Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum
J Gatesy, MS Springer - Molecular phylogenetics and evolution, 2014 - Elsevier
Large datasets are required to solve difficult phylogenetic problems that are deep in the Tree
of Life. Currently, two divergent systematic methods are commonly applied to such datasets …
of Life. Currently, two divergent systematic methods are commonly applied to such datasets …
Delimiting species without monophyletic gene trees
LL Knowles, BC Carstens - Systematic biology, 2007 - academic.oup.com
Genetic data are frequently used to delimit species, where species status is determined on
the basis of an exclusivity criterium, such as reciprocal monophyly. Not only are there …
the basis of an exclusivity criterium, such as reciprocal monophyly. Not only are there …
[PDF][PDF] Draft MrBayes version 3.2 manual: tutorials and model summaries
F Ronquist, J Huelsenbeck… - Distributed with …, 2011 - web-genobioinfo.toulouse.inrae.fr
When we started working on MrBayes in 1999-2000, we knew that there was a need for a
Bayesian MCMC package for phylogenetics, which was more flexible and easier to use than …
Bayesian MCMC package for phylogenetics, which was more flexible and easier to use than …
Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable …
The inference of the evolutionary history of a collection of organisms is a problem of
fundamental importance in evolutionary biology. The abundance of DNA sequence data …
fundamental importance in evolutionary biology. The abundance of DNA sequence data …
Integrative taxonomy, or iterative taxonomy?
The recently introduced term 'integrative taxonomy'refers to taxonomy that integrates all
available data sources to frame species limits. We survey current taxonomic methods …
available data sources to frame species limits. We survey current taxonomic methods …
[图书][B] Molecular evolution: a statistical approach
Z Yang - 2014 - books.google.com
Studies of evolution at the molecular level have experienced phenomenal growth in the last
few decades, due to rapid accumulation of genetic sequence data, improved computer …
few decades, due to rapid accumulation of genetic sequence data, improved computer …
Analysis and visualization of complex macroevolutionary dynamics: an example from Australian scincid lizards
DL Rabosky, SC Donnellan, M Grundler… - Systematic …, 2014 - academic.oup.com
The correlation between species diversification and morphological evolution has long been
of interest in evolutionary biology. We investigated the relationship between these …
of interest in evolutionary biology. We investigated the relationship between these …
Estimating species phylogenies using coalescence times among sequences
The estimation of species trees (phylogenies) is one of the most important problems in
evolutionary biology, and recently, there has been greater appreciation of the need to …
evolutionary biology, and recently, there has been greater appreciation of the need to …
Phylogenetic insights on adaptive radiation
RE Glor - Annual Review of Ecology, Evolution, and Systematics, 2010 - annualreviews.org
Adaptive radiation is a response to natural selection and ecological opportunity involving
diversification of species and associated adaptations. Although evolutionary biologists have …
diversification of species and associated adaptations. Although evolutionary biologists have …
The inference of gene trees with species trees
This article reviews the various models that have been used to describe the relationships
between gene trees and species trees. Molecular phylogeny has focused mainly on …
between gene trees and species trees. Molecular phylogeny has focused mainly on …