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BayesTraits specifications


Unique identifier OMICS_09938
Name BayesTraits
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes


No version available



  • person_outline Andrew Meade

Publication for BayesTraits

BayesTraits citations


Asynchronous evolution of interdependent nest characters across the avian phylogeny

Nat Commun
PMCID: 5951845
PMID: 29760391
DOI: 10.1038/s41467-018-04265-x
call_split See protocol

[…] e selected Sitta europaea as the representative of the family Sittidae. To reconstruct ancestral character states for each of the three nest characters (i.e., structure, site and attachment), we used BayesTraits v.2.0– with the 1,000 family trees being used to take into account the uncertainty in estimates of trees and their branch lengths. Each run of the Markov chain Monte Carlo (MCMC) algorithm […]


Coevolution of landesque capital intensive agriculture and sociopolitical hierarchy

Proc Natl Acad Sci U S A
PMCID: 5889631
PMID: 29555760
DOI: 10.1073/pnas.1714558115

[…] ets of analyses were identical.Correlated evolution was investigated using a Bayesian Reversible-Jump Markov Chain Monte Carlo approach implemented in the “Discrete” component of the computer package BayesTraits (). This method involves the testing of an independent model (in which rates are independent) against a dependent model (in which rates can covary). Each set of analyses involved four pair […]


Molecular phylogeny of Panicum s. str. (Poaceae, Panicoideae, Paniceae) and insights into its biogeography and evolution

PLoS One
PMCID: 5842878
PMID: 29466405
DOI: 10.1371/journal.pone.0191529
call_split See protocol

[…] e obtained from the examination of herbarium specimens, the taxonomic literature, and online databases cited above. Transition rate estimation and ancestral character reconstruction were performed in BayesTraits 2.0.2 []. Analyses were conducted employing a continuous-time Markov model of trait evolution with two instantaneous rates representing all possible state changes (qannual→perennial and qp […]


Fitness Tradeoffs of Antibiotic Resistance in Extraintestinal Pathogenic Escherichia coli

Genome Biol Evol
PMCID: 5817949
PMID: 29432584
DOI: 10.1093/gbe/evy030

[…] ns can be generated. Following whole-genome sequencing, a core-genome phylogeny was constructed under a general-time reversible model, and was used to infer phylogenetic-controlled correlations using BayesTraits (; see Materials and Methods for more details). We find strong evidence for trade-offs associated with antibiotic resistance (). Resistances to both ceftazidime and ciprofloxacin are negat […]


Comparative Genomics Reveals Accelerated Evolution in Conserved Pathways during the Diversification of Anole Lizards

Genome Biol Evol
PMCID: 5798147
PMID: 29360978
DOI: 10.1093/gbe/evy013

[…] rrelated (). To test this prediction, we first searched for evidence of punctuated molecular evolution across the best ML phylogeny using a phylogenetic generalized least squares (PGLS) regression in BayesTraits v3.0 (), which incorporates a species phylogeny and weights data points according to shared ancestry. We removed the nonamniote outgroup and applied a continuous model to the phylogenetic […]


Primate social group sizes exhibit a regular scaling pattern with natural attractors

PMCID: 5803586
PMID: 29343560
DOI: 10.1098/rsbl.2017.0490
call_split See protocol

[…] s might explain the patterns in the data we used the physig routine in R to calculate Blomberg's K. Evolutionary rate changes in group size were detected using the variable rates model implemented in BayesTraits []. This model partitions the phenotypic variance across the tree into two components, a background rate and a branch-specific scalar relative to the background rate. We use this approach […]


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BayesTraits institution(s)
School of Animal and Microbial Sciences, University of Reading, Whiteknights Reading, UK

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