10.5061/DRYAD.HN1VN
Rabosky, Daniel L.
University of Michigan-Ann Arbor
Data from: Automatic detection of key innovations, rate shifts, and
diversity-dependence on phylogenetic trees
Dryad
dataset
2015
Computational biology
2015-01-10T00:00:00Z
2015-01-10T00:00:00Z
en
https://doi.org/10.1371/journal.pone.0089543
21331964 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
A number of methods have been developed to infer differential rates of
species diversification through time and among clades using
time-calibrated phylogenetic trees. However, we lack a general framework
that can delineate and quantify heterogeneous mixtures of dynamic
processes within single phylogenies. I developed a method that can
identify arbitrary numbers of time-varying diversification processes on
phylogenies without specifying their locations in advance. The method uses
reversible-jump Markov Chain Monte Carlo to move between model subspaces
that vary in the number of distinct diversification regimes. The model
assumes that changes in evolutionary regimes occur across the branches of
phylogenetic trees under a compound Poisson process and explicitly
accounts for rate variation through time and among lineages. Using
simulated datasets, I demonstrate that the method can be used to quantify
complex mixtures of time-dependent, diversity-dependent, and constant-rate
diversification processes. I compared the performance of the method to the
MEDUSA model of rate variation among lineages. As an empirical example, I
analyzed the history of speciation and extinction during the radiation of
modern whales. The method described here will greatly facilitate the
exploration of macroevolutionary dynamics across large phylogenetic trees,
which may have been shaped by heterogeneous mixtures of distinct
evolutionary processes.
Phylogenetic trees simulated under multi-process macroevolutionary models
for analysis with BAMMThis file contains simulated datasets analyzed as
part of Rabosky (2014). There are 6 general simulation scenarios,
described at length in the manuscript. These include 500 phylogenetic
trees simulated under each macroevolutionary scenario. Each batch of
simulated datasets was analyzed with BAMM. This dataset contains the
simulated datasets, and also the parameters underlying the simulations.
For example, the subdirectory "constant" contains the 500
constant-rate birth-death process phylogenies that were analyzed with
BAMM. These trees are stored in the fild "simtrees.txt". Another
file in this directory, "cr_truerates.txt", contains the actual
simulation parameters. For example, the first row of that file gives the
speciation and extinction parameters that were used to simulate the first
tree in the "simtrees.txt" file. The same general idea holds for
the other subdirectories. dd_k1 for example is a pure-birth background
process with a shift to a single diversity-dependent regime on one
descendant lineage. The simulation scenarios are detailed in the master
file "DESCRIPTION.txt".BAMM-TestSIms.zip