53 research outputs found

    Revised simulation code and data

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    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

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    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

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    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

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    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

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    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.

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    <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.

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    <p>N<sub>A</sub>, 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.

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    <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).

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

    Plots of genetic diversity for cave and surface populations of Puerto Rican boas.

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    <p>A) mtDNA and nucDNA estimates for each cave and surface population. The parameters are haplotype diversity (<i>h</i>), observed heterozygosity (H<sub>O</sub>), and allelic richness (A). B) Genotypic differentiation among populations visualized in multivariate space using principal components rotations. Inset: <i>P</i>-values for Fisher’s tests for genetic differentiation between populations.</p
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