Revision and description of six species of  Choeradoplana  ( Platyhelminthes ,  Tricladida ), with an emendation to the genus

There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

Abstract

Living representatives of the Neotropical genus Choeradoplana Graff, 1896 ( Geoplaninae , Tricladida , Platyhelminthes ) are easily recognized by the typical shape of the head which is laterally expanded, rolled-up, and ventrally provided with two glandular cushions. In this study, the morphology and phylogeny (cytochrome C oxidase subunit I gene) of several species of land planarians are taxonomically investigated. Four of the six species studied are new to science, namely: Ch. eudoxiae Silva & Carbayo, sp. nov., Ch. claudioi Lago-Barcia & Carbayo, sp. nov., Ch. onae Lago-Barcia & Carbayo, sp. nov., and Ch. riutortae Lago-Barcia & Carbayo, sp. nov. The species Choeradoplana albonigra and Ch. eudoxiae deviate from the usual body shape pattern in that the head does not present lateral expansions nor glandular cushions, becoming indistinguishable from its sister genus Cephaloflexa . Pseudogeoplana tristriata (Schultze & Müller, 1857) is also redescribed from a newly collected specimen and was discovered to be a member of Choeradoplana . Graff (1899) also studied another specimen that was considered to be conspecific with P. tristriata ; however, in this new it is concluded that it is not conspecific but rather a new species. The name Pseudogeoplana aevipandemiae Lago-Barcia & Carbayo, sp. nov. is suggested for Graff’s specimen.

Related collections

Most cited references 36

Record: found
Abstract: found
Article: found

Is Open Access

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

Fredrik Ronquist, Maxim Teslenko, Paul van der Mark … (2012)

Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d N /d S rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.

0 comments Cited 4770 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: found

Is Open Access

MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization

Kazutaka Katoh, John Rozewicki, Kazunori Yamada (2017)

Abstract This article describes several features in the MAFFT online service for multiple sequence alignment (MSA). As a result of recent advances in sequencing technologies, huge numbers of biological sequences are available and the need for MSAs with large numbers of sequences is increasing. To extract biologically relevant information from such data, sophistication of algorithms is necessary but not sufficient. Intuitive and interactive tools for experimental biologists to semiautomatically handle large data are becoming important. We are working on development of MAFFT toward these two directions. Here, we explain (i) the Web interface for recently developed options for large data and (ii) interactive usage to refine sequence data sets and MSAs.

0 comments Cited 2094 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: not found

CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP.

Joseph Felsenstein (1985)

The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data. In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.

0 comments Cited 1650 times – based on 0 reviews      Review now

Bookmark

All references

Author and article information

Contributors

Domingo Lago-Barcia

Journal

Journal ID (nlm-ta): Zookeys

Journal ID (iso-abbrev): Zookeys

Journal ID (publisher-id): 2

Journal ID (index): urn:lsid:arphahub.com:pub:45048D35-BB1D-5CE8-9668-537E44BD4C7E

Journal ID (aggregator): urn:lsid:zoobank.org:pub:91BD42D4-90F1-4B45-9350-EEF175B1727A

Title: ZooKeys

Publisher: Pensoft Publishers

ISSN (Print): 1313-2989

ISSN (Electronic): 1313-2970

Publication date Collection: 2021

Publication date (Electronic): 11 February 2021

Volume: 1016

Pages: 1-48

Affiliations

[1 ] Laboratório de Ecologia e Evolução, Escola de Artes, Ciências e Humanidades (EACH), Universidade de São Paulo (USP), Av. Arlindo Bettio, 1000, São Paulo, SP, 03828-000, Brazil

[2 ] Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo (USP), Rua do Matão, Tv. 14, 321, São Paulo, SP, 05508-090, Brazil

[3 ] Programa de Pós-Graduação em Sistemática, Taxonomia Animal e Biodiversidade, Museu de Zoologia, Universidade de São Paulo, São Paulo, SP, Brazil

Author notes

Corresponding author: Domingo Lago-Barcia ( domingo.lagobarcia@ 123456gmail.com )

Academic editor: D. Gibson

Article

Publisher ID: 59617

DOI: 10.3897/zookeys.1016.59617

PMC ID: 7892534

SO-VID: 7a735ff0-57e1-4204-98c2-b9e1e211f06f

License:

This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

History

Date received : 20 October 2020

Date accepted : 29 December 2020

Funding

Funded by: Conselho Nacional de Desenvolvimento Científico e Tecnológico 501100003593 http://doi.org/10.13039/501100003593

Publish your biodiversity research with us!

Submit your article here.

Revision and description of six species of Choeradoplana (Platyhelminthes, Tricladida), with an emendation to the genus

Read this article at

Abstract

Related collections

Pensoft Biodiversity

Most cited references 36

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization

CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP.

Author and article information

Contributors

Journal

Affiliations

Author notes

Article

History

Funding

Categories

Comments

Comment on this article

Similar content 309

Most referenced authors 547