Morphological characters in light of new molecular phylogenies: the caudal-fin skeleton of Ovalentaria

The Ovalentaria is a taxon of teleosts that has been proposed based on molecular analyses only. Previously widely separated families are assembled in this taxon. For the first time, the Ovalentaria are analysed using a comparative morphological approach. The caudal-fin skeleton of 355 species covering all 48 ovalentarian families are examined in cleared and stained specimens, µCT datasets and X-ray images as well as from the literature. A total of 38 morphological characters are evaluated and used for ancestral character state reconstructions and phylogenetic analyses. Results provide hypotheses for a scenario of the evolution of the caudal-fin skeleton and its ground plan in Ovalentaria. An evolutionary trend towards the reduction of skeletal elements in the caudal fin is observed. Connections between the evolution of the caudal-fin skeleton and modes of locomotion found in ovalentarian taxa are discussed. Phylogenetic analyses based on the caudal-fin morphology provide topologies for intra-ovalentarian relationships that largely agree with molecular hypotheses.

The accessory neural arch: development, morphology, and systematic distribution

The accessory neural arch is an oddly distributed character present in several non-acanthomorph teleostean taxa. Its homology was often implied but never satisfyingly tested. In this study, we attended this pending problem. We analyzed the morphology, development, and systematic distribution of the accessory neural arch in teleosts. Using a comprehensive taxon sampling of cleared and stained specimens, we evaluated if the accessory neural arch fulfils existing homology criteria. We then combined these data with recent genetic phylogenies and ancestral character state estimation to reconstruct the evolutionary history of the accessory neural arch. While its gross morphology and development fit homology criteria, results from ancestral character state estimations suggest multiple independent evolutions within teleosts. Although the accessory neural arch cannot be homologous between several teleostean taxa, the concept of parallelism may explain the presence of such a similar character in a variety of non-acanthomorph teleostean taxa.

Taxonomy, Phylogeny, Molecular Dating and Ancestral State Reconstruction of Xylariomycetidae (Sordariomycetes)

Xylariomycetidae ( Ascomycota ) is a highly diversified group with variable stromatic characters. Our research focused on inconspicuous stromatic xylarialean taxa from China, Italy, Russia, Thailand and the United Kingdom. Detailed morphological descriptions, illustrations and combined ITS-LSU- rpb 2- tub 2- tef 1 phylogenies revealed 38 taxa from our collections belonging to Amphisphaeriales and Xylariales . A new family ( Appendicosporaceae ), five new genera ( Magnostiolata , Melanostictus , Neoamphisphaeria , Nigropunctata and Paravamsapriya ), 27 new species ( Acrocordiella photiniicola , Allocryptovalsa sichuanensis , Amphisphaeria parvispora , Anthostomella lamiacearum , Apiospora guiyangensis , Ap. sichuanensis , Biscogniauxia magna , Eutypa camelliae , Helicogermslita clypeata , Hypocopra zeae , Magnostiolata mucida , Melanostictus longiostiolatus , Me. thailandicus , Nemania longipedicellata , Ne. delonicis , Ne. paraphysata , Ne. thailandensis , Neoamphisphaeria hyalinospora , Neoanthostomella bambusicola , Nigropunctata bambusicola , Ni. nigrocircularis , Ni. thailandica , Occultitheca rosae , Paravamsapriya ostiolata , Peroneutypa leucaenae , Seiridium italicum and Vamsapriya mucosa ) and seven new host/geographical records are introduced and reported. Divergence time estimates indicate that Delonicicolales diverged from Amphisphaeriales + Xylariales at 161 (123–197) MYA. Amphisphaeriales and Xylariales diverged 154 (117–190) MYA with a crown age of 127 (92–165) MYA and 147 (111–184) MYA, respectively. Appendicosporaceae ( Amphisphaeriales ) has a stem age of 89 (65–117) MYA. Ancestral character state reconstruction indicates that astromatic, clypeate ascomata with aseptate, hyaline ascospores that lack germ slits may probably be ancestral Xylariomycetidae having plant-fungal endophytic associations. The Amphisphaeriales remained mostly astromatic with common septate, hyaline ascospores. Stromatic variations may have developed mostly during the Cretaceous period. Brown ascospores are common in Xylariales , but they first appeared in Amphisphaeriaceae , Melogrammataceae and Sporocadaceae during the early Cretaceous. The ascospore germ slits appeared only in Xylariales during the Cretaceous after the divergence of Lopadostomataceae . Hyaline, filiform and apiospores may have appeared as separate lineages providing the basis to Xylariaceae , which may have diverged independently. The future classification of polyphyletic xylarialean taxa will not be based on stromatic variations, but the type of ring, the colour of the ascospores, and the presence or absence of the type of germ slit.

Digging Up the Roots: Taxonomic and Phylogenetic Disentanglements in Corticiaceae s.s. (Corticiales, Basidiomycota) and Evolution of Nutritional Modes

Corticiaceae is one of the traditional families of the Agaricomycetes and served for a long time as a convenient placement for basidiomycetes with a resupinate, corticioid form of fruiting body. Molecular studies have helped to assign many corticioid fungi to diverse families and orders; however, Corticiaceae still lacks a phylogenetic characterization and modern circumscription. Here, we provide the first comprehensive phylogenetic and taxonomic revision of the family Corticiaceae based on extensive type studies and sequences of nLSU, ITS, IGS, nSSU, and mtSSU regions. Our analyses support the recognition of ten monophyletic genera in the Corticiaceae, and show that nutritional mode is not a robust basis for generic delimitations in the family. The genus Mycobernardia and the species Corticium thailandicum, Erythricium vernum, and Marchandiomyces allantosporus are described as new to science, and five new combinations are proposed. Moreover, ancestral character state reconstruction revealed that saprotrophy is the plesiomorphic nutritional mode in the Corticiaceae, while several transitions have occurred to diverse nutritional modes in this family. Identification keys are provided to the genera in Corticiaceae s.s. as well as to the species in Corticium, Erythricium, Laetisaria, and Marchandiomyces.

Molecular phylogeny of the grasshopper family Pyrgomorphidae (Caelifera, Orthoptera) reveals rampant paraphyly and convergence of traditionally used taxonomic characters

The grasshopper family Pyrgomorphidae is one of the most colorful orthopteran lineages, and includes biologically fascinating and culturally important species. Recent attempts to reconstruct the phylogeny of this family have resulted in a large degree of conflicts between a morphology-based study and a molecular-based study, mainly due to convergent morphological traits that affected phylogenetic reconstruction. In this study, a molecular phylogeny of Pyrgomorphidae based on 32 ingroup species and mitochondrial genome data is proposed, which is used to test the monophyly of the taxonomic groupings used in the current classification scheme. Using the ancestral character state reconstruction analyses and character mapping, we demonstrate that some of the morphological characters, including the male genitalia, which were considered to be taxonomically important, have evolved convergently across the phylogeny. We discuss the discrepancies between our phylogeny and the previous studies and propose an approach to establish a natural classification scheme for Pyrgomorphidae.

Bipedalism in Mexican Albian lizard (Squamata) and the locomotion type in other Cretaceous lizards

Representative locomotion types in lizards include terrestrial, arboreal, grass swimmer, sand swimmer and bipedal. Few studies explain the locomotion habit of extinct lizards, and even less asses those of bipedal ones. Here, we use quantitative methods to infer the type of locomotion of two Albian Mexican lizards (Lower Cretaceous) and three Cretaceous lizards from Brazil, North America and Spain, assessing the similarities of the hindlimb-forelimb length ratio amongst extinct and extant species. Additionally, an ancestral character state reconstruction analysis was performed, to evaluate the evolution of lizard locomotion habits. The species Huehuecuetzpalli mixtecus was bipedal while Tijubina pontei was facultative bipedal, Hoyalacerta sanzi, Tepexisaurus tepexii and Polyglyphanodon sternbergi cannot be differentiated amongst terrestrial or arboreal with the approach used in this work. The ancestral character state reconstruction analysis showed a terrestrial ancestral locomotion type, with a basal character state of hindlimbs longer than forelimbs. Equal length between hind and forelimbs appear to be a derivate state that evolved multiple times in lizard evolutionary history.

Molecular Phylogeny of Axonopus (Poaceae, Panicoideae, Paspaleae): Monophyly, Synapomorphies, and Taxonomic Implications for Infrageneric Classification and Species Complexes

Axonopus P. Beauv. comprises nearly 90, mostly New World, species characterized by having spikelets with the inverse position (i.e., the backs of the upper glume and the upper lemma turned away from the rachis). The genus has been divided into four sections, five series, and three subseries, based exclusively on morphological features. Previous phylogenetic analyses based on a limited sampling of species showed Axonopus to be a monophyletic genus. In this study we increased the number of species sampled (46 species in the combined tree) and sequenced four DNA regions (external transcribed spacer [ETS], internal transcribed spacer [ITS], trnL-F, and ndhF). We tested the monophyly of Axonopus and its traditional infrageneric categories using parsimony, likelihood, and Bayesian inference. Additionally, we performed ancestral character state reconstructions of 45 morphological characters to infer autapomorphies of the species and synapomorphies for the genus and clades. Our findings confirmed Axonopus as a monophyletic genus only when Centrochloa Swallen and Ophiochloa Filg., Davidse & Zuloaga are included within it. Our analyses also showed that, with the exception of section Lappagopsis, infrageneric categories from previous classifications of the genus are artificial. Twenty-one morphological character states were identified as potential autapomorphies; two were reconstructed as potential synapomorphies for Axonopus, whereas 12 were reconstructed as potential synapomorphies for specific clades within the genus. Further molecular analyses, including sequencing of unlinked nuclear genes, are needed in order to reach a robust phylogenetic classification of the genus.

The Evolution and Biogeography of Wolbachia in Ants (Hymenoptera: Formicidae)

Wolbachia bacteria are widely distributed across invertebrate taxa, including ants, but several aspects of this host-associated interaction are still poorly explored, especially with regard to the ancestral state association, origin, and dispersion patterns of this bacterium. Therefore, in this study, we explored the association of Wolbachia with Formicidae in an evolutionary context. Our data suggest that supergroup F is the ancestral character state for Wolbachia infection in ants, and there is only one transition to supergroup A, and once ants acquired infection with supergroup A, there have been no other strains introduced. Our data also reveal that the origin of Wolbachia in ants likely originated in Asia and spread to the Americas, and then back to Asia. Understanding the processes and mechanisms of dispersion of these bacteria in Formicidae is a crucial step to advance the knowledge of this symbiosis and their implications in an evolutionary context.

A new insular species of the Cyrtodactylus intermedius (Squamata: Gekkonidae) group from Cambodia with a discussion of habitat preference and ecomorphology

An integrative taxonomic analysis based on mitochondrial and morphological data recovered the population of Cyrtodactylus on Koh Rong Island, Preah Sihanouk Province, Cambodiaa as an endemic insular species belonging to the Cyrtodactylus intermedius group. This brings the number of species in the C. intermedius group to at least 10 and the number of species in Cambodia to at least seven. Species of this relatively small group vary widely in habitat preference, occurring in general, terrestrial, karstic, or granitic habitats. Ancestral character state mapping recovered a general habitat preference as the ancestral condition from which all others independently evolved even though this did not covary with morphology. The description of another new species of reptile from Cambodia continues to underscore the potentially significant amount of unrealized biodiversity in Indochina and Southeast Asia and the continued need for field surveys in unexplored or poorly explored areas.

Comprehensive analysis of Actiniopteris Link and Onychium Kaulf. (Pteridophyta) relationships according to their phylogeography, phylogeny and spore morphology

This research is the first comprehensive analysis of the intrageneric relationships of Actiniopteris and Onychium based on original data including spore morphology, phylogeny and phylogeography. Actiniopteris and Onychium are members of the large subfamily Pteridoideae of the family Pteridaceae. The Pteridaceae family is considered one of the most taxonomically confusing families due to its representatives high level of polymorphism. We used an interdisciplinary approach to study the “Onychium clade”: 13 taxa were studied using scanning electron microscopy (SEM) to characterize the morphology and morphometry of spores; 14 taxa were studied from a phylogenetic perspective, including character evolution and ancestral character state reconstructions; 15 taxa of “Onychium clade” were studied using herbarium data (B, P, PE, LE, VLA, TI, KYO, ALTB and TK) according to global botanical and geographical zones. As a result of this integrated analysis, we established a deep divergence of the taxa O. tenuifrons and O. siliculosum from the main composition of the genus Onychium and the division the genus Actiniopteris into two clades: A. radiata–A. semiflabellata and A. australis–A. dimorpha. We found that representatives of Actiniopteris and Onychium had originated in a common African-Indo-Malesian area. The “Onychium clade” center of diversity is the Indian Region, which is experiencing high levels of human impact, leading to disjunctions among the studied taxa.