Application of plastid and nuclear markers to DNA barcoding of Euro-Mediterranean oaks (Quercus, Fagaceae): problems, prospects and phylogenetic implications
Marco Cosimo Simeone,Roberta Piredda,Roberta Piredda,Alessio Papini,Federico Vessella,Bartolomeo Schirone +5 more
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TLDR
The data gathered indicate that barcoding markers may help to identify closely related species clusters and contribute to the inference of major diversification and evolutionary patterns in oaks, but the methodology per se appears to be of limited efficacy in defining species limits, unless a profound revision of traditional Quercus taxonomic categories.About:
This article is published in Botanical Journal of the Linnean Society.The article was published on 2013-08-01 and is currently open access. It has received 72 citations till now. The article focuses on the topics: DNA barcoding & Taxon.read more
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Comparative Analysis of the Complete Chloroplast Genomes of Five Quercus Species
TL;DR: The phylogenetic relationships of the Quercus species inferred from the chloroplast genomes obtained moderate-to-high support, indicating thatchloroplast genome data may be useful in resolving relationships in this genus.
Journal ArticleDOI
Model Adequacy and the Macroevolution of Angiosperm Functional Traits.
TL;DR: This work presents a general statistical framework for assessing the adequacy of phylogenetic trait models and uses this approach to evaluate the statistical performance of commonly used trait models on 337 comparative data sets covering three key angiosperm functional traits.
Journal ArticleDOI
Multiple nuclear genes stabilize the phylogenetic backbone of the genus Quercus
François Hubert,Guido W. Grimm,Emmanuelle Jousselin,Vincent Berry,Alain Franc,Antoine Kremer +5 more
TL;DR: Using a dating approach, an Eocene age for the primary divergences in Quercus and a root age of about 50–55 Ma agrees with palaeobotanical evidence, indicating that morphological differentiation pre-dates genetic isolation in this clade.
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Phylogeny and biogeography of East Asian evergreen oaks (Quercus section Cyclobalanopsis; Fagaceae): Insights into the Cenozoic history of evergreen broad-leaved forests in subtropical Asia.
TL;DR: Biogeographical reconstructions indicate that the wide northern hemisphere distribution of Quercus was disrupted in the Late Eocene, leading to the main extant groups at about 33 Ma, highlighting the importance of climatic changes and Indo-Eurasian collision-induced tectonic activities from the Neogene onward to the spatial-temporal diversification patterns of Asian EBLF lineages.
References
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Clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
TL;DR: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved and modifications are incorporated into a new program, CLUSTAL W, which is freely available.
Journal ArticleDOI
MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
Koichiro Tamura,Daniel S. Peterson,Nicholas Peterson,Glen Stecher,Masatoshi Nei,Sudhir Kumar +5 more
TL;DR: The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models, inferring ancestral states and sequences, and estimating evolutionary rates site-by-site.
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.
Book
Molecular Evolutionary Genetics
TL;DR: Recent developments of statistical methods in molecular phylogenetics are reviewed and it is shown that the mathematical foundations of these methods are not well established, but computer simulations and empirical data indicate that currently used methods produce reasonably good phylogenetic trees when a sufficiently large number of nucleotides or amino acids are used.
Journal ArticleDOI
Application of Phylogenetic Networks in Evolutionary Studies
Daniel H. Huson,David Bryant +1 more
TL;DR: This article reviews the terminology used for phylogenetic networks and covers both split networks and reticulate networks, how they are defined, and how they can be interpreted and outlines the beginnings of a comprehensive statistical framework for applying split network methods.
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