Relaxed phylogenetics and dating with confidence
(2003) Nuclear gene sequences provide evidence for the monophyly of australidelphian marsupials. Ewing G, Nicholls G, Rodrigo A (2004) Using temporally spaced sequences to simultaneously estimate migration rates, mutation rate and population sizes in measurably evolving populations.
In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a continuum.
The second step is to actually run BEAST using the input file that contains the data, model and settings.
1 The final step is to explore the output of BEAST in order to diagnose problems and to summarize the results.
W.; Phillips, Matthew J.; Rambaut, Andrew 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 evident that both are biologically unrealistic and that the real evolutionary process lies between these two extremes.
Our approach also provides a means for measuring the clocklikeness of datasets and comparing this measure between different genes and phylogenies.
Fortunately, intermediate models employing relaxed molecular clocks have been described.
These models open the gate to a new field of "relaxed phylogenetics." Here we introduce a new approach to performing relaxed phylogenetic analysis.
BEAUti The program BEAUti is a user-friendly program for setting the model parameters for BEAST. Loading the NEXUS file To load a NEXUS format alignment, simply select the Import Alignment... This file contains an alignment of sequences of 12 species of primates.
It looks like this (the lines have been truncated): #NEXUS begin data; dimensions ntax=12 nchar=898; format datatype=dna interleave=no gap=-; matrix Tarsius_syrichta AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACC Lemur_catta AAGCTTCATAGGAGCAACCATTCTAATAATCGCACATGGCCTTACA Homo_sapiens AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACA Pan AAGCTTCACCGGCGCAATTATCCTCATAATCGCCCACGGACTTACA Gorilla AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACA Pongo AAGCTTCACCGGCGCAACCACCCTCATGATTGCCCATGGACTCACA Hylobates AAGCTTTACAGGTGCAACCGTCCTCATAATCGCCCACGGACTAACC Macaca_fuscata AAGCTTTTCCGGCGCAACCATCCTTATGATCGCTCACGGACTCACC M_mulatta AAGCTTTTCTGGCGCAACCATCCTCATGATTGCTCACGGACTCACC M_fascicularis AAGCTTCTCCGGCGCAACCACCCTTATAATCGCCCACGGGCTCACC 2 M_sylvanus Saimiri_sciureus ; end; AAGCTTCTCCGGTGCAACTATCCTTATAGTTGCCCATGGACTCACC AAGCTTCACCGGCGCAATGATCCTAATAATCGCTCACGGGTTTACT begin assumptions; charset firsthalf = 1-449; charset secondhalf = 450-898; end; end; Once loaded, the two character partitions are displayed in the main panel: Defining the calibration nodes Select the Taxon Sets tab at the top of the main window.
This tutorial is written for BEAST v1.6.x, which has support for multiple partitions. • Tracer - this program is used to explore the output of BEAST (and other Bayesian MCMC programs).