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Leaf venation is a pivotal trait in the success of vascular plants. Whereas gymnosperms have single or sparsely branched parallel veins, angiosperms developed a hierarchical structure of veins that form a complex reticulum. Its physiological consequences are considered to have enabled angiosperms to dominate terrestrial ecosystems in the Late Cretaceous and Cenozoic. Although a hierarchical-reticulate venation also occurs in some groups of extinct seed plants, it is unclear whether these are stem relatives of angiosperms or have evolved these traits in parallel. Here, we re-examine the morphology of the enigmatic foliage taxon Furcula, a potential early Mesozoic angiosperm relative, and argue that its hierarchical vein network represents convergent evolution (in the Late Triassic) with flowering plants (which developed in the Early Cretaceous) based on details of vein architecture and the absence of angiosperm-like stomata and guard cells. We suggest that its nearest relatives are Peltaspermales similar to Scytophyllum and Vittaephyllum, the latter being a genus that originated during the Late Triassic (Carnian) and shares a hierarchical vein system with Furcula. We further suggest that the evolution of hierarchical venation systems in the early Permian, the Late Triassic, and the Early Cretaceous represent 'natural experiments' that might help resolve the selective pressures enabling this trait to evolve., (© 2024 The Authors New Phytologist © 2024 New Phytologist Foundation.)

The systematics of Hypotricha is one of the most puzzling problems in ciliate biology, having spanned numerous conflicting hypotheses with unstable relationships at various levels in molecular trees, for which the constant addition of newly discovered species has only increased the confusion. The hypotrichs comprise a remarkable morphologically diversified group of ciliates, and the phylogenetic potential of morphological traits is generally recognized. However, such characters were rarely used in phylogenetic reconstructions, and congruence with molecular data never assessed from simultaneous analyses. To properly reconciliate morphological and molecular information, maximum-likelihood and parsimony analyses of 79 morphological characters and 18S rDNA sequences were performed for 130 ingroup terminals, broadly sampled to represent the known hypotrich diversity. As result, well-supported and relatively stable clades were recovered, based on which the redefined Hypotricha comprises at least six higher taxa: The "arcuseriids", Holostichida, Parabirojimida, and the "amphisiellids", plus the two large clades Kentrurostylida nov. tax. (Hispidotergida nov. tax. and Simplicitergida nov. tax.) and Diatirostomata nov. tax. ("bistichellids", "kahliellids", Gonostomatida and Dorsomarginalia [Postoralida nov. tax. and Uroleptida]). Each taxon was circumscribed by synapomorphies, of which most were homoplastic, as the natural history of hypotrichs is portrayed by an outstanding quantity of convergences and reversions., (Copyright © 2020 Elsevier GmbH. All rights reserved.)

Bayesian analysis of morphological data is becoming increasingly popular mainly (but not only) because it allows for time-calibrated phylogenetic inference using relaxed morphological clocks and tip dating whenever fossils are available. As with molecular data, recent studies have shown that modeling among-character rate variation (ACRV) in morphological matrices greatly improves phylogenetic inference. In a likelihood framework this may be accomplished, for instance, by employing a hidden Markov model to assign characters to rate categories drawn from a (discretized) $\Gamma$ distribution and/or by partitioning data sets according to rate heterogeneity and estimating per-partition branch lengths, conditioned on a single topology. While the first approach is available in many phylogenetic analysis software, there is still no clear consensus on how to partition data, except perhaps in the simplest cases (e.g., "by codon" partitioning of coding sequences). Additionally, there is a trade-off between improvement in likelihood scores and the number of free parameters in the analysis, which rises quickly with the number of partitions. This trade-off may be dealt with by employing statistics that penalize overfitting of complex models, such as Akaike or Bayesian information criteria, or the more recently introduced stepping-stone method for marginal likelihood approximation. We applied the latter to three distinct matrices of discrete morphological data and demonstrated that sorting characters by homoplasy scores (obtained from implied weighting parsimony analysis) outperformed other partitioning strategies (anatomically-based and PartitionFinder2). The method was in fact so efficient in segregating characters by rates of evolution that no within-partition ACRV modeling was necessary, while among-partition rate variation was adequately accommodated by rate multipliers. We conclude that partitioning by homoplasy is a powerful and easy-to-implement strategy to address ACRV in complex data sets. We provide some guidelines focusing on morphological matrices, although this approach may be also applicable to molecular data sets., (© The Author(s) 2019. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

A homoplasy is a nucleotide identity resulting from a process other than inheritance from a common ancestor. Importantly, by distorting the ancestral relationships between nucleotide sequences, homoplasies can change the structure of the phylogeny. Homoplasies can emerge naturally, especially under high selection pressures and/or high mutation rates, or be created during the generation and processing of sequencing data. Identification of homoplasies is critical, both to understand their influence on the analyses of phylogenetic data and to allow an investigation into how they arose. Here we present HomoplasyFinder, a java application that can be used as a stand-a-lone tool or within the statistical programming environment R. Within R and Java, HomoplasyFinder is shown to be able to automatically, and quickly, identify any homoplasies present in simulated and real phylogenetic data. HomoplasyFinder can easily be incorporated into existing analysis pipelines, either within or outside of R, allowing the user to quickly identify homoplasies to inform downstream analyses and interpretation.

Convergent evolution-the appearance of the same character state in apparently unrelated organisms-is often inferred when a trait is incongruent with the species tree. However, trait incongruence can also arise from changes that occur on discordant gene trees, a process referred to as hemiplasy. Hemiplasy is rarely taken into account in studies of convergent evolution, despite the fact that phylogenomic studies have revealed rampant discordance. Here, we study the relative probabilities of homoplasy (including convergence and reversal) and hemiplasy for an incongruent trait. We derive expressions for the probabilities of the two events, showing that they depend on many of the same parameters. We find that hemiplasy is as likely-or more likely-than homoplasy for a wide range of conditions, even when levels of discordance are low. We also present a method to calculate the ratio of these two probabilities (the "hemiplasy risk factor") along the branches of a phylogeny of arbitrary length. Such calculations can be applied to any tree to identify when and where incongruent traits may be due to hemiplasy., Competing Interests: The authors declare no conflict of interest., (Copyright © 2018 the Author(s). Published by PNAS.)

Simultaneously analysing morphological, molecular and stratigraphic data suggests a potential resolution to a major remaining inconsistency in crocodylian evolution. The ancient, long-snouted thoracosaurs have always been placed near the Indian gharial Gavialis , but their antiquity ( ca 72 Ma) is highly incongruous with genomic evidence for the young age of the Gavialis lineage ( ca 40 Ma). We reconcile this contradiction with an updated morphological dataset and novel analysis, and demonstrate that thoracosaurs are an ancient iteration of long-snouted stem crocodylians unrelated to modern gharials. The extensive similarities between thoracosaurs and Gavialis are shown to be an almost 'perfect storm' of homoplasy, combining convergent adaptions to fish-eating, as well resemblances between genuinely primitive traits (thoracosaurs) and atavisms ( Gavialis ). Phylogenetic methods that ignore stratigraphy (parsimony and undated Bayesian methods) are unable to tease apart these similarities and invariably unite thoracosaurs and Gavialis. However, tip-dated Bayesian approaches additionally consider the large temporal gap separating ancient (thoracosaurs) and modern ( Gavialis ) iterations of similar long-snouted crocodyliforms. These analyses robustly favour a phylogeny which places thoracosaurs basal to crocodylians, far removed from modern gharials, which accordingly are a very young radiation. This phylogenetic uncoupling of ancient and modern gharial-like crocs is more consistent with molecular clock divergence estimates, and also the bulk of the crocodylian fossil record (e.g. all unequivocal gharial fossils are very young). Provided that the priors and models attribute appropriate relative weights to the morphological and stratigraphic signals-an issue that requires investigation-tip-dating approaches are potentially better able to detect homoplasy and improve inferences about phylogenetic relationships, character evolution and divergence dates., (© 2018 The Author(s).)

After decades of molecular phylogenetic studies, the deep phylogeny of gymnosperms has not been resolved, and the phylogenetic placement of Gnetales remains one of the most controversial issues in seed plant evolution. To resolve the deep phylogeny of seed plants and to address the sources of phylogenetic conflict, we conducted a phylotranscriptomic study with a sampling of all 13 families of gymnosperms and main lineages of angiosperms. Multiple datasets containing up to 1 296 042 sites across 1308 loci were analysed, using concatenation and coalescence approaches. Our study generated a consistent and well-resolved phylogeny of seed plants, which places Gnetales as sister to Pinaceae and thus supports the Gnepine hypothesis. Cycads plus Ginkgo is sister to the remaining gymnosperms. We also found that Gnetales and angiosperms have similar molecular evolutionary rates, which are much higher than those of other gymnosperms. This implies that Gnetales and angiosperms might have experienced similar selective pressures in evolutionary histories. Convergent molecular evolution or homoplasy is partially responsible for the phylogenetic conflicts in seed plants. Our study provides a robustly reconstructed backbone phylogeny that is important for future molecular and morphological studies of seed plants, in particular gymnosperms, in the light of evolution., (© 2018 The Author(s).)

This paper discusses the problem of whether creating a matrix with all the character state combinations that have a fixed number of steps (or extra steps) on a given tree T, produces the same tree T when analyzed with maximum parsimony or maximum likelihood. Exhaustive enumeration of cases up to 20 taxa for binary characters, and up to 12 taxa for 4-state characters, shows that the same tree is recovered (as unique most likely or most parsimonious tree) as long as the number of extra steps is within 1/4 of the number of taxa. This dependence, 1/4 of the number of taxa, is discussed with a general argumentation, in terms of the spread of the character changes on the tree used to select character state distributions. The present finding allows creating matrices which have as much homoplasy as possible for the most parsimonious or likely tree to be predictable, and examination of these matrices with hill-climbing search algorithms provides additional evidence on the (lack of a) necessary relationship between homoplasy and the ability of search methods to find optimal trees., (Copyright © 2018 Elsevier Inc. All rights reserved.)

The longhorn bee tribe Eucerini (Hymenoptera: Apidae) is a diverse, widely distributed group of solitary bees that includes important pollinators of both wild and agricultural plants. About half of the species in the tribe are currently assigned to the genus Eucera and to a few other related genera. In this large genus complex, comprising ca. 390 species, the boundaries between genera remain ambiguous due to morphological intergradation among taxa. Using ca. 6700 aligned nucleotide sites from six gene fragments, 120 morphological characters, and more than 100 taxa, we present the first comprehensive molecular, morphological, and combined phylogenetic analyses of the 'Eucera complex'. The revised generic classification that we propose is congruent with our phylogeny and maximizes both generic stability and ease of identification. Under this new classification most generic names are synonymized under an expanded genus Eucera. Thus, Tetralonia, Peponapis, Xenoglossa, Cemolobus, and Syntrichalonia are reduced to subgeneric rank within Eucera, and Synhalonia is retained as a subgenus of Eucera. Xenoglossodes is reestablished as a valid subgenus of Eucera while Tetraloniella is synonymized with Tetralonia and Cubitalia with Eucera. In contrast, we suggest that the venusta-group of species, currently placed in the subgenus Synhalonia, should be recognized as a new genus. Our results demonstrate the need to evaluate convergent loss or gain of important diagnostic traits to minimize the use of potentially homoplasious characters when establishing classifications. Lastly, we show that the Eucera complex originated in the Nearctic region in the late Oligocene, and dispersed twice into the Old World. The first dispersal event likely occurred 24.2-16.6 mya at a base of a clade of summer-active bees restricted to warm region of the Old World, and the second 13.9-12.3 mya at the base of a clade of spring-active bees found in cooler regions of the Holarctic. Our results further highlight the role of Beringia as a climate-regulated corridor for bees., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Percomorph fishes represent over 17,100 species, including several model organisms and species of economic importance. Despite continuous advances in the resolution of the percomorph Tree of Life, resolution of the sister lineage to Percomorpha remains inconsistent but restricted to a small number of candidate lineages. Here we use an anchored hybrid enrichment (AHE) dataset of 132 loci with over 99,000 base pairs to identify the sister lineage of percomorph fishes. Initial analyses of this dataset failed to recover a strongly supported sister clade to Percomorpha, however, scrutiny of the AHE dataset revealed a bias towards high GC content at fast-evolving codon partitions (GC bias). By combining several existing approaches aimed at mitigating the impacts of convergence in GC bias, including RY coding and analyses of amino acids, we consistently recovered a strongly supported clade comprised of Holocentridae (squirrelfishes), Berycidae (Alfonsinos), Melamphaidae (bigscale fishes), Cetomimidae (flabby whalefishes), and Rondeletiidae (redmouth whalefishes) as the sister lineage to Percomorpha. Additionally, implementing phylogenetic informativeness (PI) based metrics as a filtration method yielded this same topology, suggesting PI based approaches will preferentially filter these fast-evolving regions and act in a manner consistent with other phylogenetic approaches aimed at mitigating GC bias. Our results provide a new perspective on a key issue for studies investigating the evolutionary history of more than one quarter of all living species of vertebrates., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Pitheciids, one of the major radiations of New World monkeys endemic to South and Central America, are distributed in the Amazon and Orinoco basins, and include Callicebus, Cacajao, Chiropotes, and Pithecia. Molecular phylogenetics strongly support pitheciid monophyly, whereas morphological analyses infer a range of phylogenies including a sister relationship between Aotus and Callicebus. We collected geometric morphometric cranial data from pitheciids and Aotus, and used cranial data for distance-based phylogenetic analysis and tests of phylogenetic signal. Phylogenetic analyses of pitheciids were repeated with Lagothrix, Callimico, and Saimiri outgroups for Procrustes shape with and without Aotus based on the whole cranium and six anatomical regions. All phylogenetic signal tests were significant, and tree lengths were shortest and had the least morphological change over the phylogeny for Procrustes residuals from the cranial base and palate. The majority of phylogenetic analyses of Procrustes shape for pitheciids without Aotus supported the molecular phylogeny, and with Aotus included the majority inferred an Aotus-Callicebus clade, although three analyses with Callimico as outgroup supported the molecular phylogeny. The morphological similarity of Aotus and Callicebus is likely a mix of plesiomorphy, allometry, and homoplasy, and future phylogenetic inference of living and extinct platyrrhine taxa should consider the impact of these factors alongside outgroup selection and cranial region., (© 2016 Wiley Periodicals, Inc.)

Since its original inception over 150 years ago by Darwin, we have made tremendous progress toward the reconstruction of the Tree of Life. In particular, the transition from analyzing datasets comprised of small numbers of loci to those comprised of hundreds of loci, if not entire genomes, has aided in resolving some of the most vexing of evolutionary problems while giving us a new perspective on biodiversity. Correspondingly, phylogenetic trees have taken a central role in fields that span ecology, conservation, and medicine. However, the rise of big data has also presented phylogenomicists with a new set of challenges to experimental design, quantitative analyses, and computation. The sequencing of a number of very first genomes presented significant challenges to phylogenetic inference, leading fungal phylogenomicists to begin addressing pitfalls and postulating solutions to the issues that arise from genome-scale analyses relevant to any lineage across the Tree of Life. Here we highlight insights from fungal phylogenomics for topics including systematics and species delimitation, ecological and phenotypic diversification, and biogeography while providing an overview of progress made on the reconstruction of the fungal Tree of Life. Finally, we provide a review of considerations to phylogenomic experimental design for robust tree inference. We hope that this special issue of Advances in Genetics not only excites the continued progress of fungal evolutionary biology but also motivates the interdisciplinary development of new theory and methods designed to maximize the power of genomic scale data in phylogenetic analyses., (© 2017 Elsevier Inc. All rights reserved.)

Evolutionary inference can be complicated by morphological crypsis, particularly in open marine systems that may rapidly dissipate signals of evolutionary processes. These complications may be alleviated by studying systems with simpler histories and clearer boundaries, such as marine lakes-small bodies of seawater entirely surrounded by land. As an example, we consider the jellyfish Mastigias spp. which occurs in two ecotypes, one in marine lakes and one in coastal oceanic habitats, throughout the Indo-West Pacific (IWP). We tested three evolutionary hypotheses to explain the current distribution of the ecotypes: (H1) the ecotypes originated from an ancient divergence; (H2) the lake ecotype was derived recently from the ocean ecotype during a single divergence event; and (H3) the lake ecotype was derived from multiple, recent, independent, divergences. We collected specimens from 21 locations throughout the IWP, reconstructed multilocus phylogenetic and intraspecific relationships, and measured variation in up to 40 morphological characters. The species tree reveals three reciprocally monophyletic regional clades, two of which contain ocean and lake ecotypes, suggesting repeated, independent evolution of coastal ancestors into marine lake ecotypes, consistent with H3; hypothesis testing and an intraspecific haplotype network analysis of samples from Palau reaffirms this result. Phylogenetic character mapping strongly correlates morphology to environment rather than lineage (r=0.7512, p<0.00001). Considering also the deeper relationships among regional clades, morphological similarity in Mastigias spp. clearly results from three separate patterns of evolution: morphological stasis in ocean medusae, convergence of lake morphology across distinct species and parallelism between lake morphologies within species. That three evolutionary routes each result in crypsis illustrates the challenges of interpreting evolutionary processes from patterns of biogeography and diversity in the seas. Identifying cryptic species is only the first step in understanding these processes; an equally important second step is exploring and understanding the processes and patterns that create crypsis., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Octocorals are a diverse and ecologically important group of cnidarians. However, the phylogenetic relationships of many octocoral groups are not well understood and are based mostly on mitochondrial sequence data. In addition, the discovery and description of new gorgonian species displaying unusual or intermediate morphologies and uncertain phylogenetic affinities further complicates the study of octocoral systematics and raises questions about the role played by processes such as plasticity, crypsis, and convergence in the evolution of this group of organisms. Here, we use nuclear (i.e. 28S rDNA) and mitochondrial (mtMutS) markers and a sample of Eastern Pacific gorgonians thought to be remarkable from a morphological point of view to shed light on the morphological diversification among these organisms. Our study reveals the loss of the anastomosed colony morphology in two unrelated lineages of the seafan genus Pacifigorgia and offers strong evidence for the independent evolution of a whip-like morphology in two lineages of Eastern Pacific Leptogorgia. Additionally, our data revealed one instance of mito-nuclear discordance in the genera Leptogorgia and Eugorgia, which may be the results of incomplete lineage sorting or ancient hybridization-introgression events. Our study stresses the importance of comprehensive taxonomic sampling and the use of independent sources of evidence to address the phylogenetic relationships and clarifying the evolution of octocorals., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Many groups of closely related species have reticulate phylogenies. Recent genomic analyses are showing this in many insects and vertebrates, as well as in microbes and plants. In microbes, lateral gene transfer is the dominant process that spoils strictly tree-like phylogenies, but in multicellular eukaryotes hybridization and introgression among related species is probably more important. Because many species, including the ancestors of ancient major lineages, seem to evolve rapidly in adaptive radiations, some sexual compatibility may exist among them. Introgression and reticulation can thereby affect all parts of the tree of life, not just the recent species at the tips. Our understanding of adaptive evolution, speciation, phylogenetics, and comparative biology must adapt to these mostly recent findings. Introgression has important practical implications as well, not least for the management of genetically modified organisms in pest and disease control., (© 2015 The Authors. BioEssays Published by WILEY Periodicals, Inc.)

Phylogenetic methods typically rely on an appropriate model of how data evolved in order to infer an accurate phylogenetic tree. For molecular data, standard statistical methods have provided an effective strategy for extracting phylogenetic information from aligned sequence data when each site (character) is subject to a common process. However, for other types of data (e.g., morphological data), characters can be too ambiguous, homoplastic, or saturated to develop models that are effective at capturing the underlying process of change. To address this, we examine the properties of a classic but neglected method for inferring splits in an underlying tree, namely, maximum compatibility. By adopting a simple and extreme model in which each character either fits perfectly on some tree, or is entirely random (but it is not known which class any character belongs to) we are able to derive exact and explicit formulae regarding the performance of maximum compatibility. We show that this method is able to identify a set of non-trivial homoplasy-free characters, when the number [Formula: see text] of taxa is large, even when the number of random characters is large. In contrast, we show that a method that makes more uniform use of all the data-maximum parsimony-can provably estimate trees in which none of the original homoplasy-free characters support splits., (© The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.)

In this study we provide a phylogeny for the pantropical fern genus Tectaria, with emphasis on the Old World species, based on sequences of five plastid regions (atpB, ndhF plus ndhF-trnL, rbcL, rps16-matK plus matK, and trnL-F). Maximum parsimony, maximum likelihood, and Bayesian inference are used to analyze 115 individuals, representing ca. 56 species of Tectaria s.l. and 36 species of ten related genera. The results strongly support the monophyly of Tectaria in a broad sense, in which Ctenitopsis, Hemigramma, Heterogonium, Psomiocarpa, Quercifilix, Stenosemia, and Tectaridium should be submerged. Such broadly circumscribed Tectaria is supported by the arising pattern of veinlets and the base chromosome number (x=40). Four primary clades are well resolved within Tectaria, one from the Neotropic (T. trifoliata clade) and three from the Old World (T. subtriphylla clade, Ctenitopsis clade, and T. crenata clade). Tectaria crenata clade is the largest one including six subclades. Of the genera previously recognized as tectarioid ferns, Ctenitis, Lastreopsis, and Pleocnemia, are confirmed to be members in Dryopteridaceae; while Pteridrys and Triplophyllum are supported in Tectariaceae. To infer morphological evolution, 13 commonly used characters are optimized on the resulting phylogenetic trees and in result, are all homoplastic in Tectaria., (Copyright © 2014 Elsevier Inc. All rights reserved.)

Recent progress in resolving the tree of life continues to expose relationships that resist resolution, which drives the search for novel sources of information to solve these difficult phylogenetic problems. A recent example, the presence and absence of microRNA families, has been vigorously promoted as an ideal source of phylogenetic data and has been applied to several perennial phylogenetic problems. The utility of such data for phylogenetic inference hinges critically both on developing stochastic models that provide a reasonable description of the process that give rise to these data, and also on the careful validation of those models in real inference scenarios. Remarkably, however, the statistical behavior and phylogenetic utility of microRNA data have not yet been rigorously characterized. Here we explore the behavior and performance of microRNA presence/absence data under a variety of evolutionary models and reexamine datasets from several previous studies. We find that highly heterogeneous rates of microRNA gain and loss, pervasive secondary loss, and sampling error collectively render microRNA-based inference of phylogeny difficult. Moreover, our reanalyses fundamentally alter the conclusions for four of the five studies that we reexamined. Our results indicate that the capacity of miRNA data to resolve the tree of life has been overstated, and we urge caution in their application and interpretation.

Finding optimal evolutionary trees from sequence data is typically an intractable problem, and there is usually no way of knowing how close to optimal the best tree from some search truly is. The problem would seem to be particularly acute when we have many taxa and when that data has high levels of homoplasy, in which the individual characters require many changes to fit on the best tree. However, a recent mathematical result has provided a precise tool to generate a short number of high-homoplasy characters for any given tree, so that this tree is provably the optimal tree under the maximum parsimony criterion. This provides, for the first time, a rigorous way to test tree search algorithms on homoplasy-rich data, where we know in advance what the 'best' tree is. In this short note we consider just one search program (TNT) but show that it is able to locate the globally optimal tree correctly for 32,768 taxa, even though the characters in the dataset require, on average, 1148 state-changes each to fit on this tree, and the number of characters is only 57., (Copyright © 2013 Elsevier Inc. All rights reserved.)

The present publication reviews the broader evolutionary implications of our long-term study of primate musculature. It summarizes the implications of the study for our understanding of the use of myological characters for phylogenetic reconstruction, for assessing the importance of homoplasy and reversions in evolution, and for our understanding of Dollo's law, the notion of 'direction' in evolution, the common myth of human complexity, the tempo and mode of primate and human evolutionary history, adaptive radiations, the notion that 'common' equals 'primitive' and the influence of morphogenesis on the variability of head, neck, pectoral and upper limb muscles. Among other results our study shows that myological characters are useful for phylogenetic reconstruction. The results also stress the importance of homoplasy and of evolutionary reversions in morphological evolution, and they provide examples of reversions that violate Dollo's law due to the retention of ancestral developmental pathways. They also show that contrary to the idea of a 'general molecular slow-down of hominoids' the rates of muscle evolution at the nodes leading to and within the hominoid clade are higher than those in most other primate clades. However, there is no evidence of a general trend or 'directionality' towards an increasing complexity during the evolutionary history of hominoids and of modern humans in particular, at least regarding the number of muscles or of muscle bundles. The rates of muscle evolution at the major euarchontan and primate nodes are different, but within each major primate clade (Strepsirrhini, Platyrrhini, Cercopithecidae and Hominoidea) the rates at the various nodes, and particularly at the nodes leading to the higher groups (i.e. those including more than one genus) are strikingly similar. Our results also support, in general terms, the assumption that 'common is primitive' and they lend some support for the 'vertebrate-specific model' in the sense that during the divergent events that resulted in these four major primate clades there was more emphasis on postcranial changes than on cranial changes. Our study of primates does not, however, support suggestions that the distal structures of the upper limb are more prone to variation than the proximal ones, or that the topological origins of the upper limb muscles are more prone to evolutionary change than their insertions., (© 2013 The Authors. Biological Reviews © 2013 Cambridge Philosophical Society.)

Simple Summary: Sturnidae sensu lato (Muscicapoidea) consists of Sturnidae, Mimidae, and Buphagidae. However, the deep-node evolutionary relationships within this group remain undetermined, and few efforts have been made to elucidate their mitogenomic evolution. Here, we focus on Sturnidae sensu lato and present five newly sequenced mitogenomes. Together with analysis of publicly available data, comprehensive analyses of mitogenome features, codon usage and aversion, RNA and CR structures, and phylogeny are performed. In conclusion, we determine the basic organizations of Sturnidae sensu lato mitogenomes, demonstrate the pervasiveness of natural selection in forming the CUB patterns, depict the RNA secondary structures, and construct both the backbone and deep-node relationships within Sturnidae sensu lato. The main finding of our research is obtained through codon aversion motifs (CAM) analyses. The surprisingly unique CAMs from 11 mt PCGs for each species offer new opportunities for the identification of the molecular species identification of these taxa. This work can shed new light on the mitogenomic evolution of Sturnidae sensu lato. The Sturnidae family comprises 123 recognized species in 35 genera. The taxa Mimidae and Buphagidae were formerly treated as subfamilies within Sturnidae. The phylogenetic relationships among the Sturnidae and related taxa (Sturnidae sensu lato) remain unresolved due to high rates of morphological change and concomitant morphological homoplasy. This study presents five new mitogenomes of Sturnidae sensu lato and comprehensive mitogenomic analyses. The investigated mitogenomes exhibit an identical gene composition of 37 genes—including 13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes—and one control region (CR). The most important finding of this study is drawn from CAM analyses. The surprisingly unique motifs for each species provide a new direction for the molecular species identification of avian. Furthermore, the pervasiveness of the natural selection of PCGs is found in all examined species when analyzing their nucleotide composition and codon usage. We also determine the structures of mt-tRNA, mt-rRNA, and CR structures of Sturnidae sensu lato. Lastly, our phylogenetic analyses not only well support the monophyly of Sturnidae, Mimidae, and Buphagidae, but also define nine stable subclades. Taken together, our findings will enable the further elucidation of the evolutionary relationships within Sturnidae sensu lato. [ABSTRACT FROM AUTHOR]

The genus Niphargus is the most diverse subterranean amphipod genus in the western Palearctic region but, owing to the presence of cryptic species and homoplasy, its taxonomy and biogeographic scenarios are complex, making molecular methods essential to understand its evolution. We conducted a study combining DNA-based taxonomy with traditional morphotaxonomy to investigate Niphargus bihorensis Schellenberg, 1940, known from the Western Alps and Carpathians. We redescribed the type material of N. bihorensis from Bihor County, Romania, and revealed the presence of a cryptic species, N. absconditus n. sp., in the same karstic area (Pădurea Craiului Mountains). Additionally, the Alpine populations previously attributed to N. bihorensis turned out to belong to a new, not so closely related species, N. tizianoi n. sp. Phylogenetic analyses based on a concatenated dataset of one mitochondrial and two nuclear markers suggest that the N. bihorensis species complex belongs to a strongly supported clade, together with several species distributed from Switzerland to Iran. [ABSTRACT FROM AUTHOR]

Boehmeria is a taxonomically challenging group within the nettle family (Urticaceae). The polyphyly of the genus has been proposed by previous studies with respect to five genera (Debregeasia, Cypholophus, Sarcochlamys, Archiboehmeria, and Astrothalamus). Extensive homoplasy of morphological characters has made generic delimitation problematic. Previous studies in other plant groups suggest that plastome structural variations have the potential to provide characters useful in reconstructing evolutionary relationships. We aimed to test this across Boehmeria and its allied genera by mapping plastome structural variations onto a resolved strongly supported phylogeny. In doing so, we expanded the sampling of the plastome to include Cypholophus, Sarcochlamys, Archiboehmeria, and Astrothalamus for the first time. The results of our phylogenomic analyses provide strong support for Sarcochlamys as being more closely related to Leucosyke puya than to Boehmeria and for the clustering of Boehmeria s.l. into four subclades. The sizes of the plastomes in Boehmeria s.l. ranged from 142,627 bp to 170,958 bp. The plastomes recovered a typical quadripartite structure comprising 127~146 genes. We observe several obvious structural variations across the taxa such as gene loss and multiple gene duplication, inverted repeat (IR) contraction and wide expansions, and inversions. Moreover, we recover a trend for these variations that the early clades were relatively conserved in evolution, whereas the later diverging clades were variable. We propose that the structural variations documented may be linked to the adaptation of Boehmeria s.l. to a wide range of habitats, from moist broadleaf forests in Asia to xeric shrublands and deserts in Africa. This study confirms that variation in plastome gene loss/duplication, IR contraction/expansion, and inversions can provide evidence useful for the reconstruction of evolutionary relationships. [ABSTRACT FROM AUTHOR]

A formal cladistic analysis of the morphological features of taxa assigned to the Orthoseiraceae, including Phycavernosa, Guarreraea and species of the genus Orthoseira is developed for 35 taxa based on 16 characters along with two Melosira species and four biddulphioid species as ingroup taxa as well as Leptocylindrus danicus as the outgroup. A consensus tree of 266 843 most parsimonious topologies suggests that the Orthoseiraceae is monophyletic, and that Guarreraea plus all former species of Orthoseira represent a monophyletic group. This analysis of morphological data did not provide support for the members of the Orthoseiraceae being more closely related to melosiroid or biddulphioid diatoms. Relationships within the monophyletic orthoseiracean group are detailed. Due to the exclusion of the generitype of Orthoseira not possessing carinoportulae which are central tube processes, one of the diagnostic features of the former Orthoseiraceae, other taxon names are described and recognized herein. We recognize and describe a new order, the Liparogyrales, based on the genus Liparogyra for taxa that were previously assigned to Orthoseira. Two families, the Phycavernosaceae, comprising the genus Phycavernosa, and the Liparogyraceae, comprising Guarreraea and taxa formerly assigned to Orthoseira, are described. The genus Liparogyra is composed of three subgenera: the subgenus Liparogyra, the subgenus Porocyclia, and the subgenus Insularis which are diagnosed by synapomorphic features. Based on our analysis, the genus Stephanosira appears to lack synapomorphies. Liparogyra, Porocyclia and Stephanosira had previously been described as genera by Ehrenberg. Guarreraea and one newly proposed genus are also included in the Liparogyraceae. Several other lineages are aphyletic, due to them either being monotypic or without diagnostic features. Thus, a total of 29 species in five genera are recognized within the newly described order and two newly described families. Eighteen new combinations are proposed for the transfer of taxa from Orthoseira to other genera. Homoplasy amongst some of the character states is discussed. The diatom genus Orthoseira as typified by O. americana does not possess carinoportulae, requiring a new approach to the nomenclature and taxonomy of the group. A phylogenetic analysis of the group using morphological data was performed, demonstrating patterns of relationships of the species for this lineage. A new classification for this diatom lineage is presented. [ABSTRACT FROM AUTHOR]

Using molecular (COI , Cytb , H3 , wg , 12S, 16S, and 28S) and morphological data (61 characters of adults and immatures), the phylogenetic relationships of the 20 nominal genera of Liviinae were analysed, and the monophyly of the subfamily was tested relative to the other two subfamilies of Liviidae. The analyses of the molecular, morphological, and combined datasets provided similar results with a strong or moderate support in the molecular and combined analyses for the subfamilies of Liviidae and two clades in Liviinae given tribal rank (Liviini and Paurocephalini stat. rev.). Three of the six previously recognized genera were confirmed as monophyletic (Aphorma , Camarotoscena , and Livia) and three were shown to be polyphyletic: Diclidophlebia s.l. (Diclidophlebia s.s. , Haplaphalara stat. rev. Klyveria Burckhardt, Serbina and Malenovský, gen. nov. Melanastera Serbina, Malenovský, Queiroz and Burckhardt, gen. nov. and Woldaia stat. rev.), Paurocephala s.l. (Liella Burckhardt, Serbina and Malenovský, gen. nov. and Paurocephala s.s.), and Syntomoza s.l. (Anomoterga stat. rev. and Syntomoza s.s.). The new generic definitions require 38 new and eight revived combinations, including the transfer of two species to other families. All genera of Liviinae are diagnosed and keys are provided for their identification. A checklist of world Liviinae is supplemented. [ABSTRACT FROM AUTHOR]

Scolebythidae constitute the smallest family of Aculeata in number of extant species, but with a considerable diversity of extinct lineages. Twenty Cretaceous species are attributed to the family coming from deposits in Canada, Lebanon, Myanmar, New Jersey, and Spain. However, several of these taxa lack characters of the family groundplan. Although phylogenetic investigations have been conducted for the family based on a relatively small set of morphological characters, the substantial diversity of species from Burmese amber have not yet been accounted for in a phylogenetic perspective. In the present work, we reconstruct the phylogenetic relationships of Scolebythidae using a new morphological matrix and explore it through parsimony and Bayesian model evaluation. In Bayesian analyses, homoplasy-based partitioning outperformed anatomy-based partitioning and the unpartitioned models. Our phylogenetic results support the relocation of a few taxa previously attributed to Scolebythidae to the families Bethylidae and Chrysididae. We also describe †Chrysopsenellidae fam. nov. a new family of Chrysidoidea, based on an inclusion in Burmese amber. In all analyses the new family is recovered as closely related to Scolebythidae, with the whole clade being sister-group to Chrysididae + †Chrysobythidae. Finally, we discuss the origin of the Burmese amber biota distinctiveness. [ABSTRACT FROM AUTHOR]

Although molecular phylogenetics remains the most widely used method of inferring the evolutionary history of living groups, the last decade has seen a renewed interest in morphological phylogenetics, mostly driven by the promises that integrating the fossil record in phylogenetic trees offers to our understanding of macroevolutionary processes and dynamics and the possibility that the inclusion of fossil taxa could lead to more accurate phylogenetic hypotheses. The plant fossil record presents some challenges to its integration in a phylogenetic framework. Phylogenies including plant fossils often retrieve uncertain relationships with low support, or lack of resolution. This low support is due to the pervasiveness of morphological convergence among plant organs and the fragmentary nature of many plant fossils, and it is often perceived as a fundamental weakness reducing the utility of plant fossils in phylogenetics. Here I discuss the importance of uncertainty in morphological phylogenetics and how we can identify important information from different patterns and types of uncertainty. I also review a set of methodologies that can allow us to understand the causes underpinning uncertainty and how these practices can help us to further our knowledge of plant fossils. I also propose that a new visual language, including the use of networks instead of trees, represents an improvement on the old visualization based on consensus trees and more adequately serves phylogeneticists working with plant fossils. This set of methods and visualization tools represents an important way forward in a fundamental field for our understanding of the evolutionary history of plants. [ABSTRACT FROM AUTHOR]

Carrerapyrgota Aczél, 1956 is a Neotropical Diptera genus within Pyrgotidae. Currently, the genus comprise four species: C. miliaria Aczél, 1956 (type species), C. personata (Lutz & Lima, 1918), C. aczeli Mello, Lamas & Rafael, 2010, and C. bernardii Mello, Lamas & Rafael, 2010. This study investigates the phylogenetic relationships among Carrerapyrgota species, aiming to establish their monophyly as a genus. To achieve this, we conducted phylogenetic analyses based on 22 external morphological characters of adults, emploing the principle of parsimony. Analyses using both equal and implied character weighting support the monophyly of the genus, based on the following apomorphies: absence of the postscutellum, R2-3 with spurious apical vein, lower calypter with a longitudinal row of bristles, and the presence of a posterior longitudinal groove on the female fore femur. The species C. aczeli, C. bernardii, and C. miliaria form a monophyletic group, supported by the synapomorphic condition of a spot on the forehead. Within this group, C. bernardii and C. miliaria are sister species, sharing the synapomorphic condition of a less sclerotized M vein, after dm-cu compared to the anterior region, as well as the homoplastic condition of a spot on the median occipital sclerite. This phylogenetic analysis reaffirms the synonymy proposed by Bernardi (1990), which treats Anapyrgota Steyskal, 1967, as a junior synonym of Carrerapyrgota. The evolutionary relationship among the species of the genus is represented as (C. personata (C. aczeli (C. bernardii, C. miliaria))). Furthermore, this study includes an updated distributional map for the genus, featuring the first record of Pyrgotinae in the Andean region. [ABSTRACT FROM AUTHOR]

Dorometra Clark, 1917 (Comatulida: Antedonidae) is an Indo-Pacific genus of small-sized cryptic feather stars currently comprising nine species. The monophyly of this crinoid genus has been widely questioned, although only few studies have investigated the phylogeny of Antedonidae in depth. In this study we used an integrated approach combining molecular phylogenetic, morphology, and multivariate analyses to clarify the taxonomic placement of the genus Dorometra within family Antedonidae. Eight of the nine known species of the genus collected from Australia to the Sea of Japan were included in analyses. Phylogenetic analyses using sequences from two mitochondrial (COI, 16S) and one nuclear (28S) genes demonstrate that Dorometra is polyphyletic, and its species are divided into three main clades, which are spread within other Antedonidae. As a result, we herein describe Nesometra gen. nov. Four different species delimitation methods on single and multi-locus alignments also showed higher diversity than previously thought. In particular, our results highlighted the presence of cryptic diversity within the species Dorometra nana (Hartlaub, 1890) in geographically close localities within southern Japan. By multivariate analysis of morphological matrix, we confirmed the homoplasy and plasticity of the taxonomic characters used in the description of Dorometra species, providing a path forward for the general taxonomic revision of this genus and of Antedonidae and related families. [ABSTRACT FROM AUTHOR]

Coenosopsia Malloch has eight known species distributed from southern North America to south-eastern South America. The species of the genus are morphologically very homogeneous, and major differences remain in male terminalia. Remarkably, two of the main diagnostic characteristics of Anthomyiidae are absent in this genus: the setulae on the ventral surface of the scutellum and vein A1 reaching the wing margin. Some studies have attempted to propose biogeographical narratives, primarily for the Neotropical distribution of the genus. Herein, we describe three new species of Coenosopsia from north-eastern Brazil (Coenosopsia limeirai sp. nov.), southern Brazil (Coenosopsia ribeiroi sp. nov.), and central Mexico (Coenosopsia azteca sp. nov.) and present an identification key. In addition, we present an updated phylogenetic analysis based on morphological evidence, which recovered Coenosopsia as monophyletic based on five synapomorphies and four homoplasies. We also presented the first biogeographical hypothesis of Coenosopsia based on biogeographic methods (ancestral reconstruction character and S-DIVA analyses), which indicated a Mesoamerican origin of the genus. [ABSTRACT FROM AUTHOR]

The Gynoxyoid clade of the Senecioneae (Asteraceae) until now included the five genera Aequatorium, Gynoxys, Nordenstamia, Paracalia and Paragynoxys as diagnosed using selected morphological characters. In their pre-phylogenetic circumscription, the genera Aequatorium and Paragynoxys were considered to inhabit the northern Andes in contrast to Nordenstamia and Paracalia that occur in the central Andes. The most species-rich genus, Gynoxys, was believed to be distributed throughout the Andes. We use a recently established plastid phylogenomic framework that rendered Gynoxys paraphyletic to further evaluate the delimitation of genera in the Gynoxyoid clade. We examine the morphological variation of all members of the Gynoxyoid to identify characters potentially informative at genus level. This results in a matrix of eleven, mostly multistate characters, including those originally used to diagnose these genera. The ancestral character state inference displays a high level of homoplasy, but nevertheless supports the recognition of four genera. Aequatorium is characterised by white radiate capitula. Paracalia and Paragynoxys share white flowers and floral characteristics, such as flower opening and length of disc flowers lobes, as plesiomorphic states, but differ in habit (scandent shrubs vs. trees). Paracalia also retained white flowers, but its two species are characterised by the absence of outer phyllaries. The genera Gynoxys and Nordenstamia comprise species with yellow capitula which appear to be a derived feature in the Gynoxyoids. The genus Nordenstamia, with eight species, is synonymised under Gynoxys since molecular evidence shows its species nested within various parts of the Gynoxys subclade and the morphological variation of Nordenstamia falls well within that of Gynoxys. With the goal to assign all species to four genera (Aequatorium, Gynoxys, Paracalia and Paragynoxys), we assess the states for the eleven characters for all members of the Gynoxyoids and generate new ETS and ITS sequences for 171 specimens belonging to 49 species to further support their generic placement. We provide a taxonomic treatment for the four genera recognised here including amended diagnoses and morphological descriptions. Furthermore, a species-level taxonomic backbone is elaborated for all genera using electronic tools that list 158 currently accepted names and synonyms (209 names in total) with the respective protologue and type information, as well as notes on the current understanding of species limits. Eleven names are newly synonymised, two are lectotypified and eight are newly transferred to other genera. [ABSTRACT FROM AUTHOR]

Paepalanthus, in its current sense, is the most diverse genus of Eriocaulaceae in the Neotropics, comprising about 400 species. Previous studies have consistently found that the genus is not monophyletic, also being morphologically heterogeneous and diagnosable by a set of homoplasies; thus, the current circumscription needs to be revised. The new classification proposed here uses a comprehensive phylogeny of Paepalanthus and closely related genera as a framework and an evaluation of a set of morphological characters using ancestral state reconstruction, which allowed the recognition of strongly supported clades with morphological diagnosability. We propose the recognition of 12 genera in the clade encompassing Paepalanthus and allied groups, including six new genera (Coracoralina, Floralia, Giuliettia, Gnomus, Hydriade, Nisius), two new statuses (Cryptanthella, Monosperma), the reestablishment of Actinocephalus, Lachnocaulon, and Tonina, and a recircumscription of Paepalanthus. In this new circumscription, Paepalanthus comprises 257 species, most of them restricted to the Brazilian campos rupestres. Among the proposed genera, nine have potential morphological synapomorphies, one has a restricted geographical distribution, and the other two can be recognized by a combination of characters. Newly generated seed morphology data is consistent within the different genera and plays an important role in their recognition. A total of 136 new combinations are hereby proposed. We provide a genus‐level identification key, as well as generic descriptions, diagnostic features, photos illustrating their morphological diversity, maps and notes on distribution, and lists of species by genus. [ABSTRACT FROM AUTHOR]

This paper provides the first DNA sequences and phylogenetic insight into the Central Asian genus Eodorcadion. We used four molecular markers (COI, CAD, ITS2, and Histone 3) and investigated COI genetic distances to verify phylogenetic position of closely related taxa endemic to Mongolia of the 'Eodorcadion intermedium species-group'. Histone3 data are presented for the first time for Cerambycidae species. We also designed new PCR primers for better amplification of the Cerambycidae COI barcode region. Morphology of all targeted taxa was examined by means of scanning electron microscopy. Our study showed that while there were very few nucleotide differences among COI sequences of three closely related taxa, such that they shared one haplotype, two of them were grouped separately in the all-data tree, and all three were morphologically distinguishable. Conversely, there was a clear barcode gap between E. intermedium intermedium and all the remaining taxa, including E. intermedium kozlovi. Based on the phylogeny, they belong to two different species-groups; thus, E. kozlovi is herein restored to specific rank. Using Bayesian analysis, we contrasted the COI-based tree with the one supported by nuclear data and showed that COI-only data are not sufficient to resolve the phylogeny of the recently derived flightless groups such as Dorcadionini. We conclude that the Eodorcadion intermedium species-group is a polyphyletic species assemblage, established based on the pattern of the elytral stripes, which may be a case of parallel evolution driven by ecological adaptation. [ABSTRACT FROM AUTHOR]

Albanerpetontidae form an enigmatic extinct group of lissamphibians, ranging from the early Bathonian to the early Pleistocene. The Upper Jurassic outcrops of Portugal yield a large collection of material, suitable for addressing the intraspecific variation in and diagnostic potential of the characteristic fused frontals. We revise 58 specimens from the Guimarota beds of the Kimmeridgian Alcobaça Formation and describe 62 new frontal bones from the Kimmeridgian – Tithonian Lourinhã Formation. Smaller specimens exhibit a vermicular dorsal ornamentation, while it is polygonal in larger specimens and other albanerpetontids. Compared to small specimens, larger specimens display: (1) larger ventrolateral crests extending posteriorly after the parietal margin; (2) a relatively shorter internasal process; (3) a frontal width across posterior edges relatively smaller; and (4) a ventromedian crest less pronounced. Morphometric analyses suggest a single species with different ontogenetic stages. Specimens are attributed to aff. Celtedens sp., based on a bell-shaped outline with a curved orbital margin (although variable in Portuguese specimens), and a flabellate, bulbous-shaped internasal process. The species is more similar to C. megacephalus than C. ibericus, but its phylogenetic position comprises an unresolved trichotomy. Our results show that intraspecific variation and homoplasy render the fused frontal non-diagnostic below the generic level. [ABSTRACT FROM AUTHOR]

Due to classical taxonomy, the subfamily Lepturinae is divided into two large tribes Rhagiini s.l. and Lepturini s.l. However, this division is clearly artificial and does not correspond to the evolutionary relationships between the groups of genera with different morphologies that are part of these two tribes. However, there is a consensus among researchers supporting the monophyly of Lepturini s.l. while there is no such consensus for Rhagiini s.l. Over the past three decades, there have been several attempts to revise the tribe Rhagiini s.l. and divide it into smaller tribes. These attempts were somewhat successful based on larval and adult morphology. In general, eight tribes are distinguished within Rhagiini s.l. These include Teledapini, Xylosteini, Encyclopini, Oxymirini, Enoploderini, Rhamnusiini, Rhagiini and Sachalinobiini. However, the new system of Rhagiini s.l. is not always unambiguously accepted by different researchers, which causes discussions among experts. First of all, this is due to the fact that this system is only partially natural and far from fully reflects the phylogeny not only of Rhagiini s.l., but also of entire subfamily Lepturinae. In addition to the classical morphologic methods of studies, the use of the modern molecular phylogenetic methods opens up wide prospects for solving this puzzle. However, there have been very few such studies. Moreover, all of them were based on the use of only one gene. In this study, I used a general time-reversible (GTR) model of sequence evolution based on three mitochondrial (12S rRNA, 16S rRNA, COI) and two nuclear (18S rRNA, 28S rRNA) genes. My analysis yielded a well-resolved phylogenetic maximum likelihood tree, which clearly demonstrates the paraphyly of Rhagiini s.l. It consists of at least three clades representing different and distantly related evolutionary branches: 1) PaRh, 2) OSaXyR-SEP, 3) GAC. The extant Rhagiini s.l. are mostly heterogeneous relict groups with an intricate evolutionary and phylogeographic history. Most of these groups are represented by one or very few species, often isolated geographically on different continents. In particular, numerous cases of parallel and convergent evolution and homoplasy, a chimeric combination of plesiomorphic and apomorphic morphological characters, were found in all clades. Therefore, the evolutionary "tree" of Rhagiini s.l. is more like a "bush" with numerous relict branches. Finally, I proposed a new taxonomic model of Rhagiini s.l., which is the most consistent with their natural phylogeny, with new developments in nomenclature.

The Carthamus‐Carduncellus complex is formed by approximately 50 taxa that are widely distributed throughout the Mediterranean basin and western Asia. The generic delineation of this complex has always been controversial. Currently, there are three widely diverging taxonomical proposals, suggesting that the complex is formed by (1) a single genus, Carthamus; (2) two genera, Carduncellus and Carthamus; and (3) four genera, Carduncellus, Carthamus, Femeniasia, and Phonus. The generic classification has varied depending on the importance assigned to some morphological characters, i.e., the morphology/structure of pappus, achenes, and involucral bracts. All these generic changes have complicated the nomenclature of the complex, leading to species wandering between four different genera. To objectively assess the taxonomic delimitation of this complex, we carried out phylogenetic analyses using nuclear (external and internal transcribed spacers of rDNA) and plastid (ndhF, trnH, rpl32, trnT) data, as well as multispecies coalescent model analyses on near‐complete sampling. Phylogenetic reconstructions resolved two monophyletic groups, Carthamus s.str. and Carduncellus s.l. Within the latter, some groups could be differentiated, such as the monophyletic genus Phonus and the monospecific Femeniasia. Our multispecies coalescent analyses strongly support a classification based on four genera in the complex Carthamus‐Carduncellus. In contrast, classifications based on only one or two genera lack relevant support. However, the absence of synapomorphic morphological characters that define the Carduncellus lineage (Carduncellus, Phonus, Femeniasia), and the possible hybridization in the ancestral lineages detected by incongruences between plastid and nuclear markers make it difficult to define clear generic boundaries. We propose maintaining the hypothesis of four genera, which was the first classification supported by molecular evidence, pending a broader study (both molecular and morphological) to reach a more definitive delineation and avoid more unfounded generic changes. [ABSTRACT FROM AUTHOR]

Helicarionid land snails with large shells have been placed in three genera: Malandena, Pravonitor and Elatonitor. These taxa are revised herein using comparative morpho-anatomy and mitochondrial phylogenetics. We demonstrate that these species represent three independent radiations, but this is not reflected in the current generic arrangement. Phylogenetic reconstruction revealed that these genera do not form a monophyletic group, and we conclude that large shells have evolved multiple times among helicarionids in Queensland, Australia, presumably as an adaptation to moist environments. Species belonging to Pravonitor have a medium-sized to large, glossy shell, often with a peripheral band. Among other traits, they always have a single-chambered, internally pustulose or ridged penis, an epiphallus with a slender flagellum, and a long epiphallic caecum with medial penial retractor muscle attachment. This genus comprises eight species: Pravonitor kreffti, P. ferrugineus, P. insularum, P. annulus, P. aquilonia comb. nov., P. monteithi comb. nov., P. septentrionalis sp. nov. and P. stuarti sp. nov. We describe Geminitor gen. nov. for Geminitor laura comb. nov., G. villaris comb. nov., G. kullaensis sp. nov., G. macveae sp. nov. and G. wenlockensis sp. nov. Geminitor has a small to medium-sized shell, a long, two-chambered penis, an epiphallus with a slender flagellum, and an epiphallic caecum with basal penial retractor muscle attachment. The unavailable genus name Malandena is subsumed under Elatonitor, which now contains Elatonitor montanus and E. suturalis comb. nov. Elatonitor has a large glossy shell with an angulate periphery, a long, narrow, single-chambered penis with longitudinal pilasters, an epiphallus with a broad flagellum, and no epiphallic caecum. While this study has nearly doubled the number of known large helicarionid species in Far North Queensland, there are still knowledge gaps and we recommend further surveys to search for undocumented species, improve our understanding of species distribution and undertake vital conservation assessments. [ABSTRACT FROM AUTHOR]

Simple Summary: Rampant morphological homoplasy in Mantodea has confused systematists for a long time. The leaf-like pronotum was long thought to be one of the key characteristics of Rhombodera in Hierodulinae. In this study, we describe a new species of Rhombodera and discuss the phylogeny as well as complex convergent evolution of leaf-like pronotum in Hierodulinae based on the combination of morphological and mitogenome data. The results reveal the unnatural grouping of the current classification in Hierodula and Rhombodera, rendering the well-developed lateral expansion invalid as the diagnosis of Rhombodera. Mapping the pronotal-foliaceous trait onto our phylogenetic tree show that the origin in multiple lineages of this trait in Hierodulinae may have adaptive significance. The congruent results of the group division between mitochondrial phylogenomics and morphology of male genitalia also highlight the capacity of the use of mitogenomes in resolving the derived mantodean phylogenetic relationship. Hierodulinae is a species-rich mantid subfamily, with some species bearing a notable leaf-like pronotum. However, the evolutionary pattern and taxonomic significance of the leaf-like pronotum are largely unknown. Here, we present a phylogenomic analysis of the Hierodulinae genera Rhombodera Burmeister, 1838, and Hierodula Burmeister, 1838 based on mitochondrial genomes. We also describe a new species, namely Rhombodera hyalina sp. nov. from Guangxi, China. Our phylogenetic result, together with the evidence from male genitalia, suggests the division of the Oriental Hierodula and Rhombodera complex into three clades. We find a complex pattern on the evolution of the leaf-like pronotum, which is present in at least five lineages, respectively, of the above three clades. [ABSTRACT FROM AUTHOR]

Augochlorini comprise 646 described bee species primarily distributed in the Neotropical region. According to molecular and morphological phylogenies, the tribe is monophyletic and subdivided into seven genus groups. Our main objective is to propose a revised phylogeny of Augochlorini based on a comprehensive data set including fossil species as terminals and new characters from the internal skeleton. We also aim to develop a total-evidence framework incorporating a morphological-partitioned homoplasy approach and molecular data and propose a detailed biogeographic and evolutionary scenario based on ancestor range estimation. Our results recovered Augochlorini and most genus groups as monophyletic, despite some uncertainties about monophyly of the Megalopta and Neocorynura groups. The position of the cleptoparasite Temonosoma is still uncertain. All analyses recovered Augochloropsis s.l. as related to the Megaloptidia group. Internal characters from the head, mesosoma and sting apparatus provided important synapomorphies for most internal nodes, genus groups and genera. Augochlorini diversification occurred in the uplands of the Neotropical region, especially the Brazilian Plateau. Multiple dispersals to Amazonia, Central America and North America with returns to the Atlantic endemism area were recovered in our analysis. Total evidence, including morphological partitioning, was shown to be a reliable approach for phylogenetic reconstruction. [ABSTRACT FROM AUTHOR]

The subfamily Typhlocybinae is a ubiquitous, highly diverse group of mostly tiny, delicate leafhoppers. The tribal classification has long been controversial and phylogenetic methods have only recently begun to test the phylogenetic status and relationships of tribes. To shed light on the evolution of Typhlocybinae, we performed phylogenetic analyses based on 28 newly sequenced and 19 previously sequenced mitochondrial genomes representing all currently recognized tribes. The results support the monophyly of the subfamily and its sister‐group relationship to Mileewinae. The tribe Zyginellini is polyphyletic with some included genera derived independently within Typhlocybini. Ancestral character state reconstruction suggests that some morphological characters traditionally considered important for diagnosing tribes (presence/absence of ocelli, development of hind wing submarginal vein) are homoplastic. Divergence time estimates indicate that the subfamily arose during the Middle Cretaceous and that the extant tribes arose during the Late Cretaceous. Phylogenetic results support establishment of a new genus, Subtilissimia Yan & Yang gen. nov., with two new species, Subtilissimia fulva Yan & Yang sp. nov. and Subtilissimia pellicula Yan & Yang sp. nov.; but indicate that two previously recognized species of Farynala distinguished only by the direction of curvature of the processes of the aedeagus are synonyms, that is, Farynala dextra Yan & Yang, 2017 equals Farynala sinistra Yan & Yang, 2017 syn. nov. A key to tribes of Typhlocybinae is provided. [ABSTRACT FROM AUTHOR]

Lachenalia (Asparagaceae; Scilloideae; Hyacintheae) is a large and morphologically diverse genus of more than 140 bulbous species endemic to southern Africa. Previous attempts to infer a well‐resolved and robustly supported phylogeny of Lachenalia using Sanger sequencing of candidate loci and/or morphological characters have been largely unsuccessful. Consequently, the current infrageneric classification is artificial, and there is a need to explore alternative avenues to produce a phylogenetic classification. In this paper, we present a novel phylogenetic hypothesis for Lachenalia inferred using maximum likelihood and coalescent‐based species tree estimation (ASTRAL) as applied to 378 hybrid‐enrichment loci. Our tree is well resolved and well supported, providing strong support for a monophyletic radiation of the genus in southern Africa and a solid foundation for a revised infrageneric classification. The well‐supported placement of L. isopetala Jacq. as sister to Lachenalia + Massonia supports the establishment of a new monotypic genus, Pseudolachenalia, to accommodate this species. Conversely, the inclusion of species previously classified as Polyxena within the Lachenalia clade supports the transfer of these species to Lachenalia. Within Lachenalia, the delimitation of subgenera and sections is complicated by the highly imbalanced character of the phylogeny and by the high levels of homoplasy shown by most morphological characters traditionally used to delimit species in this group. Nonetheless, we propose an infrageneric taxonomy comprising 10 morphologically distinct, monophyletic sections. The largest of these, L. sect. Lachenalia, is further divided into 13 more‐or‐less diagnosable, monophyletic subsections. Keys to the sections of Lachenalia, and to the subsections of L. sect. Lachenalia, are provided. [ABSTRACT FROM AUTHOR]

Few clades of plants have proven as difficult to classify as cacti. One explanation may be an unusually high level of convergent and parallel evolution (homoplasy). To evaluate support for this phylogenetic hypothesis at the molecular level, we sequenced the genomes of four cacti in the especially problematic tribe Pachycereeae, which contains most of the large columnar cacti of Mexico and adjacent areas, including the iconic saguaro cactus (Carnegiea gigantea) of the Sonoran Desert. We assembled a high-coverage draft genome for saguaro and lower coverage genomes for three other genera of tribe Pachycereeae (Pachycereus, Lophocereus, and Stenocereus) and a more distant outgroup cactus, Pereskia We used these to construct 4,436 orthologous gene alignments. Species tree inference consistently returned the same phylogeny, but gene tree discordance was high: 37% of gene trees having at least 90% bootstrap support conflicted with the species tree. Evidently, discordance is a product of long generation times and moderately large effective population sizes, leading to extensive incomplete lineage sorting (ILS). In the best supported gene trees, 58% of apparent homoplasy at amino sites in the species tree is due to gene tree-species tree discordance rather than parallel substitutions in the gene trees themselves, a phenomenon termed "hemiplasy." The high rate of genomic hemiplasy may contribute to apparent parallelisms in phenotypic traits, which could confound understanding of species relationships and character evolution in cacti.

This paper provides the first DNA sequences and phylogenetic insight into the Central Asian genus Eodorcadion. We used four molecular markers (COI, CAD, ITS2, and Histone 3) and investigated COI genetic distances to verify phylogenetic position of closely related taxa endemic to Mongolia of the ‘Eodorcadion intermedium species-group’. Histone3 data are presented for the first time for Cerambycidae species. We also designed new PCR primers for better amplification of the Cerambycidae COI barcode region. Morphology of all targeted taxa was examined by means of scanning electron microscopy. Our study showed that while there were very few nucleotide differences among COI sequences of three closely related taxa, such that they shared one haplotype, two of them were grouped separately in the all-data tree, and all three were morphologically distinguishable. Conversely, there was a clear barcode gap between E. intermedium intermedium and all the remaining taxa, including E. intermedium kozlovi. Based on the phylogeny, they belong to two different species-groups; thus, E. kozlovi is herein restored to specific rank. Using Bayesian analysis, we contrasted the COI-based tree with the one supported by nuclear data and showed that COI-only data are not sufficient to resolve the phylogeny of the recently derived flightless groups such as Dorcadionini. We conclude that the Eodorcadion intermedium species-group is a polyphyletic species assemblage, established based on the pattern of the elytral stripes, which may be a case of parallel evolution driven by ecological adaptation.

Building natural classifications for genera with complex morphological variations such as Centaurea needs the support of molecular analysis and knowledge of morphological character diversification. Here we use parsimony and Bayesian analyses of nuclear ribosomal ITS sequences to gain insight into the sectional relationships and character evolution in Centaurea sections Chartolepis, Cheirolepis, Cynaroides, Grosheimia, Microlophus, Paraphysis, Phaeopappus, Plumosipappus, Pseudoserida, Pseudophaeopappus, Ptheracantha, Ptosimopappus, and Rhizocalathium, from Turkey. In particular, we increase sampling in Turkish endemic species of Centaurea sect. Cynaroides and related taxa. The new ITS sequences for 26 taxa from 48 locations are given. Sequences of 17 taxa are given here the first time. The phylogeny derived from ITS data provides a reasonably resolved and reasonably supported phylogenetic framework for the genus. Our analysis shows characters traditionally used in Centaurea taxonomy such as flower colour, appendage width, spine length, and pappus length evolved several times independently and show a lot of homoplasies. However, we can confirm the validity of character combinations for a reliable subgeneric classification of Centaurea. [ABSTRACT FROM AUTHOR]

Acalypha (Euphorbiaceae: Acalyphoideae) is a large, monophyletic genus distributed worldwide in tropical and subtropical regions, with a few species extending into temperate areas of southern Africa, Asia, and North and South America. We reconstructed phylogenetic relationships within the genus using DNA sequences from the plastid ndhF and trnL-F regions and the nuclear ribosomal ITS region, sampling 142 species to represent the geographic, morphologic, and taxonomic diversity with the genus, resulting in a 162 (158 in Acalypha) terminal and 3847 character combined dataset. Bayesian and maximum likelihood reconstructions based on the combined dataset yielded a tree with a generally well-supported backbone and several strongly supported clades. Our results strongly supported the monophyly of Acalypha subg. Acalypha as currently recognized but showed that A. subg. Linostachys and almost all other infrageneric taxa recognized in the most recent comprehensive classification of the genus were not monophyletic. We therefore propose a new subgeneric classification comprising A. subg. Acalypha, A. subg. Androcephala, A. subg. Hypandrae, and A. subg. Linostachys (s.s.). Our results also shed light on relationships within some species groups, including in what has been treated as a broadly defined A. amentacea, in which we recognize A. amentacea, A. palauensis comb. nov., and A. wilkesiana as distinct species. Bayesian ancestral state estimations based on the phylogeny of Acalypha demonstrated that inflorescence position and sexuality and habit show high homoplasy, especially within A. subg. Acalypha, and that inflorescence position and habit exhibit correlated evolution. [ABSTRACT FROM AUTHOR]

The terrestrial isopod family Armadillidiidae presents higher diversity in karstic areas, with fewer species present in areas with reduced suitable subterranean habitats, such as siliceous sandy soils. Myrmecophily, although not widespread in the family Armadillidiidae, can help these animals to colonize sandy substrates, as is observed in several populations of myrmecophilous Armadillidiidae species in central and southern Spain. Morphological examination and multilocus phylogenetic analyses, including mitochondrial DNA (Cox1) and nuclear DNA (18S, 28S and H3) markers, indicate that these myrmecophilous populations represent four new taxa: Iberiarmadillidium pinicola gen. & sp. nov. Iberiarmadillidium psammophilum sp. nov. , Iberiarmadillidium sakura sp. nov. and Cristarmadillidium myrmecophilum sp. nov. Some of the main diagnostic characters used in the taxonomy of Armadillidiidae are not clearly apomorphic. Among head morphologies, Eluma type seems to be the ancestral state, being typical of several unrelated lineages; duplocarinate and Armadillidium types are derived states observed in unrelated lineages. The presence of a schisma is a convergent character state, because it has been identified in several taxa nested in unrelated clades. The newly described taxa present patterns of morphological stasis and homoplasy, likely to be associated with their shared myrmecophilous habits. The generic taxonomy of the family needs a deep revision including phylogenetic approaches and thorough taxon sampling. [ABSTRACT FROM AUTHOR]

Haustoriid amphipods have received little recent attention and their systematics and phylogenetics are largely unresolved. Some efforts have been made at classifying the family within the broader Amphipoda, but there is persistent incongruence in its placement among different authors and techniques. Furthermore, there exists no phylogenetic hypothesis of intrafamilial relationships. In this work, we evaluate the competing hypotheses on the phylogenetic position of the Haustoriidae within Amphipoda by examining new and previously published sequences of nearly 100 species across 38 families. We find strong support for the Haustoriidae as basal gammarids, and that other families placed within the parvorder 'Haustoriidira' are spread across Amphipoda. The radiation began during the Eocene and may have been driven in North America by the rapid filling of a coastal niche opened by the Chesapeake Bay impact crater. Unlike previous work, we find that the Pacific-endemic genus Eohaustorius is the most basal haustoriid, and that it separated from the rest of the family ~31 Mya. Finally, we provide taxonomic recommendations for relationships within Haustoriidae, including the elevation of a new genus, Cryptohaustorius gen. nov.. We conclude by recommending that the 'Haustoriidira' be abandoned. [ABSTRACT FROM AUTHOR]

Despite increased use of genomic data in phylogenetics, morphological information remains vital for resolving evolutionary relationships, particularly for fossil taxa. The properties and models of evolution of molecular sequence data are well characterized and mature, relative to those of morphological data. Furthermore, heterogeneity, integration and relative homoplasy of empirical morphological data could prove problematic for phylogenetic reconstruction. Here we compare osteological and non-osteological characters of 28 morphological datasets of extant saurians in terms of their homoplasy relative to molecular trees. Analysis of individual avian datasets finds osteological characters to be significantly more consistent with molecular data than soft characters are. Significant differences between morphological partitions were also observed in the age at which characters resolved on molecular trees. Osteological character changes occur relatively earlier in deep branches, whilst soft-tissue character transitions are more recent in shallow branches. The combined results demonstrate differences in evolutionary dynamics between morphological partitions. This may reflect evolutionary constraints acting on osteological characters, compared with the relative lability of soft characters. Furthermore, it provides some support to phylogenetic interpretations of fossil data, including dinosaurs, which are predominately osteological. Recent advances in amphibian and mammal phylogenetics may make these patterns possible to test for all tetrapods. [ABSTRACT FROM AUTHOR]

The phylogeny of coelacanths (Devonian-Recent) has been a matter of discussion at least since 1940s following the discovery of Latimeria chalumnae, and it remains as a revisited issue in most recent works. In this contribution, an updated phylogenetic analysis based on a new consensual data matrix is presented, merging most of the emendations proposed over the past two decades, and including a completely reviewed character scoring for some genera. Also, a complete Stratigraphic Tree Analysis is introduced, calibrating divergence times, branch lengths, potential ghost ranges and quantifying the stratigraphic fit of the trees. The topologies are congruent with previous analyses, with exceptions: Mawsoniidae and Latimeriidae include some genera previously not considered as such. Implied weights analysis indicates that this result is influenced by homoplasies. Time-scaled phylogenies show a great proportion of cladogenetic events concentrated in the Permian-Triassic transition, leading to the diversification of the Mesozoic modern stock of the group (Latimerioidei). In spite of some large ghost ranges (e.g. Latimeria, ranging from Middle-Upper Jurassic), the metrics indicate relatively good stratigraphic fits. Although additional reviews of both the character codings and the scorings of several taxa are still needed, these preliminary results can constitute an input for future macroevolutionary studies. [ABSTRACT FROM AUTHOR]

Cyrtandra (Gesneriaceae), with over 800 species, is a mega-diverse genus which presents considerable taxonomic challenges due to its size. A well-sampled phylogeny of the genus across Southeast Asia has confirmed that all but one of the sections within Clarke's 1883 genus-wide infrageneric classification are polyphyletic. It also shows that there are high levels of homoplasy in key morphological characters, although it is possible to use morphological characters to define clades in parts of the phylogenetic tree. There is some geographic structure in the phylogeny, but there is also evidence of dispersal between islands. A practical approach for tackling the taxonomy of Cyrtandra in the region, through phylogenetically informed taxonomic revisions of geographic areas, an approach which combines evidence from molecular, morphological and distribution data, is discussed. Completing our understanding of species diversity and delimitation in this genus will allow us to maximise the use of Cyrtandra as a tool for studying biogeography, speciation, diversification and conservation prioritisation in the rainforests of Southeast Asia. [ABSTRACT FROM AUTHOR]