis Vain., while Dichomera Cooke is reduced under Botryosphaeria Ces. & De Not. (Art. 59).

We present the first large-scale phylogenetic hypothesis for the genus Carex based on 996 of the 1983 accepted species (50.23%). We used a supermatrix approach using three DNA regions: ETS, ITS and matK. Every concatenated sequence was derived from a single specimen. The topology of our phylogenetic reconstruction largely agreed with previous studies. We also gained new insights into the early divergence structure of the two largest clades, core Carex and Vignea clades, challenging some previous evolutionary hypotheses about inflorescence structure. Most sections were recovered as non-monophyletic. Homoplasy of characters traditionally selected as relevant for classification, historical misunderstanding of how morphology varies across Carex, and regional rather than global views of Carex diversity seem to be the main reasons for the high levels of polyphyly and paraphyly in the current infrageneric classification.

The proliferation of DNA data is revolutionizing all fields of systematic research. DNA barcode sequences, now available for millions of specimens and several hundred thousand species, are increasingly used in algorithmic species delimitations. This is complicated by occasional incongruences between species and gene genealogies, as indicated by situations where conspecific individuals do not form a monophyletic cluster in a gene tree. In two previous reviews, non-monophyly has been reported as being common in mitochondrial DNA gene trees. We developed a novel web service “Monophylizer” to detect non-monophyly in phylogenetic trees and used it to ascertain the incidence of species non-monophyly in COI (a.k.a. cox1) barcode sequence data from 4977 species and 41,583 specimens of European Lepidoptera, the largest data set of DNA barcodes analyzed from this regard. Particular attention was paid to accurate species identification to ensure data integrity. We investigated the effects of tree-building method, sampling effort, and other methodological issues, all of which can influence estimates of non-monophyly. We found a 12% incidence of non-monophyly, a value significantly lower than that observed in previous studies. Neighbor joining (NJ) and maximum likelihood (ML) methods yielded almost equal numbers of non-monophyletic species, but 24.1% of these cases of non-monophyly were only found by one of these methods. Non-monophyletic species tend to show either low genetic distances to their nearest neighbors or exceptionally high levels of intraspecific variability. Cases of polyphyly in COI trees arising as a result of deep intraspecific divergence are negligible, as the detected cases reflected misidentifications or methodological errors. Taking into consideration variation in sampling effort, we estimate that the true incidence of non-monophyly is ∼23%, but with operational factors still being included. Within the operational factors, we separately assessed the frequency of taxonomic limitations (presence of overlooked cryptic and oversplit species) and identification uncertainties. We observed that operational factors are potentially present in more than half (58.6%) of the detected cases of non-monophyly. Furthermore, we observed that in about 20% of non-monophyletic species and entangled species, the lineages involved are either allopatric or parapatric—conditions where species delimitation is inherently subjective and particularly dependent on the species concept that has been adopted. These observations suggest that species-level non-monophyly in COI gene trees is less common than previously supposed, with many cases reflecting misidentifications, the subjectivity of species delimitation or other operational factors.

The tropical ginger genus Amomum (Zingiberaceae) has always posed challenges for classification based on morphological characters. Previous molecular phylogenetic studies showed Amomum to be paraphyletic but limited sampling and absence of the data of the type Amomum subulatum made it impossible to resolve the paraphyly and make nomenclatural changes. Here, Amomum is further investigated in a multi-marker phylogenetic framework using matK and nrITS including multiple accessions of the type, the genus Elettaria and additional accessions of Amomum, Alpinia, Elettariopsis, Geocharis, Geostachys and Hornstedtia. Amomum is shown to consist of nine clades and Alpinia of six. The genera Elettaria, Elettariopsis, Plagiostachys, and species in Hornstedtia are nested within these clades. Morphological studies of species previously subsumed in Amomum support recognition of new genera that correspond to well-delimited clades in the phylogenetic framework presented here. Recircumscription of the paraphyletic genus Amomum facilitates identification and creates nomenclatural stability. Three genera, Conamomum, Meistera and Wurfbainia, are resurrected, and three new genera Epiamomum, Lanxangia and Sundamomum are described, together with a key to the genera and a nomenclatural synopsis placing 384 specific names (incl. all synonyms) into the new generic framework. Of these 129 represent new combinations and 3 are replacement names. Types of Geocharis and Geostachys are designated. Further studies and specific sampling will be needed to resolve other branches of Alpinioideae containing other polyphyletic genera.

• The evolution of L-DOPA 4,5-dioxygenase activity, encoded by the gene DODA, was a key step in the origin of betalain biosynthesis in Caryophyllales. We previously proposed that L-DOPA 4,5-dioxygenase activity evolved via a single Caryophyllales-specific neofunctionalisation event within the DODA gene lineage. However, this neofunctionalisation event has not been confirmed and the DODA gene lineage exhibits numerous gene duplication events, whose evolutionary significance is unclear. • To address this, we functionally characterised 23 distinct DODA proteins for L-DOPA 4,5-dioxygenase activity, from four betalain-pigmented and five anthocyanin-pigmented species, representing key evolutionary transitions across Caryophyllales. By mapping these functional data to an updated DODA phylogeny, we then explored the evolution of L-DOPA 4,5-dioxygenase activity. • We find that low L-DOPA 4,5-dioxygenase activity is distributed across the DODA gene lineage. In this context, repeated gene duplication events within the DODA gene lineage give rise to polyphyletic occurrences of elevated L-DOPA 4,5-dioxygenase activity, accompanied by convergent shifts in key functional residues and distinct genomic patterns of micro-synteny. • In the context of an updated organismal phylogeny and newly inferred pigment reconstructions, we argue that repeated convergent acquisition of elevated L-DOPA 4,5-dioxygenase activity is consistent with recurrent specialisation to betalain synthesis in Caryophyllales.

The reconstruction of the Tree of Life has relied almost entirely on concatenation methods, which do not accommodate gene tree heterogeneity, a property that simulations and theory have identified as a likely cause of incongruent phytogenies. However, this incongruence has not yet been demonstrated in empirical studies. Several key relationships among eutherian mammals remain controversial and conflicting among previous studies, including the root of eutherian tree and the relationships within Euarchontoglires and Laurasiatheria. Both Bayesian and maximum-likelihood analysis of genome-wide data of 447 nuclear genes from 37 species show that concatenation methods indeed yield strong incongruence in the phylogeny of eutherian mammals, as revealed by subsampling analyses of loci and taxa, which produced strongly conflicting topologies. In contrast, the coalescent methods, which accommodate gene tree heterogeneity, yield a phylogeny that is robust to variable gene and taxon sampling and is congruent with geographic data. The data also demonstrate that incomplete lineage sorting, a major source of gene tree heterogeneity, is relevant to deep-level phylogenies, such as those among eutherian mammals. Our results firmly place the eutherian root between Atlantogenata and Boreoeutheria and support ungulate polyphyly and a sister-group relationship between Scandentia and Primates. This study demonstrates that the incongruence introduced by concatenation methods is a major cause of longstanding uncertainty in the phylogeny of eutherian mammals, and the same may apply to other clades. Our analyses suggest that such incongruence can be resolved using phylogenomic data and coalescent methods that deal explicitly with gene tree heterogeneity.

The Ramalinaceae is the fourth-largest family of lichenized ascomycetes with 42 genera and 913 species exhibiting considerable morphological variation. Historically, generic boundaries in the Ramalinaceae were primarily based on morphological characters. However, molecular systematic investigations of subgroups revealed that current taxonomy is at odds with evolutionary relationships. Tropical members of the family remain particularly understudied, including the large genus Phyllopsora. We have generated and collected multilocus sequence data (mtSSU, nrITS, nrLSU, RPB1, RPB2) for 149 species associated with the Ramalinaceae and present the first comprehensive molecular phylogeny of the family. We used ancestral state reconstructions on our molecular family phylogeny to trace the evolution of character states. Our results indicate that the Ramalinaceae have arisen from an ancestor with long, multiseptate ascospores living in humid temperate forests, and that the phyllopsoroid growth form has evolved multiple times within the family. Based on our results using integrative taxonomy, we discuss sister-relations and taxon-delimitation within five well-supported clades: The Bacidia, Biatora-, Ramalina-, Rolfidium-, and Toninia-groups. We reduce six genera into synonymy and make 49 new nomenclatural combinations. The genera Bacidia, Phyllopsora, Physcidia and Toninia are polyphyletic and herein split into segregates. We describe the two genera Bellicidia and Parallopsora and resurrect the genera Bibbya, Kiliasia, Sporacestra, and Thalloidima. According to our new circumscription, which also includes some additional changes, the family Ramalinaceae now comprises 39 genera.

Coelomycetous fungi are an artificial taxonomic group which produce conidia inside a cavity i.e. conidiomata. Coelomycetes comprise about, 1000 genera and 7000 species, which can be endophytic, pathogenic or saprobic. Traditional classification of coelomycetes was previously based on morphology, such as the shape of conidiomata and mode of conidiogenesis, while it was treated as a distinct group i.e. Deuteromycotina. Sequence based taxonomic studies has been used to accommodate asexual fungi in a natural classification system, resolve generic boundaries of polyphyletic genera and species complexes, as well as establish asexual-sexual links. Nevertheless, most of genera lack sequence data, thus, morphology based identification is still important when introducing new genera or species. In this paper we illustrate, describe, and provide taxonomic notes for 235 dematiaceous coelomycetous genera, including five new genera viz. Apiculospora, Didymellocamarosporium, Melanocamarosporium, Melnikia and Paulkirkia. Phylogenetic analyses of combined sequence data are provided to show placements of dematiaceous coelomycetes in Dothideomycetes, Leotiomycetes and Sordariomycetes. One-hundred and fifty-two (65 %) of genera have sequence data, thus, their taxonomic placement in a natural classification system, is listed as an outline. However, 83 genera still lack sequence data, hence, they are treated as Ascomycota, genera incertae sedis. In addition, separate analyses are provided where better taxonomic resolution is needed.

Robust evidence from phylogenomic analyses of 997 nuclear genes has recently shown, beyond doubt, that the genus Prosopis is polyphyletic with three separate lineages, each with affinities to other genera of mimosoids: (i) Prosopis africana is an isolated lineage placed in the grade of Plathymenia , Newtonia and Fillaeopsis that subtends the core mimosoid clade; (ii) the remaining Old World species of Prosopis form a clade that is sister to the Indo-Nepalese monospecific genus Indopiptadenia and (iii) New World Prosopis has the Namibian / Namaqualand monospecific endemic genus Xerocladia nested within it. This means that it is now clear that maintaining the unity of the genus Prosopis sensu Burkart (1976) is no longer tenable. These three distinct lineages of Prosopis species correspond directly to Burkart’s (1976) sectional classification of the genus, to previously recognised genera and to the differences in types of armature that underpin Burkart’s sections. Here, we address this non-monophyly by resurrecting three segregate genera – Anonychium , Neltuma and Strombocarpa and provide 57 new name combinations where necessary, while maintaining the morphologically distinctive and geographically isolated genera Xerocladia and Indopiptadenia . The genus Prosopis itself is reduced to just three species and an emended description is presented. The impacts of these name changes for a genus of such high ecological and human use importance are discussed. These impacts are mitigated by clear differences in armature which facilitate identification and by potential benefits from the deeper biological understanding brought about by recognition of these divergent lineages at generic rank. We provide an identification key to genera and present a map showing the distributions of the segregate genera, as well as drawings and photos illustrating variation in armature and fruits.