Molecular phylogenetic relationships and phenotypic diversity in miniaturized toadlets, genus Brachycephalus (Amphibia: Anura: Brachycephalidae)
Rute B. G. Clemente-Carvalho,Julia Klaczko,S. Ivan Perez,Ana C. R. Alves,Célio F. B. Haddad,Sérgio F. dos Reis +5 more
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TLDR
Comparison of the log likelihoods for the concatenated and BEST trees suggests that the method implemented in BEST explains the multilocus data for Brachycephalus better than the Bayesian analysis of concatenate data.About:
This article is published in Molecular Phylogenetics and Evolution.The article was published on 2011-10-01 and is currently open access. It has received 45 citations till now. The article focuses on the topics: Phylogenetic tree & Coalescent theory.read more
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Journal ArticleDOI
Mathematics in the Archaeological and Historical Sciences. Edited by F. R. Hodson, D. G. Kendall and P. Tăutu. Pp. vii, 565. £10. 1971. (Edinburgh University Press.)
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Molecular systematics of terraranas (Anura: Brachycephaloidea) with an assessment of the effects of alignment and optimality criteria.
TL;DR: The optimal tree-alignment indicates that insertions and deletions occurred in twice as many aligned positions as implied by the optimal similarity-Alignment, confirming previous findings that sequence turnover through insertion and deletion events plays a greater role in molecular evolution than indicated by similarity-alignments.
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Poor Fit to the Multispecies Coalescent is Widely Detectable in Empirical Data
Noah M. Reid,Sarah M. Hird,Jeremy M. Brown,Tara A. Pelletier,John D. McVay,Jordan D. Satler,Bryan C. Carstens +6 more
TL;DR: It is shown that poor model fit is detectable in the majority of data sets; that this poor fit can mislead phylogenetic estimation; and that in some cases it stems from processes of inherent interest to systematists.
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Size-Dependent Selective Mechanisms on Males and Females and the Evolution of Sexual Size Dimorphism in Frogs
TL;DR: The data indicate that the fecundity advantage associated with female body size may not be linear, such that intermediate and large females benefit less with body size increases, and underscores the fact that lineage-specific ecology and behavior should be incorporated in comparative analyses of animal SSD.
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From widespread to microendemic: molecular and acoustic analyses show that Ischnocnema guentheri (Amphibia: Brachycephalidae) is endemic to Rio de Janeiro, Brazil
TL;DR: Although none of the species studied appears highly threatened with extinction, their IUCN threat status is recommended to be re-evaluated carefully for the next comprehensive update of the Red List of Brazil’s amphibians.
References
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Book
Molecular Cloning: A Laboratory Manual
TL;DR: Molecular Cloning has served as the foundation of technical expertise in labs worldwide for 30 years as mentioned in this paper and has been so popular, or so influential, that no other manual has been more widely used and influential.
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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Stephen F. Altschul,Thomas L. Madden,Alejandro A. Schäffer,Jinghui Zhang,Zheng Zhang,Webb Miller,David J. Lipman +6 more
TL;DR: A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.
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MrBayes 3: Bayesian phylogenetic inference under mixed models
TL;DR: MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models to analyze heterogeneous data sets and explore a wide variety of structured models mixing partition-unique and shared parameters.
Journal ArticleDOI
Clustal W and Clustal X version 2.0
Mark A. Larkin,Gordon Blackshields,Nigel P. Brown,R. Chenna,Paul A. McGettigan,Hamish McWilliam,Franck Valentin,Iain M. Wallace,Andreas Wilm,Rodrigo Lopez,J.D. Thompson,Toby J. Gibson,Desmond G. Higgins +12 more
TL;DR: The Clustal W and ClUSTal X multiple sequence alignment programs have been completely rewritten in C++ to facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems.
Journal ArticleDOI
MRBAYES: Bayesian inference of phylogenetic trees
TL;DR: The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo, and an executable is available at http://brahms.rochester.edu/software.html.
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