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 …
Evolutionary insights into host–pathogen interactions from mammalian sequence data
Infections are one of the major selective pressures acting on humans, and host-pathogen
interactions contribute to shaping the genetic diversity of both organisms. Evolutionary …
interactions contribute to shaping the genetic diversity of both organisms. Evolutionary …
Less is more: an adaptive branch-site random effects model for efficient detection of episodic diversifying selection
Over the past two decades, comparative sequence analysis using codon-substitution
models has been honed into a powerful and popular approach for detecting signatures of …
models has been honed into a powerful and popular approach for detecting signatures of …
Gene-wide identification of episodic selection
We present BUSTED, a new approach to identifying gene-wide evidence of episodic
positive selection, where the non-synonymous substitution rate is transiently greater than the …
positive selection, where the non-synonymous substitution rate is transiently greater than the …
Detecting individual sites subject to episodic diversifying selection
The imprint of natural selection on protein coding genes is often difficult to identify because
selection is frequently transient or episodic, ie it affects only a subset of lineages. Existing …
selection is frequently transient or episodic, ie it affects only a subset of lineages. Existing …
Bayes empirical Bayes inference of amino acid sites under positive selection
Codon-based substitution models have been widely used to identify amino acid sites under
positive selection in comparative analysis of protein-coding DNA sequences. The …
positive selection in comparative analysis of protein-coding DNA sequences. The …
The population genetics of dN/dS
S Kryazhimskiy, JB Plotkin - PLoS genetics, 2008 - journals.plos.org
Evolutionary pressures on proteins are often quantified by the ratio of substitution rates at
non-synonymous and synonymous sites. The dN/dS ratio was originally developed for …
non-synonymous and synonymous sites. The dN/dS ratio was originally developed for …
[图书][B] Computational molecular evolution
Z Yang - 2006 - books.google.com
The field of molecular evolution has experienced explosive growth in recent years due to the
rapid accumulation of genetic sequence data, continuous improvements to computer …
rapid accumulation of genetic sequence data, continuous improvements to computer …
A random effects branch-site model for detecting episodic diversifying selection
SL Kosakovsky Pond, B Murrell… - Molecular biology …, 2011 - academic.oup.com
Adaptive evolution frequently occurs in episodic bursts, localized to a few sites in a gene,
and to a small number of lineages in a phylogenetic tree. A popular class of “branch-site” …
and to a small number of lineages in a phylogenetic tree. A popular class of “branch-site” …
Patterns of positive selection in six mammalian genomes
Genome-wide scans for positively selected genes (PSGs) in mammals have provided insight
into the dynamics of genome evolution, the genetic basis of differences between species …
into the dynamics of genome evolution, the genetic basis of differences between species …