Molecular‐clock methods for estimating evolutionary rates and timescales
The molecular clock presents a means of estimating evolutionary rates and timescales using
genetic data. These estimates can lead to important insights into evolutionary processes and …
genetic data. These estimates can lead to important insights into evolutionary processes and …
Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA
DNA data has been widely used in animal phylogenetic studies over the past 15 years. Here
we review how these studies have used advances in knowledge of molecular evolutionary …
we review how these studies have used advances in knowledge of molecular evolutionary …
[KNJIGA][B] Bayesian evolutionary analysis with BEAST
AJ Drummond, RR Bouckaert - 2015 - books.google.com
What are the models used in phylogenetic analysis and what exactly is involved in Bayesian
evolutionary analysis using Markov chain Monte Carlo (MCMC) methods? How can you …
evolutionary analysis using Markov chain Monte Carlo (MCMC) methods? How can you …
Relaxed phylogenetics and dating with confidence
In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are
two extremes of a continuum. Despite their dominance in phylogenetic inference, it is …
two extremes of a continuum. Despite their dominance in phylogenetic inference, it is …
A 4000-species dataset provides new insight into the evolution of ferns
Ferns are the second-most diverse lineage of vascular plants on Earth, yet the best-sampled
time-calibrated phylogeny of the group to date includes fewer than 5% of global diversity …
time-calibrated phylogeny of the group to date includes fewer than 5% of global diversity …
Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times
The estimation of phylogenetic divergence times from sequence data is an important
component of many molecular evolutionary studies. There is now a general appreciation …
component of many molecular evolutionary studies. There is now a general appreciation …
Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified
Background In recent years, model based approaches such as maximum likelihood have
become the methods of choice for constructing phylogenies. A number of authors have …
become the methods of choice for constructing phylogenies. A number of authors have …
Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds
Abstract We implement a Bayesian Markov chain Monte Carlo algorithm for estimating
species divergence times that uses heterogeneous data from multiple gene loci and …
species divergence times that uses heterogeneous data from multiple gene loci and …
A general comparison of relaxed molecular clock models
Several models have been proposed to relax the molecular clock in order to estimate
divergence times. However, it is unclear which model has the best fit to real data and should …
divergence times. However, it is unclear which model has the best fit to real data and should …
Using phylogenomic data to explore the effects of relaxed clocks and calibration strategies on divergence time estimation: primates as a test case
Primates have long been a test case for the development of phylogenetic methods for
divergence time estimation. Despite a large number of studies, however, the timing of …
divergence time estimation. Despite a large number of studies, however, the timing of …