Phylogeny of Amathusiini butterflies based on adult morphology (Lepidoptera, Nymphalidae, Satyrinae)

Based on comparative morphology of adults, a phylogeny is proposed for the butterfly tribe Amathusiini (Nymphalidae, Satyrinae). The dataset includes 92 characters scored for 45 species in 12 genera, representing the most comprehensive phylogenetic analysis for this group. Parsimony analyses produced a well-resolved strict consensus tree where genera were divided in three main groups: (clade 1) Stichophthalma; (clade 2) Aemona, Faunis, Melanocyma and Taenaris; (clade 3) Enispe, Discophora, Thaumantis, Thauria, Amathusia, Amathuxidia, and Zeuxidia. While genera in clades 1 and 2 were found to be morphologically homogeneous, clade 3 showed remarkable morphological divergence between and within genera. The monophyly of most genera was recovered with variable levels of support, but Melanocyma and Taenaris nested within Faunis. Therefore, here Melanocyma NEW SYN. is subsumed within Faunis, and Taenaris STAT. REV. is regarded as a subgenus of Faunis. Mimicry likely evolved a single time within the Faunis-Taenaris assemblage, as species of Taenaris formed a monophyletic group. Results are compared to early classifications and recent DNA-based analyses, and points of agreement and conflicts are discussed.

ConTreeDP: A consensus method of tumor trees based on maximum directed partition support problem

Phylogenetic inference has become a crucial tool for interpreting cancer genomic data, but continuing advances in our understanding of somatic mutability in cancer, genomic technolo- gies for profiling it, and the scale of data available have created a persistent need for new algorithms able to deal with these challenges. One particular need has been for new forms of consensus tree algorithms, which present special challenges in the cancer space for dealing with heterogeneous data, short evolutionary time scales, and rapid mutation by a wide variety of somatic mutability mechanisms. We develop a new consensus tree method for clonal phy- logenetics, ConTreeDP, based on a formulation of the Maximum Directed Partition Support Consensus Tree (MDPSCT) problem. We demonstrate theoretically and empirically that our approach can efficiently and accurately compute clonal consensus trees from cancer genomic data.

CoVizu: Rapid analysis and visualization of the global diversity of SARS-CoV-2 genomes

Phylogenetics has played a pivotal role in the genomic epidemiology of SARS-CoV-2, such as tracking the emergence and global spread of variants, and scientific communication. However, the rapid accumulation of genomic data from around the world - with over two million genomes currently available in the GISAID database - is testing the limits of standard phylogenetic methods. Here, we describe a new approach to rapidly analyze and visualize large numbers of SARS-CoV-2 genomes. Using Python, genomes are filtered for problematic sites, incomplete coverage, and excessive divergence from a strict molecular clock. All differences from the reference genome, including indels, are extracted using minimap2, and compactly stored as a set of features for each genome. For each Pango lineage (https://cov-lineages.org), we collapse genomes with identical features into 'variants', generate 100 bootstrap samples of the feature set union to generate weights, and compute the symmetric differences between the weighted feature sets for every pair of variants. The resulting distance matrices are used to generate neigihbor-joining trees in RapidNJ and converted into a majority-rule consensus tree for the lineage. Branches with support values below 50% or mean lengths below 0.5 differences are collapsed, and tip labels on affected branches are mapped to internal nodes as directly-sampled ancestral variants. Currently, we process about 1.6 million genomes in approximately nine hours on 34 cores. The resulting trees are visualized using the JavaScript framework D3.js as 'beadplots', in which variants are represented by horizontal line segments, annotated with beads representing samples by collection date. Variants are linked by vertical edges to represent branches in the consensus tree. These visualizations are published at https://filogeneti.ca/CoVizu. All source code was released under an MIT license at https://github.com/PoonLab/covizu.

Rapid radiation of the inner Indo-European languages: an advanced approach to Indo-European lexicostatistics

In this article we present a new reconstruction of Indo-European phylogeny based on 13 110-item basic wordlists for protolanguages of IE subgroups (Proto-Germanic, Proto-Slavic, etc.) or ancient languages of the corresponding subgroups (Hittite, Ancient Greek, etc.). We apply reasonably formal techniques of linguistic data collection and post-processing (onomasiological reconstruction, derivational drift elimination, homoplastic optimization) that have been recently proposed or specially developed for the present study. We use sequential phylogenetic workflow and obtain a consensus tree based on several algorithms (Bayesian inference, maximum parsimony, neighbor joining; without topological constraints applied). The resulting tree topology and datings are entirely compatible with established expert views. Our main finding is the multifurcation of the Inner IE clade into four branches ca. 3357–2162 bc: (1) Greek-Armenian, (2) Albanian, (3) Italic-Germanic-Celtic, (4) Balto-Slavic–Indo-Iranian. The proposed radiation scenario may be reconciled with diverse opinions on Inner IE branchings previously expressed by Indo-Europeanists.

Building alternative consensus trees and supertrees using k-means and Robinson and Foulds distance

Each gene has its own evolutionary history which can substantially differ from the evolutionary histories of other genes. For example, some individual genes or operons can be affected by specific horizontal gene transfer and recombination events. Thus, the evolutionary history of each gene should be represented by its own phylogenetic tree which may display different evolutionary patterns from the species tree that accounts for the main patterns of vertical descent. The output of traditional consensus tree or supertree inference methods is a unique consensus tree or supertree. Here, we describe a new efficient method for inferring multiple alternative consensus trees and supertrees to best represent the most important evolutionary patterns of a given set of phylogenetic trees (i.e. additive trees or X-trees). We show how a specific version of the popular k-means clustering algorithm, based on some interesting properties of the Robinson and Foulds topological distance, can be used to partition a given set of trees into one (when the data are homogeneous) or multiple (when the data are heterogeneous) cluster(s) of trees. We adapt the popular Caliński-Harabasz, Silhouette, Ball and Hall, and Gap cluster validity indices to tree clustering with k-means. A special attention is paid to the relevant but very challenging problem of inferring alternative supertrees, built from phylogenies constructed for different, but mutually overlapping, sets of taxa. The use of the Euclidean approximation in the objective function of the method makes it faster than the existing tree clustering techniques, and thus perfectly suitable for the analysis of large genomic datasets. In this study, we apply it to discover alternative supertrees characterizing the main patterns of evolution of SARS-CoV-2 and the related betacoronaviruses.

Molecular phylogeny of Atractocarpus (Rubiaceae): taxonomic implications for several New Caledonian Gardenieae species

Background and aims – New Caledonia is a hotspot of biodiversity in the world. Among the most diverse New Caledonian plant families is Rubiaceae, which consist of 30 genera containing 220 species, with a level of endemism of 93%. The tribe Gardenieae is represented by four genera, Gardenia (8 species), Aidia (2 species), Randia (7 species), and Atractocarpus (10 species). As Randia has now been restricted to the Neotropics, the New Caledonian Randia species remain unplaced within the tribe. Atractocarpus is a Pacific genus, easily characterized by long imbricated stipules, a feature also present in the Randia species and in several Gardenia species in New Caledonia. The aims of the present study are to test the monophyly of Atractocarpus and to assess the phylogenetic placement of the Randia and Gardenia species with long imbricated stipules within Gardenieae and specifically their relationships with taxa of the Porterandia group to which Atractocarpus belongs. Material and methods – We investigated 63 species of Pacific Gardenieae, with a focus on the Porterandia group, in a Bayesian phylogenetic reconstruction (cpDNA: trnTF and rpl32, and nrDNA: ITS). Key results – Our study provides a mostly supported consensus tree topology of the Porterandia group. Five Gardenia and seven Randia species fall within a clade that comprises the New Caledonian Atractocarpus species, rendering both Atractocarpus and Gardenia polyphyletic. Conclusion – We enlarge the delimitation of Atractocarpus to include 12 New Caledonian Randia and Gardenia species. New Caledonia is consequently confirmed as the centre of diversity for Atractocarpus with 31 species. According to our study, three genera of Gardenieae occur in the archipelago: Aidia, Gardenia, and Atractocarpus.

A combined molecular and morphological phylogeny of the Loricariinae (Siluriformes: Loricariidae), with emphasis on the Harttiini and Farlowellini

We present a combined molecular and morphological phylogenetic analysis of the Loricariinae, with emphasis on the Harttiini (Cteniloricaria, Harttia, and Harttiella) and Farlowellini (Aposturisoma, Farlowella, Lamontichthys, Pterosturisoma, Sturisoma, and Sturisomatichthys). Character sampling comprised seven molecular markers (the mitochondrial Cytb, nd2, 12S and 16S, and the nuclear MyH6, RAG1 and RAG2) and 196 morphological characters. A total of 1,059 specimens, and 159 tissue samples were analized, representing 100 species. A Bayesian Inference analysis was performed using the concatenated data matrix, which is comprised of 6,819 characters. The Loricariinae were found to comprise the tribes (Hartiini (Loricariini, Farlowellini)), the latter two elevated from subtribes. A Maximum Parsimony analysis was also performed using the same data matrix in order to reveal phenotypical synapomorphies to diagnose each clade. Two MP trees were found with a length of 14,704 steps, consistency index of 0.29 and retention index of 0.61, which were summarized in a strict consensus tree. Harttiini includes (Harttiella (Cteniloricaria, Harttia), and Farlowellini includes (Lamontichthys (Pterosturisoma (Sturisoma (Sturisomatichthys, Farlowella)))). Aposturisoma was recovered nested within Farlowella and is synonymyzed to the latter. Sturisoma was corroborated as strictly cis-Andean, while Sturisomatichthys encompasses, besides the valid species already included in the genus, the trans-Andean species once belonging to Sturisoma sensu lato. Identification keys and phylogenetic diagnoses of family-group taxa and genera of both the Harttiini and the Farlowellini are provided.

A complete time-calibrated multi-gene phylogeny of the European butterflies

With the aim of supporting ecological analyses in butterflies, the third most species-rich superfamily of Lepidoptera, this paper presents the first time-calibrated phylogeny of all 496 extant butterfly species in Europe, including 18 very localised endemics for which no public DNA sequences had been available previously. It is based on a concatenated alignment of the mitochondrial gene COI and up to eleven nuclear gene fragments, using Bayesian inferences of phylogeny. To avoid analytical biases that could result from our region-focussed sampling, our European tree was grafted upon a global genus-level backbone butterfly phylogeny for analyses. In addition to a consensus tree, the posterior distribution of trees and the fully concatenated alignment are provided for future analyses. Altogether a complete phylogenetic framework of European butterflies for use by the ecological and evolutionary communities is presented.

Detection and skeletonization of single neurons and tracer injections using topological methods

Neuroscientific data analysis has traditionally relied on linear algebra and stochastic process theory. However, the tree-like shapes of neurons cannot be described easily as points in a vector space (the subtraction of two neuronal shapes is not a meaningful operation), and methods from computational topology are better suited to their analysis. Here we introduce methods from Discrete Morse (DM) Theory to extract the tree-skeletons of individual neurons from volumetric brain image data, and to summarize collections of neurons labelled by tracer injections. Since individual neurons are topologically trees, it is sensible to summarize the collection of neurons using a consensus tree-shape that provides a richer information summary than the traditional regional ‘connectivity matrix’ approach. The conceptually elegant DM approach lacks hand-tuned parameters and captures global properties of the data as opposed to previous approaches which are inherently local. For individual skeletonization of sparsely labelled neurons we obtain substantial performance gains over state-of-the-art non-topological methods (over 10% improvements in precision and faster proofreading). The consensus-tree summary of tracer injections incorporates the regional connectivity matrix information, but in addition captures the collective collateral branching patterns of the set of neurons connected to the injection site, and provides a bridge between single-neuron morphology and tracer-injection data.

Estimating Bifurcating Consensus Phylogenetic Trees Using Evolutionary Imperialist Competitive Algorithm

Background:One of the important goals of phylogenetic studies is the estimation of species-level phylogeny. A phylogenetic tree is an evolutionary classification of different species of creatures. There are several methods to generate such trees, where each method may produce a number of different trees for the species. By choosing the same proteins of all species, it is possible that the topology and arrangement of trees would be different.Objective:There are methods by which biologists summarize different phylogenetic trees to a tree, called consensus tree. A consensus method deals with the combination of gene trees to estimate a species tree. As the phylogenetic trees grow and their number is increased, estimating a consensus tree based on the species-level phylogenetic trees becomes a challenge.Methods:The current study aims at using the Imperialist Competitive Algorithm (ICA) to estimate bifurcating consensus trees. Evolutionary algorithms like ICA are suitable to resolve problems with the large space of candidate solutions.Results:The obtained consensus tree has more similarity to the native phylogenetic tree than related studies.Conclusion:The proposed method enjoys mechanisms and policies that enable us more than other evolutionary algorithms in tuning the proposed algorithm. Thanks to these policies and the mechanisms, the algorithm enjoyed efficiently in obtaining the optimum consensus tree. The algorithm increased the possibility of selecting an optimum solution by imposing some changes in its parameters.