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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]

Aquilaria (Thymelaeaceae), a tropical and subtropical plant, is one of the main genera that can produce agarwood. Aquilaria sinensis and Aquilaria yunnanensis are native Chinese tree species, and A. sinensis is China's main agarwood source. Agarwood is a nontimber forest product with high economic and medicinal value. First‐grade agarwood is sold as much as $100 000 per kilogram. There has been little research on the saprobic fungi associated with Aquilaria, with only 11 records having been reported. In the present study, 10 terrestrial saprobic fungi associated with A. sinensis and A. yunnanensis were collected in China. Based on morphological and phylogenetic studies, these 10 collections are introduced herein as one new genus (Aquilariomyces), nine new species – Aquilariomyces aquilariae, Corynespora aquilariae, Melomastia maomingensis, Nigrograna aquilariae, Parathyridariella aquilariae, Peroneutypa maomingensis, Phaeoseptum aquilariae, Pseudothyridariella aquilariae, and Triangularia aquilariae, and one known species (Camarographium clematidis). Descriptions, illustrations of morphological characteristics, photo plates, phylogenetic trees, and the results of a pairwise homoplasy index test (PHI) test results are provided. [ABSTRACT FROM AUTHOR]

The hypervariable region (HVR) in the control region of the mitochondrial DNA has frequently been used for population genetics and phylogeographic studies because of its highly variable nature. Although the HVR is beneficial for evaluating recent evolutionary history, including population demography, recent studies have implied the incidence of homoplasy in this region. To assess the accuracy of relying solely on the HVR for population genetics studies, molecular evolutionary analysis of the HVR, NADH-dehydrogenase subunit 2 (ND2), and cytochrome b genes were performed using 120 individuals of marbled flounder Pseudopleuronectes yokohamae. The HVR exhibited the highest genetic variability among the three regions, with sites showing high site-specific substitution rates. Considering the reticulate haplotype network structure and evolutionary linkages between regions, homoplastic mutations were indicated in the HVR in addition to ND2, underestimating genetic diversity. We found that homoplasy was less likely to affect coalescent-based demographic inferences in the population; however, there is still a potential risk of misinterpretation of population demography when solely using the HVR owing to its hypervariable nature. Collectively, we suggest analyzing other regions in addition to the HVR in fish population genetic research to improve accuracy and eliminate biases caused by homoplasy. [ABSTRACT FROM AUTHOR]

Abstract In addition to the type locality (the summit of Aprada-tepui, Bolívar State of Venezuela), the distribution of the egg-brooding frog Stefania satelles was long thought to include several isolated tabletop mountain (tepui) summits surrounding the large Chimantá Massif in Bolívar State (hence the Latin name “satelles”). However, multilocus molecular phylogenetic analyses have revealed that this taxon includes several undescribed morphologically cryptic species, and that S. satelles should be restricted to its type locality. Two tepui-summit species confused under that name in the literature remain to be named, and the present paper aims at describing these populations previously referred to as Stefania sp. 3 and S. sp. 5. Stefania sp. 3 is only known from the small summit of Angasima-tepui, while S. sp. 5 is only reported from the small summit of Upuigma-tepui, both mountains being located south of the Chimantá Massif. These new, phylogenetically distinct species are described based on external morphology and osteology and in comparison to close relatives in the S. ginesi clade, which consists exclusively of tepui summit species. Both new species have highly restricted geographic ranges (less than 3 km2) and should be listed as Critically Endangered according to IUCN criteria.

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]

In addition to the type locality (the summit of Aprada-tepui, Bolívar State of Venezuela), the distribution of the egg-brooding frog Stefania satelles was long thought to include several isolated tabletop mountain (tepui) summits surrounding the large Chimantá Massif in Bolívar State (hence the Latin name "satelles"). However, multilocus molecular phylogenetic analyses have revealed that this taxon includes several undescribed morphologically cryptic species, and that S. satelles should be restricted to its type locality. Two tepui-summit species confused under that name in the literature remain to be named, and the present paper aims at describing these populations previously referred to as Stefania sp. 3 and S. sp. 5. Stefania sp. 3 is only known from the small summit of Angasima-tepui, while S. sp. 5 is only reported from the small summit of Upuigma-tepui, both mountains being located south of the Chimantá Massif. These new, phylogenetically distinct species are described based on external morphology and osteology and in comparison to close relatives in the S. ginesi clade, which consists exclusively of tepui summit species. Both new species have highly restricted geographic ranges (less than 3 km2) and should be listed as Critically Endangered according to IUCN criteria. [ABSTRACT FROM AUTHOR]

Here, we propose, prove mathematically and discuss maximum and minimum measures of maximum parsimony evolution across 12 discrete phylogenetic character types, classified across 4467 morphological and molecular datasets. Covered character types are: constant, binary symmetric, multistate unordered (non‐additive) symmetric, multistate linear ordered symmetric, multistate non‐linear ordered symmetric, binary irreversible, multistate irreversible, binary Dollo, multistate Dollo, multistate custom symmetric, binary custom asymmetric and multistate custom asymmetric characters. We summarize published solutions and provide and prove a range of new formulae for the algebraic calculation of minimum (m), maximum (g) and maximum possible (gmax) character cost for applicable character types. Algorithms for exhaustive calculation of m, g and gmax applicable to all classified character types (within computational limits on the numbers of taxa and states) are also provided. The general algorithmic solution for minimum steps (m) is identical to a minimum spanning tree on the state graph or minimum weight spanning arborescence on the state digraph. Algorithmic solutions for character g and gmax are based on matrix mathematics equivalent to optimization on the star tree, respectively for given state frequencies and all possible state frequencies meeting specified numbers of taxa and states. We show that maximizing possible cost (gmax) with given transition costs can be equivalent to maximizing, across all possible state frequency combinations, the lowest implied cost of state transitions if any one state is ancestral on the star tree, via the solution of systems of linear equations. The methods we present, implemented in the Claddis R package, extend to a comprehensive range, the fundamental character types for which homoplasy may be measured under parsimony using m, g and gmax, including extra cost (h), consistency index (ci), retention index (ri) or indices based thereon. [ABSTRACT FROM AUTHOR]

Summary: 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. [ABSTRACT FROM AUTHOR]

The Brazilian Atlantic Forest, one the five main biodiversity hotspots in the world, still houses many organisms that are rare and unknown to science, mostly concentrated in mountain ranges. Herein, we describe a rare new species of Cambeva from the Rio Tietê drainage at the Serra da Mantiqueira, exhibiting a caudal fin color pattern comprising a light-yellowish–white bar posteriorly edged by a black pigmented area. A similar color pattern was described for C. castroi, C. diabola, and C. melanoptera, also endemic to the Rio Paraná basin, and considered evidence of close relationships among these three species. However, other morphological characteristics highly suggest that the new species is not closely related to C. castroi, C. diabola, and C. melanoptera). Herein, we perform a molecular phylogenetic analysis using two mitochondrial genes and one nuclear gene, including all species with that bicolored caudal pattern. The analysis strongly supports the new species as a member of the alpha-clade, and therefore as distantly related to those three species belonging to the beta-clade, indicating that this color pattern has homoplastically arisen in Cambeva. The data reported here reinforce the urgent need for field studies to better understand the different evolutionary patterns found in the genus, since an intense process of environmental degradation is in course. [ABSTRACT FROM AUTHOR]

Although simulations have shown that implied weighting (IW) outperforms equal weighting (EW) in phylogenetic parsimony analyses, weighting against homoplasy lacks extensive usage in palaeontology. Iterative modifications of several phylogenetic matrices in the last decades resulted in extensive genealogies of datasets that allow the evaluation of differences in the stability of results for alternative character weighting methods directly on empirical data. Each generation was compared against the most recent generation in each genealogy because it is assumed that it is the most comprehensive (higher sampling), revised (fewer misscorings) and complete (lower amount of missing data) matrix of the genealogy. The analyses were conducted on six different genealogies under EW and IW and extended implied weighting (EIW) with a range of concavity constant values (k) between 3 and 30. Pairwise comparisons between trees were conducted using Robinson–Foulds distances normalized by the total number of groups, distortion coefficient, subtree pruning and regrafting moves, and the proportional sum of group dissimilarities. The results consistently show that IW and EIW produce results more similar to those of the last dataset than EW in the vast majority of genealogies and for all comparative measures. This is significant because almost all of these matrices were originally analysed only under EW. Implied weighting and EIW do not outperform each other unambiguously. Euclidean distances based on a principal components analysis of the comparative measures show that different ranges of k‐values retrieve the most similar results to the last generation in different genealogies. There is a significant positive linear correlation between the optimal k‐values and the number of terminals of the last generations. This could be employed to inform about the range of k‐values to be used in phylogenetic analyses based on matrix size but with the caveat that this emergent relationship still relies on a low sample size of genealogies. [ABSTRACT FROM AUTHOR]

The Asteroidea, Ophiuroidea, and Stenuroidea are the derived classes of the subphylum Asterozoa, the class Somasteroidea stemward within the subphylum. The Stenuroidea, originally recognized at the ordinal level and assigned to the Ophiuroidea, was judged unique and therefore cannot be subsumed within the Ophiuroidea and has been separated at the class level. Somasteroidea have multiple adaxial ossicles, and Asteroidea and Ophiuroidea both a single adaxial. The necessary and sufficient condition for assignment to the Stenuroidea is strict presence of either two, or rarely three or four, adaxial ossicles. Aside from ambulacral column configuration, many stenuroid genera are similar to non-stenuroid asterozoans of all ages, natural selection apparently separating overall form from ambulacral column expression. Selective advantage(s) of the 'extra' adaxial might relate to presence of enlarged podia seated in the enlarged podial receptacles, and/or enhanced ambulacral flexibility. Intrageneric uniformity of expression is taken as favoring enduring selective advantage(s) that arose with a monophyletic stenuroid origin. Alternatively, similarities between certain stenuroids and certain asteroids and ophiuroids can be considered indicative of homoplasy, an approach given the current state of knowledge that imposes serious difficulties on phylogenetic interpretation. To place the Stenuroidea in context, the concept of the subphylum Asterozoa is surveyed along with concepts of those early echinoderm groups that have been the preferred subphylum outgroup candidates. Because a phylogenetic analysis failed to yield clear stenuroid clustering between the class and generic levels, intermediate taxonomic categories remain problematic. Eight available familial names are retained and the new families Hystrigasteridae, Stuertzasteridae, Erinaceasteridae, and Ptilonasteridae are recognized. The eighteen known stenuroid genera are reviewed. [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]

ABSTRACT The retention index (r or ri) is used to compute the amount of similarity in a character that can be interpreted as a synapomorphy on a given cladogram. In the case of autapomorphies, the retention index assumes the form 0 / 0, which is a mathematically indeterminate form. Originally, this issue was resolved by assigning a value of one to the retention index in such cases. However, some authors did not follow this original interpretation and assumed that, in this case, the retention index must assume a value of zero. In this note, we present two arguments supporting the original definition. The first argument is an application of the concept of limit from calculus to determine the assumed value of the retention index function in this specific situation. The second argument is a biological one that invokes the original definitions of autapomorphy and synapomorphy.

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]

The Inonotus linteus complex, predominantly reported from East Asia, Mesoamerica and Caribbean countries, was circumscribed into Tropicoporus as one of the new genera, based on morphological and phylogenetic data. The present paper describes four new species of Tropicoporus from India. Morphological characteristics and phylogenetic analyses, based on ITS and nLSU data, delimited the new species, which are named T. cleistanthicola, T. indicus, T. pseudoindicus and T. tamilnaduensis. The pairwise homoplasy index (PHI) test was done to confirm the distinctive nature of the new species. The traits of Indian species remain distinct from one another, except for the pileate basidiome with the mono-dimitic hyphal system, cystidioles and broadly ellipsoid basidiospores. Descriptions, illustrations, PHI test results and a phylogenetic tree to show the position of the new species are provided. In addition, an identification key to Tropicoporus in Asia and an African species is given. [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]

This article discusses the concept of homology in neural systems across different animal phyla. The authors argue that there are no recognized neuronal homologies among three basal eumetazoan lineages: Ctenophora, Cnidaria, and Bilateria. The article explores the genealogy of neurons and the hypothesis of neuronal polyphyly, as well as the molecular markers of different neurotransmitters and neurons in various animal species. It emphasizes the challenges in identifying homologous neurons across taxa and suggests the need for comprehensive comparative single-cell genomic data. The document provides a list of references and citations related to the topic of neuronal identity and the evolution of nervous systems, offering valuable insights into the diversity and origins of neurons and neurotransmitters. Another document is a list of references to scientific articles exploring different aspects of homology thinking and its applications in evolutionary biology and neurobiology, providing valuable resources for library patrons interested in studying homology and its significance in different fields of science. [Extracted from the article]

Members of the genus Phrynosoma all exhibit asperities upon the parietal and squamosal. We examined μ‐CT scans of the dermatocrania of ontogenetic series of all but two of the species of Phrynosoma, and defined parietal and squamosal "horns", distinguishing them from tubercles. We counted parietal and squamosal horns and used phylogenetic analysis to reconstruct the plesiomorphic horn numbers for these bones. Based upon this, we propose and test hypotheses of evolutionary homology for these asperities and conclude the following: (1) a plesiomorphic horn array is retained among the species of Phrynosoma; the horns are paramorphs, each identifiable as an evolutionary homologue; (2) an autapomorphic additional pair of parietal horns in P. solare has been recruited from a pair of tubercles associated with the plesiomorphic parietal horns; (3) an additional anterior squamosal horn in P. solare and the Brevicauda species is derived from a tubercle recruited homoplasiously in these taxa; (4) the anteriormost squamosal horn of the plesiomorphic series in the species of the coronatum species group is highly reduced and is subsumed within the posteriormost jugal asperity and (5) an apparent additional squamosal horn exhibited by P. ditmarsi and P. modestum is instead an enlarged submarginal tubercle, a homoplasy for these species. [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]

Interspecific hybridization events are on the rise in natural systems due to climate change disrupting species barriers. Across taxa, microsatellites have long been the molecular markers of choice to identify admixed individuals. However, with the advent of high‐throughput sequencing easing the generation of genome‐wide datasets, incorrect reports of hybridization resulting from microsatellite technical artefacts have been uncovered in a growing number of taxa. In the marine zooplankton genus Calanus (Copepoda), whose species are used as climate change indicators, microsatellite markers have suggested hybridization between C. finmarchicus and C. glacialis, while other nuclear markers (InDels) never detected any admixed individuals, leaving the scientific community divided. Here, for the first time, we investigated the potential for hybridization among C. finmarchicus, C. glacialis, C. helgolandicus and C. hyperboreus using two large and independent SNP datasets. These were derived firstly from a protocol of target‐capture applied to 179 individuals collected from 17 sites across the North Atlantic and Arctic Oceans, including sympatric areas, and second from published RNA sequences. All SNP‐based analyses were congruent in showing that Calanus species are distinct and do not appear to hybridize. We then thoroughly re‐assessed the microsatellites showing hybrids, with the support of published transcriptomes, and identified technical issues plaguing eight out of 10 microsatellites, including size homoplasy, paralogy, potential for null alleles and even two primer pairs targeting the same locus. Our study illustrates how deceptive microsatellites can be when applied to the investigation of hybridization. [ABSTRACT FROM AUTHOR]

Recent phylogenetic studies have challenged the traditional classification of the subtribe Cynoglossinae, which was based on nutlet characteristics. To investigate the evolution of fruit traits related to dispersal modes in this complex group, we conducted a study using scanning electron microscopy to examine 28 taxa representing all previously recognized lineages of the subtribe. Cynoglossinae displays four main types of nutlets: marginate, emarginate, flat wing, and incurved wing. Our findings reveal the arrangement of glochids and their structure, including the number of apical hooks, and their surface ornamentation is highly variable both across and within these four main types. We reconstructed the phylogenetic tree with four main clades (i.e., Clades I–IV) using Maximum likelihood analysis. In addition, we mapped four nutlet traits (i.e., nutlet margin, nutlet glochid, glochid sculpture, and glochid hooks) associated with different dispersal modes using ancestral state reconstruction analysis. The ancestor of subtribe Cynoglossinae was inferred to have marginate and glochidiate nutlets, with glochids externally provided with complex spiny tubercles and bearing at least four hooks at the tip as well as epizoochory dispersal mode. These ancestral states have been retained in Clade II (East Asian-Australian-African Cynoglossum-Lindelofia clade) and Clade III (Mediterranean-Asian Cynoglossum-Solenanthus-Trachelanthus clade), with several independent shifts to emarginate fruits. Transitions from marginate to wide-winged nutlets have occurred at least four independent times, facilitating wind-assisted dispersal in Clade I (Microparacaryum clade), Clade IV (Paracaryum-Mattiastrum-Rindera clade), Rindera tetraspis, and Mattiastrum crista-galli (both belonging to Clade III), where a transition from tuberculate to papillate surface has also occurred. [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]

Selaginella is the largest and most taxonomically complex genus in lycophytes. The fact that over 750 species are currently treated in a single genus makes Selaginellales/Selaginellaceae unique in pteridophytes. Here we assembled a dataset of six existing and newly sampled plastid and nuclear loci with a total of 684 accessions (74% increase of the earlier largest sampling) representing ca. 300 species to infer a new phylogeny. The evolution of 10 morphological characters is studied in the new phylogenetic context. Our major results include: (1) the nuclear and plastid phylogenies are congruent with each other and combined analysis well resolved and strongly supported the relationships of all but two major clades; (2) the Sinensis group is resolved as sister to S. subg. Pulviniella with strong support in two of the three analyses; (3) most morphological characters are highly homoplasious but some characters alone or combinations of characters well define the major clades in the family; and (4) an infrafamilial classification of Selaginellaceae is proposed and the currently defined Selaginella s.l. is split into seven subfamilies (corresponding to the current six subgenera + the Sinensis group) and 19 genera (the major diagnosable clades) with nine new species-poor genera. We support the conservation of Selaginella with a new type, S. flabellata, to minimize nomenclatural instability. We provide a key to subfamilies and genera, images illustrating their morphology, their morphological and geographical synopses, a list of constituent species, and necessary new combinations. This new classification will hopefully facilitate communication, promote further studies, and help conservation.

Background A general view in the study of pollination syndromes is that floral traits usually represent convergent floral adaptations to specific functional pollinator groups. However, the definition of convergence is elusive and contradictory in the literature. Is convergence the independent evolution of either the same trait or similar traits with the same function? A review of the concept of convergence in developmental biology and phylogenetic systematics may shed new light in studies of pollination syndromes. Scope The aims of this article are (1) to explore the notion of convergence and other concepts (analogy, homoplasy and parallelism) within the theory and practice of developmental evolution and phylogenetic systematics; (2) to modify the definitions of syndromes in order to embrace the concepts of analogy and convergence; (3) to revisit the bat pollination syndrome in the context of angiosperm phylogeny, with focus on the showy 'petaloid' organs associated with the syndrome; (4) to revisit the genetic-developmental basis of flower colour; (5) to raise evolutionary hypotheses of floral evolution associated with the bat pollination syndrome; and (6) to highlight some of the current frontiers of research on the origin and evolution of flowers and its impact on pollination syndrome studies in the 21st century. Conclusions The inclusion of the concepts of analogy and convergence within the concept of syndromes will constitute a new agenda of inquiry that integrates floral biology, phylogenetic systematics and developmental biology. Phyllostomid and pteropodid bat pollination syndrome traits in eudicots and monocots represent cases of analogous and convergent evolution. Pollination syndromes are a multivariate concept intrinsically related to the understanding of flower organogenesis and evolution. The formulation of hypotheses of pollination syndromes must consider the phylogenetic levels of universality for both plant and animal taxa, flower development, genetics, homology and evolution, and a clear definition of evolutionary concepts, including analogy, convergence, homoplasy and parallelism. [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]

We present a novel identification tool called PhyloKey , based on the method of morphology-based, phylogenetic binning developed within the software package RAxML. This method takes a reference data set of species for which both molecular and morphological data are available, computes a molecular reference tree, maps the morphological characters on the tree, and computes weights based on their level of consistency versus homoplasy using maximum likelihood (ML) and maximum parsimony (MP). Additional units for which only morphological data are known are then binned onto the reference tree, calculating bootstrap support values for alternative placements. This approach is modified here to work as an identification tool which uses the same character coding approach as interactive keys. However, rather than identifying individual samples through a progressive filtering process when entering or selecting characters, query samples are binned in batch mode to all possible alternative species in the tree, with each placement receiving a bootstrap support adding to 100% for all alternative placements. In addition to the fact that, after scoring a character matrix, a large number of specimens can be identified at once in short time, all possible alternative identifications are immediately apparent and can be evaluated based on their bootstrap support values. We illustrate this approach using the basidiolichen genus Cora , which was recently shown to contain hundreds of species. We also demonstrate how the PhyloKey approach can aid the restudying of herbarium samples, adding further value to these collections and contributing with large quantitative data matrices to 'non-molecular museomics'. Our analysis showed that PhyloKey identifies species correctly with as low as 50% of the characters sampled, depending on the nature of the reference tree and the character weighting scheme. Overall, a molecular reference tree worked best, but a randomized reference tree gave more consistent results, whereas a morphological reference tree performed less well. Surprisingly, even character weighting gave the best results, followed by parsimony weighting and then maximum likelihood weighting. [ABSTRACT FROM AUTHOR]

Geometric morphometrics (GM) is a powerful analytical tool that enables complete quantification of shapes. Its use in Botany has a great potential for complementing plant evolutionary and ecological studies. Taxonomic delimitation in Carex has been complicated due to reduction of characters and frequent homoplasy. This problem is more marked in cases where the species exhibit dwarfism. South America is the continent with the least understood Carex flora. The systematic relationships of some bizarre-looking groups were not unraveled until molecular phylogenetic studies resolved their relationships. In particular, there are two species only known from their type material whose affinities remain uncertain: Carex herteri and C. hypsipedos. These two taxa are acaulescent plants that respectively grow in the Uruguayan pampa and Peruvian high-altitude meadows. Recently, both species were ascribed to the Carex phalaroides group (subgen. Psyllophorae, sect. Junciformes) due to superficial morphological similarities, such as the androgynous peduncled spikes. However, their character combination is also coincident for its circumscription to sect. Abditispicae species. Nevertheless, in the absence of confirmation from molecular analyses, their placement must be considered preliminary until additional data can be provided. In this work we employ for the first time geometric morphometrics (GM) tools to assess the systematic affinities of two taxonomically problematic sedge species based on fruit shape. We compared utricle morphology of C. herteri and C. hypsipedos with that of C. phalaroides group and species in sect. Abditispicae. To this end we used GM and traditional morphometric approaches. Utricle shape variation along with other morphological features support the exclusion of these two species from the C. phalaroides gr. and, at the same time, show clear affinities of C. herteri to sect. Abditispicae. Carex hypsipedos remains as an incertae sedis species. Our work shows the potential utility of GM for the exploration of systematic affinities in sedges and in other graminoids. [ABSTRACT FROM AUTHOR]

Retrotransposon insertion patterns facilitate a virtually homoplasy-free picture of phylogenetic history. Still, a few most likely random parallel insertions or deletions result in rare cases of homoplasy in primates. The following question arises: how frequent is retrotransposon homoplasy in other phylogenetic clades? Here, we derived genome insertion data of toothed whales to evaluate the extension of homoplasy in a representative laurasiatherian group. Among more than a thousand extracted and aligned retrotransposon loci, we detected 37 cases of precise parallel insertions in species that are separated by over more than 10 million years, a time frame which minimizes the effects of incomplete lineage sorting. We compared the phylogenetic signal of insertions with the flanking sequences of these loci to further exclude potential polymorphic loci derived by incomplete lineage sorting. We found that the phylogenetic signals of retrotransposon insertion patterns exhibiting true homoplasy differ from the signals of their flanking sequences. In toothed whales, precise parallel insertions account for around 0.18–0.29% of insertion cases, which is about 12.5 times the frequency of such insertions among Alus in primates. We also detected five specific deletions of retrotransposons on various lineages of toothed whale evolution, a frequency of 0.003%, which is slightly higher than such occurrences in primates. Overall, the level of retrotransposon homoplasy in toothed whales is still marginal compared to the phylogenetic diagnostic retrotransposon presence/absence signal. [ABSTRACT FROM AUTHOR]

Despite the obstacles facing marine colonists, most lineages of aquatic organisms have colonized and diversified in freshwaters repeatedly. These transitions can trigger rapid morphological or physiological change and, on longer timescales, lead to increased rates of speciation and extinction. Diatoms are a lineage of ancestrally marine microalgae that have diversified throughout freshwater habitats worldwide. We generated a phylogenomic data set of genomes and transcriptomes for 59 diatom taxa to resolve freshwater transitions in one lineage, the Thalassiosirales. Although most parts of the species tree were consistently resolved with strong support, we had difficulties resolving a Paleocene radiation, which affected the placement of one freshwater lineage. This and other parts of the tree were characterized by high levels of gene tree discordance caused by incomplete lineage sorting and low phylogenetic signal. Despite differences in species trees inferred from concatenation versus summary methods and codons versus amino acids, traditional methods of ancestral state reconstruction supported six transitions into freshwaters, two of which led to subsequent species diversification. Evidence from gene trees, protein alignments, and diatom life history together suggest that habitat transitions were largely the product of homoplasy rather than hemiplasy, a condition where transitions occur on branches in gene trees not shared with the species tree. Nevertheless, we identified a set of putatively hemiplasious genes, many of which have been associated with shifts to low salinity, indicating that hemiplasy played a small but potentially important role in freshwater adaptation. Accounting for differences in evolutionary outcomes, in which some taxa became locked into freshwaters while others were able to return to the ocean or become salinity generalists, might help further distinguish different sources of adaptive mutation in freshwater diatoms. [ABSTRACT FROM AUTHOR]

Abstract The hemiphractid frog genus Stefania is one of the many ancient (near-) endemic lineages of vertebrates inhabiting the biodiverse Pantepui biogeographical region in the Guiana Shield Highlands of northern South America—the famous “Lost World” of Arthur Conan Doyle. Previous molecular analyses of the genus Stefania have indicated that species boundaries and phylogenetic relationships are often incongruent with morphological traits in that clade. A substantial number of “taxonomically cryptic” species, often microendemic, remain to be described. This is notably the case for an isolated population from the summit of Wei-Assipu-tepui, a small table-top mountain at the border between Guyana and Brazil. That population was previously known as Stefania sp. 6 and belongs to the S. riveroi clade. The new species is phylogenetically distinct, but phenotypically extremely similar to S. riveroi, a taxon found only on the summit of Yuruaní-tepui in Venezuela and recovered as sister to all the other known species in the S. riveroi clade. The new taxon is described based on morphology and osteology. Data about genetic divergences within the S. riveroi clade are provided. A new synapomorphy for the genus Stefania is proposed: the presence of a distal process on the third metacarpal. Amended definitions are offered for the three other species in the S. riveroi clade (S. ayangannae, S. coxi, S. riveroi). The new species should be listed as Critically Endangered according to IUCN criteria.

Previous molecular analyses of the frog genus Stefania have shown that species boundaries in that group are often difficult to delineate when solely based on morphology. As a consequence, "taxonomically cryptic" species are not uncommon in the genus. Several highland Stefania species remain to be described, some potentially critically endangered due to their highly restricted geographic ranges. One case is the microendemic Stefania population from the summit of Murisipán-tepui, a poorly explored table-top mountain in the Los Testigos Massif, a small tepui mountain range located north to the much larger Chimantá Massif in southern Venezuela. That population, mistaken as S. satelles for two decades, was later reported as Stefania sp. 2 and belongs to the S. ginesi clade. The new species is phylogenetically distinct but phenotypically similar to S. satelles, a taxon restricted to its type-locality, i.e. the summit of Aprada-tepui in Venezuela. The new species is described based on morphology and cranial osteology. Molecular divergences with S. satelles are high (> 8%) in the barcoding fragment of 16S rRNA. Amended definitions for the two other described species in the S. ginesi clade (S. ginesi and S. satelles) are also provided. The new species should be listed as critically endangered according to IUCN criteria. [ABSTRACT FROM AUTHOR]

There is widespread agreement that "homology" designates something of fundamental biological importance, but no consensus as to how precisely that "something" should be defined, recognized, or theorized. Philosophical observers of this situation commonly focus on tensions between historical and mechanistic explications of homological sameness by appeal, respectively, to common ancestry and shared developmental resources. This paper uses select historical episodes to decenter those tensions and challenge standard narratives about how they arose. Haas and Simpson (1946) influentially defined "homology" simply as "similarity due to common ancestry." They claimed historical precedent in Lankester (1870) but seriously oversimplified his views in the process. Lankester did prioritize common ancestry, but he also raised mechanistic questions that resonate with contemporary evo devo work on homology. The rise of genetics inspired similar speculations in twentieth-century workers like Boyden (1943), a zoologist who engaged Simpson in a 15-year debate over homology. Though he shared Simpson's devotion to taxonomy and his interest in evolutionary history, he favored a more operational and less theoretical homology concept. Their dispute is poorly captured by current analyses of the homology problem. It calls for further study of the complex relationship between concepts and the epistemic goals they serve. • G. G. Simpson advanced a familiar but flawed narrative about the development of 'homology'. • Contra Simpson, Lankester (1870) saw 'homogeny' and 'homoplasy' as overlapping categories. • Lankester and others anticipate recent attempts to integrate mechanistic and historical views. • Simpson insisted that the definition of 'homology' should be explanatory; Alan Boyden disagreed. • Previous work has likely underestimated the variability of epistemic goals for 'homology'. [ABSTRACT FROM AUTHOR]

The sauropod genus Mamenchisaurus, from the Late Jurassic–Early Cretaceous of East Asia, has a convoluted taxonomic history. Although included in the first cladistic analysis of sauropods, only recently has the monophyly of Mamenchisaurus, and the anatomical diversity of the many penecontemporaneous East Asian eusauropods, been evaluated critically. Here, we re-describe the holotype and only specimen of M. sinocanadorum. Although the original diagnosis is no longer adequate, we identify several autapomorphies that support the validity of this species, including an elongate external mandibular fenestra and distinctive pneumatic structures on the cervical centra. We incorporate new data into a phylogenetic character matrix that also includes Bellusaurus and Daanosaurus, both of which are known only from juvenile material and are often hypothesized to be neosauropods (or close relatives thereof). We recover all species of Mamenchisaurus as part of a radiation of predominantly Middle–Late Jurassic East Asian eusauropods, but the genus is non-monophyletic, underscoring the need for further systematic revision of mamenchisaurid taxonomy. Analyses that score ontogenetically variable characters ambiguously recover Bellusaurus and Daanosaurus as juvenile mamenchisaurids, a hypothesis supported by several features that are unique to mamenchisaurids or exhibit little homoplasy, including anteriorly bifurcate cervical ribs. Finally, computed-tomography reveals extensive vertebral pneumaticity in M. sinocanadorum that is comparable to that of the largest sauropods, and updated scaling analyses imply a neck over 14 m long, rivalling estimates for other exceptionally long-necked sauropods. Previous work has suggested that the elongated cervical ribs of particularly long-necked sauropods such as M. sinocanadorum stabilized the neck by limiting its mobility. Given that extent of pneumaticity responds dynamically to a bone's habitual loading, we propose that long cervical ribs – and other structural modifications that limited flexibility – promoted the evolution of increasingly long necks by producing a more predictable biomechanical milieu amenable to increased pneumatization. [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]

The hemiphractid frog genus Stefania is one of the many ancient (near-) endemic lineages of vertebrates inhabiting the biodiverse Pantepui biogeographical region in the Guiana Shield Highlands of northern South America—the famous "Lost World" of Arthur Conan Doyle. Previous molecular analyses of the genus Stefania have indicated that species boundaries and phylogenetic relationships are often incongruent with morphological traits in that clade. A substantial number of "taxonomically cryptic" species, often microendemic, remain to be described. This is notably the case for an isolated population from the summit of Wei-Assipu-tepui, a small table-top mountain at the border between Guyana and Brazil. That population was previously known as Stefania sp. 6 and belongs to the S. riveroi clade. The new species is phylogenetically distinct, but phenotypically extremely similar to S. riveroi, a taxon found only on the summit of Yuruaní-tepui in Venezuela and recovered as sister to all the other known species in the S. riveroi clade. The new taxon is described based on morphology and osteology. Data about genetic divergences within the S. riveroi clade are provided. A new synapomorphy for the genus Stefania is proposed: the presence of a distal process on the third metacarpal. Amended definitions are offered for the three other species in the S. riveroi clade (S. ayangannae, S. coxi, S. riveroi). The new species should be listed as Critically Endangered according to IUCN criteria. [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]

The earthworm genus Helodrilus comprises about 20 species with distributions ranging from the Iberian Peninsula to the Caucasus, through Central Europe, the Balkans, Anatolia and the Levant. The species prefer moist habitats and are often found in the mud of river banks, in swamps or in caves. Although a high degree of morphological variability is observed in the taxonomic characters, the genus shares a common feature: the absence of nephridial bladders. In this study, we clarify the phylogeny and taxonomy of the genus Helodrilus using an integrated approach including a multilocus molecular phylogenetic analysis and thorough morphological examination of several species across the putative Helodrilus area of distribution. The findings of this study have led to the genus Helodrilus being split and to the description of two new genera and two new species: Coventina Szederjesi, Sarbu & Csuzdi gen. nov. and Imetescolex movilensis Szederjesi, Sarbu & Csuzdi gen. & sp. nov. The highly homoplasic nature of the absence of nephridial bladders was also revealed. [ABSTRACT FROM AUTHOR]

The hyper‐diverse clade Passeriformes (crown group passerines) comprises over half of extant bird diversity, yet disproportionately few studies have targeted passerine comparative anatomy on a broad phylogenetic scale. This general lack of research attention hinders efforts to interpret the passerine fossil record and obscures patterns of morphological evolution across one of the most diverse clades of extant vertebrates. Numerous potentially important crown passeriform fossils have proven challenging to place phylogenetically, due in part to a paucity of phylogenetically informative characters from across the passerine skeleton. Here, we present a detailed analysis of the morphology of extant passerine carpometacarpi, which are relatively abundant components of the passerine fossil record. We sampled >70% of extant family‐level passerine clades (132 extant species) as well as several fossils from the Oligocene of Europe and scored them for 54 phylogenetically informative carpometacarpus characters optimised on a recently published phylogenomic scaffold. We document a considerable amount of previously undescribed morphological variation among passerine carpometacarpi, and, despite high levels of homoplasy, our results support the presence of representatives of both crown Passeri and crown Tyranni in Europe during the Oligocene. [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.

Abstract Background Citrus species are among the most important and widely consumed fruit trees in the world and are subjected to increasing global cultivation. Sweet orange (Citrus sinensis L. Osbeck) is one of 30 species of citrus which is cultivated in different regions of Iran. In this study, 80 trees of 13 sweet orange cultivars of Mazandaran province were studied for genetic diversity and fingerprinting by five short simple repeat (SSR) marker. Results The studied cultivars showed a high degree of genetic variability with an average genetic polymorphism of 98.46%. Behshahr and Jadeh Ghadim2 genotypes had the highest and lowest values in Nei genetic diversity, number of effective alleles, and Shannon index, respectively. Based on k-means clustering, the studied genotypes were divided into two main different groups. The high magnitude of genetic similarity between replicates of different cultivars indicated a potential case of homonymy or synonymy. DAPC analysis showed genetic admixture among some of the cultivars. The heatmap plot illustrated the alleles involved in cultivar differentiation. The CAPs analysis of monomorphic alleles of SSR loci indicated that these alleles differ in their sequences which add up to the genetic variability of citrus germplasm. Conclusion In general, SSR markers, due to their codominant nature and abundance in genome, are a good indicator for cultivar fingerprinting and hybrid prediction in orange cultivars. The present results showed the high diversity of sweet orange trees in different cultivars in the north of the country.

This paper addresses a recent claim by Miyashita and co-authors that the filter-feeding larval lamprey is a new evolutionary addition to the lamprey life-cycle and does not provide information about early vertebrates, in contrast to the traditional view that this ammocoete stage resembles the first vertebrates. The evidence behind this revolutionary claim comes from fossil lampreys from 360–306 Mya that include young stages – even yolk-sac hatchlings – with adult (predacious) feeding structures. However, the traditional view is not so easily dismissed. The phylogeny on which the non-ammocoete theory is based was not tested in a statistically meaningful way. Additionally, the target article did not consider the known evidence for the traditional view, namely that the complex filter-feeding structures are highly similar in ammocoetes and the invertebrate chordates, amphioxus and tunicates. In further support of the traditional view, I show that ammocoetes are helpful for reconstructing the first vertebrates and the jawless, fossil stem gnathostomes called ostracoderms – their pharynx, oral cavity, mouth opening, lips and filter-feeding mode (but, ironically, not their mandibular/jaw region). From these considerations, I offer a scenario for the evolution of vertebrate life-cycles that fits the traditional, ammocoete-informed theory and puts filter feeding at centre stage. [ABSTRACT FROM AUTHOR]

Osteostraci and Galeaspida are stem-gnathostomes, occupying a key phylogenetic position for resolving the nature of the jawless ancestor from which jawed vertebrates evolved more than 400 million years ago. Both groups are characterized by the presence of rigid headshields that share a number of common morphological traits, in some cases hindering the resolution of their interrelationships and the exact nature of their affinities with jawed vertebrates. Here, we explore the morphological and functional diversity of osteostracan and galeaspid headshields using geometric morphometrics and computational fluid dynamics to constrain the factors that promoted the evolution of their similar morphologies and informing on the ecological scenario under which jawed vertebrates emerged. Phylomorphospace, Mantel analysis and Stayton metrics demonstrate a high degree of homoplasy. Computational fluid dynamics reveals similar hydrodynamic performance among morphologically convergent species, indicating the independent acquisition of the same morphofunctional traits and, potentially, equivalent lifestyles. These results confirm that a number of the characters typically used to infer the evolutionary relationships among galeaspids, osteostracans and jawed vertebrates are convergent in nature, potentially obscuring understanding of the assembly of the gnathostome bodyplan. Ultimately, our results reveal that while the jawless relatives of the earliest jawed vertebrates were ecologically diverse, widespread convergence on the same hydrodynamic adaptations suggests they had reached the limits of their potential ecological diversity—overcome by jawed vertebrates and their later innovations. [ABSTRACT FROM AUTHOR]

Karooprosbole magnifica gen. et sp. nov., oldest African cicadomorphan Prosbolidae, is described from middle Permian deposits (Abrahamskraal Formation, Karoo Supergoup) at the Onder Karoo locality in South Africa. It is compared to the genera currently included in Prosbolidae but also those in the Tettigarctidae: Cicadoprosbolinae. The limits and definitions of the two groups are discussed, because the new taxon has diagnostic characters of venation common to both groups. Also, some characters currently used to define these groups are clearly subject to homoplasy. This suggests that a phylogenetic analysis of the whole extant and fossil Cicadomorpha is needed to better define these families and verify their monophyly. [ABSTRACT FROM AUTHOR]

Examples of evolution, extinction and homoplasy of the larger benthic foraminifera (LBF) occur throughout their history. Since the Carboniferous, LBF have thrived in carbonate-rich tropical and subtropical shallow-marine shelf environments. Their high abundance and diversity are due primarily to their extraordinary ability to inhabit a range of ecological niches and by hosting a variety of symbionts. Attaining relatively large, centimetre-scale sizes, made some forms very specialized and vulnerable to rapid ecological changes. For this reason, some LBF have shown a tendency to suffer periodically during major extinctions, especially when environmental conditions have changed rapidly and/or substantially. This, however, makes them valuable biostratigraphic microfossils and, in addition, gives invaluable insight into the spatial and temporal process of biological evolution, such as convergent/homoplasy and homology/iterative evolution. Here the evolutionary behavior of two important morphological types that occurred throughout the history of the LBF are discussed, namely the planispiral-fusiform test as typified by the fusulinids in the Late Paleozoic and the alveolinids in the Mid-Cretaceous and Neogene, and the three-layered discoid lenticular test as characterized by the orbitoids in the Mid- to Late Cretaceous, the orthophragminids in the Paleogene, and lepidocyclinids in the Oligocene to Quaternary. Understanding the propensity of these forms to convergent and iterative evolution, with the repeated re-occurrence of certain morphological features, is essential in understanding and constructing their phylogenetic relationships more generally within the main groups of the LBF. The insights gained from the history of these LBF have wider implications, and provide a more general understanding of the impacts of climate and ecological changes as driving forces for biological evolution. [ABSTRACT FROM AUTHOR]

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]