January 21, 2014
This Dryad submission contains data and analytical information for the manuscript:
Crandall, E.D., Treml, E.A., Liggins, L., Gleeson, L., Yasuda, N., Barber, P.H., Wörheide, G. and C.R. Riginos (2014). Return of the ghosts of dispersal past: historical spread and contemporary gene flow in the blue seastar Linckia laevigata. In press at Bulletin of Marine Science.

1. Data
Linckia_MASTER_workingcopy.nex - the master copy of the mitochondrial dataset we worked with
Linckia_orig.arp - the same data in Arlequin format
Linckia_reduced_biophys model.arp - the same data including only pops that were included in the biophysical model
Linckia_reduced_N10.arp - the same dataset reduced to only include pop with n>=10


2. Analyses:

The folder Diffusion_analysis contains .xml files that can be run in the phylogenetic software BEAST, and which describe the relevant priors and settings used in the analysis.
Linckia_diffusion_treml4.xml - describes setting used in the final analysis, run over 4 replicates
Linkcia_diffusion_randomized - the same file, but adds an operator that randomizes the tip state, allowing us to explore the effect of sample size on the inference of root location.

The folder MRDM+MDS contains R scripts and data that were used for Multiple Regression on Distance matrices (MRDM) and Multi-dimensional scaling (MDS) analyses in the paper.
Biophys_Gen_dists.R contains R scripts for reading in the data, and readying it for analysis
MDS_Mantel_MRDM contains R scripts for the MRDM and MDS analyses described in the paper.
Other files contain either genetic distances (Gst, Phist, Jost's D), or geographic distances (overwater distance, biophysical model distance, euclidean distance).

Please contact Eric Crandall at eric.d.crandall@gmail.com if you have any questions.