New long-horned caddisfly genus and species of Leptoceridae (Insecta: Trichoptera) from Brazil

Ibyacerina caparao new genus, new species (Trichoptera: Leptoceridae) is described and illustrated from specimens collected at Serra do Caparaó, Minas Gerais, Brazil. The monotypic genus is characterized by tibial spur formula 0,2,2; preanal appendages originating from a single base with a median process; tergum X broad, heavily sclerotized, saddle-like, wider at apex, and upturned, bearing small stout setae; inferior appendages each 3-branched, setose; and phallic apparatus tubular, curved slightly ventrad, with pair of lateral processes. Phylogenetic Bayesian and maximum likelihood analyses based on concatenated cytochrome oxidase I (COI) and carbamoyl-phosphate synthetase (CAD) partial sequences (1,504 bp) including representatives of 38 leptocerid genera positioned Ibyacerina gen. nov. with good support within Leptocerinae. However, due to low branch support of most relationships among genera within the clade of Leptocerinae, except Mystacidini, Setodini, and Leptocerini, its close affinities and tribal placement are still unknown.

Standardized genome-wide function prediction enables comparative functional genomics in plants: a new application area for Gene Ontologies

BackgroundGenome-wide gene function annotations are useful for hypothesis generation and for prioritizing candidate genes responsible for phenotypes of interest. We functionally annotated the genes of 18 crop plant genomes across 14 species using the GOMAP pipeline.ResultsBy comparison to existing GO annotation datasets available for a subset of these genomes, GOMAP-generated datasets cover more genes, assign more GO terms, and produce datasets similar in quality (based on precision and recall metrics using existing gold standards as the basis for comparison). From there, we sought to determine whether the datasets could be used in tandem to carry out comparative functional genomics analyses. As a test of the idea and a proof of concept, we created parsimony and distance-based dendrograms of relatedness based on functions for all 18 genomes. These dendrograms were compared to well-established species-level phylogenies to determine whether trees derived through the analysis of gene function agree with known evolutionary histories, which they largely do. Where discrepancies were observed, we determined branch support based on jack-knifing then removed individual annotation sets by genome to identify the annotation sets causing errant relationships.ConclusionsBased on the results of these analyses, it is clear that for genome assembly and annotation products of similar quality, GOMAP-derived functional annotations used together across species do retain sufficient biological signal to recover known phylogenetic relationships, indicating that comparative functional genomics across species based on GO data hold promise as a tool for generating novel hypotheses about gene function and traits.

Evaluating Results

This chapter explores the tools used to evaluate the quality and plausibility of results of phylogenetic analyses. The term “fit” has been widely used in the phylogenetic literature to indicate the degree to which data conform to (or are explained by) a cladogram. The most commonly used measure of fit applied to discrete character data is the consistency index, or ci. Meanwhile, measures of synapomorphy are less frequently reported than the consistency index. The chapter then considers the resolution of branches; multiple equally parsimonious cladograms; successive approximations weighing; and data decisiveness. It also differentiates between total evidence and consensus, before describing supertrees. Finally, the chapter looks at approaches for evaluating support or stability of phylogenetic results, including branch support, jackknifing, bootstrapping, randomization tests, and sensitivity analysis.

Exploring the impact of unstable terminals on branch support values in paleontological data

Recent studies have acknowledged the many benefits of including fossils in phylogenetic inference (e.g., reducing long-branch attraction). However, unstable taxa are known to be problematic, as they can reduce either the resolution of the strict consensus or branch support. In this study, we evaluate whether unstable taxa that reduce consensus resolution affect support values, and the extent of such impact, under equal and extended implied weighting. Two sets of analyses were conducted across 30 morphological datasets to evaluate complementary aspects. The first focused on the analytical conditions incrementing the terminal instability, while the second assessed whether pruning wildcards improves support. Changes in support were compared with the “number of nodes collapsed by unstable terminals,” their “distance to the root,” the “proportion of missing data in a dataset,” and the “proportion of sampled characters.” Our results indicate that the proportion of missing entries distributed among closely related taxa (for a given character) might be as detrimental for stability as those distributed among characters (for a given terminal). Unstable terminals that (1) collapse few nodes or (2) are closely located to the root node have more influence on the estimated support values. Weighting characters according to their extra steps while assuming that missing entries contribute to their homoplasy reduced the instability of wildcards. Our results suggest that increasing character sampling and using extended implied weighting decreases the impact of wildcard terminals. This study provides insights for designing future research dealing with unstable terminals, a typical problem of paleontological data.

What can genome analysis offer for bacteria?

This book chapter is organized as follows: (i) the main approaches to the philosophy of taxonomic classification are recapitulated; (ii) the paradigm of polyphasic taxonomy is discussed in this context; (iii) the causes of conflict between previous classifications and genome-scale analyses are investigated, using examples from recent phylum-wide studies, with a discussion of how markers used in polyphasic taxonomy can be replaced by genome-derived ones; and (iv) the challenges in assigning taxonomic ranks using genome-scale or other data are revisited. The conclusion assesses the chances, or lack thereof, of reconciling taxonomic classifications. Phenetic and phylogenetic thinking still compete with each other on the classification of bacteria, with potentially conflicting and confusing results. Some causes of problematic taxonomic classifications are independent of the type and number of characters that can be used and can only be mitigated if, for example, taxon sampling and branch support are more appropriately taken into account. It may be possible to devise objective criteria for separating bacterial species, but the currently dominating approaches for microbial species delineation may be inadequate. It is even harder to delineate higher taxa; in contrast to claims in the literature, it may prove to be impossible to objectively assign taxonomic ranks above species level.

Figs S1-S3

Fig. S1. Maximum likelihood tree based on ITS dataset. Branch support values >75 % and Bayesian posterior probabilities > 0.90 are indicated. Symbols with closed circles represent gasteroid taxa, symbols with half circles represent secotoid taxa, and all other taxa are agaricoid. Limacella glioderma was used as an outgroup.Fig. S2. Maximum likelihood tree based on LSU dataset. Branch support values >75 % and Bayesian posterior probabilities > 0.90 are indicated. Symbols with closed circles represent gasteroid taxa, symbols with half circles represent secotoid taxa, and all other taxa are agaricoid. Limacella glioderma was used as an outgroup. Fig. S3. Maximum likelihood tree based on concatenated LSU, rpb2, and tef1 dataset with ambiguously aligned regions excluded. Branch bootstrap support values >75 % and Bayesian posterior probabilities > 0.90 are indicated. Limacella delicata, Limacella glioderma and Limacella guttata were used as an outgroup.

Target-capture phylogenomics provide insights on gene and species tree discordances in Old World treefrogs (Anura: Rhacophoridae)

Genome-scale data have greatly facilitated the resolution of recalcitrant nodes that Sanger-based datasets have been unable to resolve. However, phylogenomic studies continue to use traditional methods such as bootstrapping to estimate branch support; and high bootstrap values are still interpreted as providing strong support for the correct topology. Furthermore, relatively little attention has been given to assessing discordances between gene and species trees, and the underlying processes that produce phylogenetic conflict. We generated novel genomic datasets to characterize and determine the causes of discordance in Old World treefrogs (Family: Rhacophoridae)—a group that is fraught with conflicting and poorly supported topologies among major clades. Additionally, a suite of data filtering strategies and analytical methods were applied to assess their impact on phylogenetic inference. We showed that incomplete lineage sorting was detected at all nodes that exhibited high levels of discordance. Those nodes were also associated with extremely short internal branches. We also clearly demonstrate that bootstrap values do not reflect uncertainty or confidence for the correct topology and, hence, should not be used as a measure of branch support in phylogenomic datasets. Overall, we showed that phylogenetic discordances in Old World treefrogs resulted from incomplete lineage sorting and that species tree inference can be improved using a multi-faceted, total-evidence approach, which uses the most amount of data and considers results from different analytical methods and datasets.

A new species of Nidirana from the N. pleuraden group (Anura, Ranidae) from western Yunnan, China

The Music Frog genus Nidirana was recently resurrected as a distinct genus and contains 14 species distributed in subtropical eastern and southeastern Asia. The species diversity of Nidirana is dramatically underestimated, and half of its species was described in the last five years. In this study, Nidirana occidentalis sp. nov., a new species of Music Frog from western Yunnan, China, is proposed based on morphological and molecular evidences. The new species was previously misidentified as N. pleuraden, but can be distinguished from the true N. pleuraden from eastern Yunnan, and all other congeners, by a combination of morphological characteristics, and significant divergence in the mitochondrial genes (≥ 5.1% in 16S and ≥ 8.9% in CO1). Nidirana occidentalis sp. nov. is assigned to the N. pleuraden group on the basis of morphological characters, but its phylogenetic placement remains unresolved due to weak branch support. Geographically, these two species are isolated by the Red River in Yunnan, supporting the hypothesis that the Red River is an important geographical barrier that drives speciation in flora and fauna. Nidirana occidentalis sp. nov. represents the second species of N. pleuraden group and the 15th species of the genus.

An Evolving View of Phylogenetic Support

If all nucleotide sites evolved at the same rate within molecules and throughout the history of lineages, if all nucleotides were in equal proportion, if any nucleotide or amino acid evolved to any other with equal probability, if all taxa could be sampled, if diversification happened at well-spaced intervals, and if all gene segments had the same history, then tree building would be easy. But of course, none of those conditions are true. Hence, the need for evaluating the information content and accuracy of phylogenetic trees. The symposium for which this historical essay and presentation were developed focused on the importance of phylogenetic support, specifically branch support for individual clades. Here, I present a timeline and review significant events in the history of systematics that set the stage for the development of the sophisticated measures of branch support and examinations of the information content of data highlighted in this symposium. [Bayes factors; bootstrap; branch support; concordance factors; internode certainty; posterior probabilities; spectral analysis; transfer bootstrap expectation.]

A new genus Vittaliana belonging to the tribe Opsiini (Hemiptera: Cicadellidae) from India and its molecular phylogeny

The new leafhopper genus Vittalianareticulata gen. nov., sp. nov., is described from India, and placed in the tribe Opsiini based on ocelli close to eyes, without carina on anterior margin of the face and bifurcate aedeagus with two gonopores. Phylogenetic analysis with maximum likelihood (ML) using IQtree v1.4.1 of combined data (Histone H3 and 28S rDNA) reveals that the new genus Vittaliana belongs to a clade consisting of Opsius versicolor (Distant, 1908), Opsiini gen. sp., Libengaia sp., Hishimonus phycitis (Distant, 1908) and Yinfomibus menglaensis Du, Liang & Dai (2019) with good branch support, and that the tribe Opsiini is paraphyletic. This resolves the placement of a new genus in the tribe Opsiini under Deltocephalinae.