BAMMtools-data {BAMMtools}R Documentation

BAMMtools datasets

Description

Example datasets and sample BAMM output for the package BAMMtools.

Details

This includes both the raw data and the BAMM output for three example analyses. The first is an analysis of speciation and extinction rates during the radiation of modern whales, using a time-calibrated tree from Steeman et al. (2009). The second is a BAMM analysis of phenotypic evolutionary rates (body mass) during the radiation of extant primates, taken from Vos and Mooers (2006) and Redding et al. (2010).The third is a BAMM analysis of speciation and extinction rates for a 300-species subset of ray-finned fishes, along with body size data for these species from Rabosky et al. (2013).

Dataset whales is the raw time-calibrated tree that was analyzed with BAMM, primates is the corresponding time-calibrated phylogeny of 233 primate species, and fishes is the time-calibrated phylogeny of 300 fish species. Log-transformed body masses for primates are in dataset mass.primates, and fish body sizes are in dataset traits.fishes.

The MCMC output files (mcmc.whales and mcmc.primates) are dataframes containing the raw MCMC output as generated by BAMM. Column headers in the dataframes includes the sampling generation, the current number of shifts in the simulation (N_shifts), the log-prior density of the parameters (logPrior), the log-likelihood of the data (logLik), the current parameter of the Poisson process governing the number of regime shifts (eventRate), and the MCMC acceptance rate (acceptRate). This is the file that would typically be analyzed as a first step towards assessing MCMC convergence (e.g., analyzing effective sample sizes of logLik and N_shifts).

The "core" BAMM output is included in the event data files (events.whales, events.primates and events.fishes). These are all the parameters sampled with MCMC that are relevant to reconstructing the nature and location of evolutionary rate dynamics across a phylogeny. Please refer to BAMM documentation for a detailed overview of this output, but a brief description is as follows:

generation: The index value of the state in the MCMC simulation (the "generation").

leftchild, rightchild: This defines a unique topological location where a rate shift was sampled. Specifically, for given right-left pair, the shift is sampled on the branch leading to the node from which rightchild and leftchild are descended (these two taxa are part of the spanning set of taxa for the node). If leftchild is "NA", this simply means that the shift was sampled on a terminal branch.

abstime: The absolute occurrence time of the shift, assuming that the time of the root node is 0.0.

lambdainit, lambdashift: For speciation extinction model, the initial speciation rate and rate change parameter for the process.

muinit: For speciation extinction model, the extinction rate (time-invariant).

betainit, betashift: For phenotypic evolutionary model, the initial (betainit) rate of phenotypic evolution and the rate change parameter (betashift).

Source

Vos R.A., A.O. Mooers. 2006. A new dated supertree of the Primates. Chapter 5. In Inferring large phylogenies: the big tree problem (R Vos, Ph.D. thesis) Simon Fraser University.

Redding D.W., C. DeWolff, A.O. Mooers. 2010. Evolutionary distinctiveness, threat status and ecological oddity in primates. Conservation Biology 24: 1052-1058. DOI: 10.1111/j.1523-1739.2010.01532.x

Steeman, M.E., M.B. Hebsgaard, R.E. Fordyce, S.W.Y. Ho, D.L. Rabosky, R. Nielsen, C. Rahbek, H. Glenner, M.V. Sorensen, E. Willerslev. 2009. Radiation of Extant Cetaceans Driven by Restructuring of the Oceans. Systematic Biology. 58: 573-585. DOI: 10.1093/sysbio/syp060

Rabosky, D. L., F. Santini, J.T. Eastman, S. . Smith, B.L. Sidlauskas, J. Chang, and M.E. Alfaro. 2013. Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation. Nature Communications DOI: 10.1038/ncomms2958.


[Package BAMMtools version 2.1.11 Index]