Revised simulation code and data

The zipped tarball contains revised simulation code and data for my revisions of 23 August 2012. 1) combined.results.RData (combined results from all simulations; 2) Fig1.simulation.R (R code use for simulating the example of Figure 1); 3) Five files named according to the convention qX.Y.R - these contain the code used in simulation for each value of q=X.Y; 4) Five files named according to the convention qX.Y.RData - these contain the results from simulation for each value of q=X.Y; 5) summary.code.R (R code for summarizing the results from simulation); 6) a folder comparison.to.SIMMAP containing comparison code in R, an .RData file with results, and the input (.xml) and output (.nex) files from SIMMAP

All code & scripts

This zipped tarball contains all the code & scripts necessary (combined with R packages available through CRAN) to reproduce the analyses of this study. All files are plain text and contain a short description of the specific analysis or analyses that will be generated by the script

Simulation code and data

This zipped tarball contains the following files to accompany my submitted manuscript: 1) combined.results.RData (combined results from all simulations; 2) Fig1.simulation.R (R code use for simulating the example of Figure 1); 3) Five files named according to the convention qX.Y.R - these contain the code used in simulation for each value of q=X.Y; 4) Five files named according to the convention qX.Y.RData - these contain the results from simulation for each value of q=X.Y; 5) summary.code.R (R code for summarizing the results from simulation)

Cyprinid_tree

Tree file used for analysis of empirical data. Tree is from Hulsey and Hollingsworth (2011; Biol. J. Linn. Soc. 103: 136-146)

cyprinid_morphometric_data

Morphological data for cyprinid minnows used in empirical data analysis. Data from Hulsey and Hollingsworth (2011; Biol. J. Linn. Soc 103: 136-146)

Map of Puerto Rico overlaid with the karst region (brown) and mtDNA haplogroups found in the Puerto Rican Boa, mapped by sampling locality on the island.

<p>Sampling locations with a single individual are labeled with a “1.” Note that no distinct phylogeographic signal is found, and that Haplogroup I appears restricted to a single population.</p

Microsatellite loci used to genotype samples in this study.

<p>N_A, number of alleles per locus; HWE, <i>P</i>-value for test of Hardy-Weinberg equilibrium.</p

Genetic diversity and test statistics of selective neutrality with populations of <i>Epicrates inornatus</i> for the concatenated mitochondrial dataset.

<p>S: number of segregating sites, <i>n</i>: number of haplotypes, K: number of private haplotypes, <i>h</i>: haplotype diversity, π: nucleotide diversity. Significance for neutrality tests were based on 10,000 permutations with α = 0.05.</p

Pairwise genetic divergence between sampling locations (cave and surface populations only).

<p>Above diagonal: mtDNA distances (<i>Φ_ST</i>); below diagonal, microsatellite distances (<i>F_ST</i>). P-values (* significant at <i>P</i><0.05) were obtained through 99,999 permutations.</p

A hypomelanistic endemic endangered Puerto Rican Boa (<i>Epicrates inornatus</i>) consuming a bat (<i>Monophyllus redmani</i>), Mata de Plátano Cave, Arecibo municipality.

<p>Photo by ARPR.</p