Blepharostoma trichophyllum  S.L. (Marchantiophyta): The Complex of Sibling Species and Hybrids

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

Blepharostoma trichophyllum was found to be a species collectiva formed by several strongly genetically different species. The taxonomic diversity in the group is the possible result of radiation in early stages; then, these taxa likely survived for a long time in similar environmental conditions, which resulted in stasis. Presently, the existing taxa are similar one to another and may be morphologically distinguished with difficulties. The most taxonomically valuable morphological characteristics include oil bodies and cells in the leaf segment features. The most diverse genotypes (the vast majority of which are treated here as distinct species) were found in amphi-Pacific Asia, which may reflect the evolutionary history of the genus or may be the consequence of more profound sampling in the macro-region in comparison with other parts of the Holarctic.

Related collections

Most cited references 37

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 4335 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: not found

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

Stéphane Guindon, Jean-François Dufayard, Vincent Lefort … (2010)

PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.

0 comments Cited 2763 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: not found
Book Chapter: not found

AMPLIFICATION AND DIRECT SEQUENCING OF FUNGAL RIBOSOMAL RNA GENES FOR PHYLOGENETICS

T.J White, T. Bruns, S. Lee … (1990)

0 comments Cited 2655 times – based on 0 reviews

Bookmark

All references

Author and article information

Journal

Journal ID (nlm-ta): Plants (Basel)

Journal ID (iso-abbrev): Plants (Basel)

Journal ID (publisher-id): plants

Title: Plants

Publisher: MDPI

ISSN (Electronic): 2223-7747

Publication date (Electronic): 23 October 2020

Publication date Collection: November 2020

Volume: 9

Issue: 11

Electronic Location Identifier: 1423

Affiliations

[1 ]Laboratory of Cryptogamic Biota, Botanical Garden-Institute FEB RAS, Vladivostok 690024, Russia; vabakalin@ 123456gmail.com

[2 ]Laboratory of Flora and Vegetation, Polar-Alpine Botanical Garden-Institute Kola SC RAS, Apatity 184209, Russia; anya_v@ 123456list.ru

[3 ]Team of National Ecosystem Survey, National Institute of Ecology, Seocheon 33657, Korea

[4 ]Institute of Ecology and Biological Resources, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Ha Noi 10000, Vietnam; vansinh.nguyen@ 123456iebr.ac.vn

Author notes

[* ]Correspondence: hepaticae@ 123456nie.re.kr

Author information

Vadim A. Bakalin https://orcid.org/0000-0001-7897-4305

Article

Publisher ID: plants-09-01423

DOI: 10.3390/plants9111423

PMC ID: 7716226

PubMed ID: 33114166

SO-VID: b8216705-8f96-4d58-95f6-e79298878381

License:

Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

Blepharostoma trichophyllum S.L. (Marchantiophyta): The Complex of Sibling Species and Hybrids

Read this article at

Abstract

Related collections

Taxonomic intelligence

Most cited references 37

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

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

AMPLIFICATION AND DIRECT SEQUENCING OF FUNGAL RIBOSOMAL RNA GENES FOR PHYLOGENETICS

Author and article information

Journal

Affiliations

Author notes

Author information

Article

History

Categories

Comments

Comment on this article

Similar content 296

Cited by 4

Most referenced authors 1,228