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

Diversity ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 426
Author(s):  
Manuela O. Ramalho ◽  
Corrie S. Moreau
Keyword(s):  
Wolbachia Infection ◽  
Character State ◽  
Ancestral State ◽  
Crucial Step ◽  
Ancestral Character State ◽  
Dispersion Patterns ◽  
State Association ◽  
Evolutionary Context

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.

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

2021 ◽  
Author(s):  
Milan C. Samarakoon ◽  
Kevin D Hyde ◽  
Sajeewa S. N. Maharachchikumbura ◽  
Marc Stadler ◽  
E. B. Gareth Jones ◽  
...  
Keyword(s):  
Divergence Time ◽  
Molecular Dating ◽  
Character State ◽  
Ancestral State ◽  
New Host ◽  
State Reconstruction ◽  
Divergence Time Estimates ◽  
New Family ◽  
Ancestral Character State ◽  
Time Estimates

Abstract 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.

scholarly journals Exploring and Reconstructing Ancestral Anatomies using Ontology-Informed Approaches

2019 ◽  
Vol 3 ◽  
Author(s):  
Sergei Tarasov ◽  
Istvan Miko ◽  
Matthew Yoder ◽  
Josef Uyeda
Keyword(s):  
Phylogenetic Trees ◽  
Character State ◽  
Ancestral Reconstruction ◽  
Anatomy Ontology ◽  
Insect Order ◽  
Ancestral Character State ◽  
Body Regions ◽  
Individual Traits ◽  
History Of ◽  
Complex Characters

Ancestral character state reconstruction has been long used to gain insight into the evolution of individual traits in organisms. However, organismal anatomies (= entire phenotypes) are not merely ensembles of individual traits, rather they are complex systems where traits interact with each other due to anatomical dependencies (when one trait depends on the presence of another trait) and developmental constraints. Comparative phylogenetics has been largely lacking a method for reconstructing the evolution of entire organismal anatomies or organismal body regions. Herein, we present a new approach named PARAMO (Phylogenetic Ancestral Reconstruction of Anatomy by Mapping Ontologies, Tarasov and Uyeda 2019) that takes into account anatomical dependencies and uses stochastic maps (i.e., phylogenetic trees with an instance of mapped evolutionary history of characters, Huelsenbeck et al. 2003) along with anatomy ontologies to reconstruct organismal anatomies. Our approach treats the entire phenotype or its component body regions as single complex characters and allows exploring and comparing phenotypic evolution at different levels of anatomical hierarchy. These complex characters are constructed by ontology-informed amalgamation of elementary characters (i.e., those coded in character matrix) using stochastic maps. In our approach, characters are linked with the terms from an anatomy ontology, which allows viewing them not just as an ensemble of character state tokens but as entities that have their own biological meaning provided by the ontology. This ontology-informed framework provides new opportunities for tracking phenotypic radiations and anatomical evolution of organisms, which we explore using a large dataset for the insect order Hymenoptera (sawflies, wasps, ants and bees).

scholarly journals Integration of Anatomy Ontologies and Evo-Devo Using Structured Markov Models Suggests a New Framework for Modeling Discrete Phenotypic Traits

2019 ◽  
Vol 68 (5) ◽  
pp. 698-716 ◽  
Author(s):  
Sergei Tarasov
Keyword(s):  
Regulatory Networks ◽  
Markov Models ◽  
Phylogenetic Inference ◽  
Phenotypic Traits ◽  
Character State ◽  
Body Parts ◽  
Ancestral Character State ◽  
State Models ◽  
Hidden States ◽  
New Framework

Abstract Modeling discrete phenotypic traits for either ancestral character state reconstruction or morphology-based phylogenetic inference suffers from ambiguities of character coding, homology assessment, dependencies, and selection of adequate models. These drawbacks occur because trait evolution is driven by two key processes—hierarchical and hidden—which are not accommodated simultaneously by the available phylogenetic methods. The hierarchical process refers to the dependencies between anatomical body parts, while the hidden process refers to the evolution of gene regulatory networks (GRNs) underlying trait development. Herein, I demonstrate that these processes can be efficiently modeled using structured Markov models (SMM) equipped with hidden states, which resolves the majority of the problems associated with discrete traits. Integration of SMM with anatomy ontologies can adequately incorporate the hierarchical dependencies, while the use of the hidden states accommodates hidden evolution of GRNs and substitution rate heterogeneity. I assess the new models using simulations and theoretical synthesis. The new approach solves the long-standing “tail color problem,” in which the trait is scored for species with tails of different colors or no tails. It also presents a previously unknown issue called the “two-scientist paradox,” in which the nature of coding the trait and the hidden processes driving the trait’s evolution are confounded; failing to account for the hidden process may result in a bias, which can be avoided by using hidden state models. All this provides a clear guideline for coding traits into characters. This article gives practical examples of using the new framework for phylogenetic inference and comparative analysis.

scholarly journals Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota)

IMA Fungus ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Claudio G. Ametrano ◽  
Felix Grewe ◽  
Pedro W. Crous ◽  
Stephen B. Goodwin ◽  
Chen Liang ◽  
...  
Keyword(s):  
Character State ◽  
Ancestral Character State ◽  
Wide Range ◽  
Tree Inference ◽  
Ancestral Character State Reconstruction ◽  
Inference Methods ◽  
Genome Scale ◽  
The Impact ◽  
Rock Inhabiting Fungi ◽  
Scale Data

Abstract Dothideomycetes is the most diverse fungal class in Ascomycota and includes species with a wide range of lifestyles. Previous multilocus studies have investigated the taxonomic and evolutionary relationships of these taxa but often failed to resolve early diverging nodes and frequently generated inconsistent placements of some clades. Here, we use a phylogenomic approach to resolve relationships in Dothideomycetes, focusing on two genera of melanized, extremotolerant rock-inhabiting fungi, Lichenothelia and Saxomyces, that have been suggested to be early diverging lineages. We assembled phylogenomic datasets from newly sequenced (4) and previously available genomes (238) of 242 taxa. We explored the influence of tree inference methods, supermatrix vs. coalescent-based species tree, and the impact of varying amounts of genomic data. Overall, our phylogenetic reconstructions provide consistent and well-supported topologies for Dothideomycetes, recovering Lichenothelia and Saxomyces among the earliest diverging lineages in the class. In addition, many of the major lineages within Dothideomycetes are recovered as monophyletic, and the phylogenomic approach implemented strongly supports their relationships. Ancestral character state reconstruction suggest that the rock-inhabiting lifestyle is ancestral within the class.

Convergence to the tiniest detail: vocal sac structure in torrent-dwelling frogs

2019 ◽  
Author(s):  
Agustín J Elias-Costa ◽  
Julián Faivovich
Keyword(s):  
Background Noise ◽  
Evolutionary History ◽  
Visual Display ◽  
Character State ◽  
Visual Displays ◽  
State Reconstruction ◽  
Ancestral Character State ◽  
History Of ◽  
Ancestral Character State Reconstruction ◽  
Detection And Recognition

Abstract Cascades and fast-flowing streams impose severe restrictions on acoustic communication, with loud broadband background noise hampering signal detection and recognition. In this context, diverse behavioural features, such as ultrasound production and visual displays, have arisen in the evolutionary history of torrent-dwelling amphibians. The importance of the vocal sac in multimodal communication is being increasingly recognized, and recently a new vocal sac visual display has been discovered: unilateral inflation of paired vocal sacs. In the diurnal stream-breeding Hylodidae from the Atlantic forest, where it was first described, this behaviour is likely to be enabled by a unique anatomical configuration of the vocal sacs. To assess whether other taxa share this exceptional structure, we surveyed torrent-dwelling species with paired vocal sacs across the anuran tree of life and examined the vocal sac anatomy of exemplar species across 18 families. We found striking anatomical convergence among hylodids and species of the distantly related basal ranid genera Staurois, Huia, Meristogenys and Amolops. Ancestral character state reconstruction identified three new synapomorphies for Ranidae. Furthermore, we surveyed the vocal sac configuration of other anuran species that perform visual displays and report observations on what appears to be unilateral inflation of paired vocal sacs, in Staurois guttatus – an extremely rare behaviour in anurans.

Quantifying morphological change during an evolutionary radiation of Devonian trilobites

Paleobiology ◽  
2012 ◽  
Vol 38 (2) ◽  
pp. 292-307 ◽  
Author(s):  
Francine R. Abe ◽  
Bruce S. Lieberman
Keyword(s):  
Morphological Change ◽  
Fossil Record ◽  
Character State ◽  
Geometric Morphometric ◽  
Biogeographic Patterns ◽  
Ancestral Character State ◽  
Speciation Rates ◽  
Adaptive Radiations ◽  
Geometric Morphometric Analysis ◽  
Heterogeneous Region

The fossil record provides an important source of data on adaptive radiations, and indeed some of the earliest theoretical insights on the nature of these radiations were made by paleontologists. Here we focus on the diverse DevonianMetacryphaeusgroup calmoniid trilobites, known from the Malvinokaffric Realm, which have been considered a classic example of an adaptive radiation preserved in the fossil record. We use a geometric morphometric analysis in conjunction with phylogenetic and biogeographic patterns and data on speciation rates. Using ancestral character state reconstruction during speciation events, we quantify patterns of morphological change in order to assess the role ecological and geographical factors may have played in mediating this radiation. We found no significant differences between the amount of morphological change that occurred during speciation events when ancestors and descendants were in the same area as opposed to when they occupied different areas. Further, the magnitude of morphological divergence did not change through time or with cladogenetic rank. These patterns, in conjunction with the fact that the radiation occurs in a geographically heterogeneous region subjected to repeated episodes of sea-level rise and fall, suggest that at the macroevolutionary scale this radiation may have been motivated more by phenomena that facilitated geographic isolation than by competition.

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

Zoomorphology ◽  
2021 ◽  
Author(s):  
Philipp Thieme ◽  
Timo Moritz
Keyword(s):  
State Estimation ◽  
Evolutionary History ◽  
Taxon Sampling ◽  
Character State ◽  
Neural Arch ◽  
Ancestral Character State ◽  
History Of ◽  
Similar Character ◽  
Morphology Development ◽  
State Estimations

AbstractThe 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.

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