Harpetid Character Matrix [X24940] Character Matrix 1

2021 ◽  
Author(s):  
J Beech ◽  
J Lamsdell
Keyword(s):  
Character Matrix

scholarly journals Character evolution of modern fly-speck fungi and implications for interpreting thyriothecial fossils

2020 ◽  
Author(s):  
Ludovic Le Renard ◽  
André L. Firmino ◽  
Olinto L. Pereira ◽  
Ruth A. Stockey ◽  
Mary. L. Berbee
Keyword(s):  
Morphological Evolution ◽  
Morphological Characters ◽  
Small Subunit ◽  
Leaf Surfaces ◽  
The Matrix ◽  
Character Matrix ◽  
Phylogenetic Framework ◽  
Single Hypha ◽  
Objective Basis ◽  
Ancestral Character States

AbstractPREMISE OF THE STUDYFossils show that fly-speck fungi have been reproducing with small, black thyriothecia on leaf surfaces for ∼250 million years. We analyze morphological characters of extant thyriothecial fungi to develop a phylogenetic framework for interpreting fossil taxa.METHODSWe placed 59 extant fly-speck fungi in a phylogeny of 320 Ascomycota using nuclear ribosomal large and small subunit sequences, including newly determined sequences from nine taxa. We reconstructed ancestral character states using BayesTraits and maximum likelihood after coding 11 morphological characters based on original observations and literature. We analyzed the relationships of three previously published Mesozoic fossils using parsimony and our morphological character matrix, constrained by the molecular phylogeny.KEY RESULTSThyriothecia evolved convergently in multiple lineages of superficial, leaf- inhabiting ascomycetes. The radiate and ostiolate scutellum organization is restricted to Dothideomycetes. Scutellum initiation by intercalary septation of a single hypha characterizes Asterinales and Asterotexiales, and initiation by coordinated growth of two or more adjacent hyphae characterizes Aulographaceae (order incertae sedis). Scutella in Microthyriales are initiated apically on a lateral hyphal branch. Patterns of hyphal branching in scutella contribute to distinguishing among orders. Parsimony resolves three fossil taxa as Dothideomycetes; one is further resolved as a member of a Microthyriales-Zeloasperisporiales clade within Dothideomycetes.CONCLUSIONSThis is the most comprehensive systematic study of thyriothecial fungi and their relatives to date. Parsimony analysis of the matrix of character states of modern taxa provides an objective basis for interpreting fossils, leading to insights into morphological evolution and geological ages of Dothideomycetes clades.

scholarly journals Chromosomal phylogeny and comparative chromosome painting among Neacomys species (Rodentia, Sigmodontinae) from eastern Amazonia

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Willam Oliveira da Silva ◽  
Julio Cesar Pieczarka ◽  
Marlyson Jeremias Rodrigues da Costa ◽  
Malcolm Andrew Ferguson-Smith ◽  
Patricia Caroline Mary O’Brien ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Chromosome Painting ◽  
Chromosomal Evolution ◽  
Distribution Area ◽  
Comparative Chromosome Painting ◽  
Candidate Species ◽  
Character Matrix ◽  
Coi Sequences ◽  
Molecular Relationships ◽  
Chromosomal Phylogeny

Abstract Background The Neacomys genus is predominantly found in the Amazon region, and belongs to the most diverse tribe of the Sigmodontinae subfamily (Rodentia, Cricetidae, Oryzomyini). The systematics of this genus and questions about its diversity and range have been investigated by morphological, molecular (Cytb and COI sequences) and karyotype analysis (classic cytogenetics and chromosome painting), which have revealed candidate species and new distribution areas. Here we analyzed four species of Neacomys by chromosome painting with Hylaeamys megacephalus (HME) whole-chromosome probes, and compared the results with two previously studied Neacomys species and with other taxa from Oryzomyini and Akodontini tribes that have been hybridized with HME probes. Maximum Parsimony (MP) analyses were performed with the PAUP and T.N.T. software packages, using a non-additive (unordered) multi-state character matrix, based on chromosomal morphology, number and syntenic blocks. We also compared the chromosomal phylogeny obtained in this study with molecular topologies (Cytb and COI) that included eastern Amazonian species of Neacomys, to define the phylogenetic relationships of these taxa. Results The comparative chromosome painting analysis of the seven karyotypes of the six species of Neacomys shows that their diversity is due to 17 fusion/fission events and one translocation, pericentric inversions in four syntenic blocks, and constitutive heterochromatin (CH) amplification/deletion of six syntenic autosomal blocks plus the X chromosome. The chromosomal phylogeny is consistent with the molecular relationships of species of Neacomys. We describe new karyotypes and expand the distribution area for species from eastern Amazonia and detect complex rearrangements by chromosome painting among the karyotypes. Conclusions Our phylogeny reflects the molecular relationships of the Akodontini and Oryzomyini taxa and supports the monophyly of Neacomys. This work presents new insights about the chromosomal evolution of this group, and we conclude that the karyotypic divergence is in accord with phylogenetic relationships.

When Chinese Masks Meet Phylogenetics

2016 ◽  
Vol 78 (3) ◽  
pp. 241-247 ◽  
Author(s):  
Claudia A. M. Russo ◽  
Bárbara Aguiar ◽  
Carolina M. Voloch ◽  
Alexandre P. Selvatti
Keyword(s):  
Biological Sciences ◽  
Undergraduate Students ◽  
Data Matrix ◽  
Complex Objects ◽  
Single Character ◽  
Topological Pattern ◽  
Hands On ◽  
Character Matrix ◽  
The Common ◽  
Character Coding

Phylogenetics has a central role in the biological sciences. We suggest a hands-on exercise to demonstrate the task of character coding and its importance in phylogenetic systematics. This exercise is appropriate for undergraduate students in life sciences and related courses. The teacher must provide a single group of masks in which color patterns, textures, and formats provide the characters to fill the data matrix. (The masks could be replaced by a set of other complex objects.) In this case, because there is no actual phylogeny, students will not be concerned with recovering the correct topology. Character coding is the aim of the exercise. After the character matrix is completed, a phylogenetic tree is drawn and the students interpret the evolution of a single character, starting from the common ancestor, based on the topological pattern of the tree and on the data matrix. In sequence, the students name and provide a full diagnosis for the group of masks as revealed by the topological pattern. The comparison between group results is also educational: there will be some common patterns between trees, but others will differ as in biological systematics.

scholarly journals Toward synthesizing our knowledge of morphology: using ontologies and machine reasoning to extract presence/absence evolutionary phenotypes across studies

2015 ◽  
Author(s):  
T. Alexander Dececchi ◽  
James P Balhoff ◽  
Hilmar Lapp ◽  
Paula M Mabee
Keyword(s):  
Formal Semantics ◽  
Model Organism ◽  
Future Research ◽  
Data Provenance ◽  
Character State ◽  
Phenotypic Data ◽  
Large Numbers ◽  
Molecular Databases ◽  
Variable Character ◽  
Character Matrix

The reality of larger and larger molecular databases and the need to integrate data scalably have presented a major challenge for the use of phenotypic data. Morphology is currently primarily described in discrete publications, entrenched in non-computer readable text, and requires enormous investments of time and resources to integrate across large numbers of taxa and studies. Here we present a new methodology, using ontology-based reasoning systems working with the Phenoscape Knowledgebase (KB), to automatically integrate large amounts of evolutionary character state descriptions into a synthetic character matrix of neomorphic (presence/absence) data. Using the KB, which includes more than 55 studies of sarcopterygian taxa, we generated a synthetic supermatrix of 1051 variable characters scored for 639 taxa resulting in over 145,000 populated cells. Of these characters, over 76% were made variable through the addition of inferred presence/absence states derived by machine reasoning over the formal semantics of the source ontologies. Inferred data reduced the missing data in the variable character-subset from 98.5% to 78.2%. Machine reasoning also enables the isolation of conflicts in the data, i.e., cells where both presence and absence are indicated; reports regarding conflicting data provenance can be generated automatically. Further, reasoning enables quantification and new visualizations of the data, here for example, allowing identification of character space that has been undersampled across the fin to limb transition. The approach and methods demonstrated here to compute synthetic presence/absence supermatrices are applicable to any taxonomic and phenotypic slice across the tree of life, providing the data are semantically annotated. Because such data can also be linked to model organism genetics through computational scoring of phenotypic similarity, they open a rich set of future research questions into phenotype to genome relationships.

scholarly journals Physcraper: a python package for continual update of evolutionary estimates using the Open Tree of Life

2020 ◽  
Author(s):  
Luna L. Sanchez Reyes ◽  
Martha Kandziora ◽  
Emily Jane McTavish
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Reconstruction ◽  
Open Science ◽  
Tree Of Life ◽  
List Type ◽  
Matrix Assembly ◽  
Life Project ◽  
Character Matrix ◽  
Molecular Dataset ◽  
Phylogenetic Hypotheses

AbstractPhylogenies are a key part of research in many areas of biology. Tools that automate some parts of the process of phylogenetic reconstruction, mainly molecular character matrix assembly, have been developed for the advantage of both specialists in the field of phylogenetics and nonspecialists. However, interpretation of results, comparison with previously available phylogenetic hypotheses, and selection of one phylogeny for downstream analyses and discussion still impose difficulties to one that is not a specialist either on phylogenetic methods or on a particular group of study.Physcraper is a command-line Python program that automates the update of published phylogenies by adding public DNA sequences to underlying alignments of previously published phylogenies. It also provides a framework for straightforward comparison of published phylogenies with their updated versions, by leveraging upon tools from the Open Tree of Life project to link taxonomic information across databases.Physcraper can be used by the nonspecialist, as a tool to generate phylogenetic hypotheses based on publicly available expert phylogenetic knowledge. Phylogeneticists and taxonomic group specialists will find it useful as a tool to facilitate molecular dataset gathering and comparison of alternative phylogenetic hypotheses (topologies).The Physcraper workflow demonstrates the benefits of doing open science for phylogenetics, encour-aging researchers to strive for better sharing practices. Physcraper can be used with any OS and is released under an open-source license. Detailed instructions for installation and use are available at https://physcraper.readthedocs.

Here Be Dragons: Using Dragons as Models for Phylogenetic Analysis

2017 ◽  
Vol 79 (7) ◽  
pp. 544-551
Author(s):  
Ronald Allan L. Cruz
Keyword(s):  
Phylogenetic Analysis ◽  
Evolutionary History ◽  
Computer Software ◽  
Fantasy Literature ◽  
General Biology ◽  
Anatomical Characteristics ◽  
Character Matrix ◽  
Conventional Computer

Dragons are a staple of fantasy literature, and various aspects of the creatures (most notably their anatomy) have been explored scientifically across different forms of media. Their distinct anatomical characteristics and the variations therein among the recognized “species” of dragons make the taxa appropriate models for basic phylogenetic analysis in an undergraduate general biology or systematics class. The wyvern, an obviously more primitive, distant cousin of the “true” dragons, is also an appropriate outgroup for these estimations of shared evolutionary history. Separating metallic from chromatic dragons, the generated tree shows relationships among the species that are consistent with their separation in the Dungeons & Dragons games according to alignment, scale color, and religion, three characters that are not used in the analysis. Manual construction of a character matrix and cladogram of dragons followed by repetition of this process via conventional computer software allows the students to track their progress not only in terms of understanding such concepts as choice of character states and parsimony but also in terms of the applicability of said software.

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