11 research outputs found

    Additional file 1: Table S1. of Fine-scale genetic structure among greater sage-grouse leks in central Nevada

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    Geographic coordinates and number of individuals included in final analyses (N‚ÄČ=‚ÄČ140) for each lek and lek complex. Table S2. Mean observed F ST estimates among leks was compared to a null distribution of F ST values (based on 100 permutations of lek assignment). Figure S1. Histograms display the distribution of (A) yearly and (B) summer movement distances for sage-grouse individuals in this system based on telemetry data. Figure S2. Histograms display the distribution of Euclidean genetic distances for 1000 permutations of randomly sampled subsets of sage grouse pairs. These permutations were used to test if sage-grouse within a (A) lek complex and (B) lek were genetically more similar than expected from a null distribution. Figure S3. The correlation between the genomic and geographic matrices obtained from the Procrustes analysis (0.695) is compared to the distribution of correlations from 999 random permutations. Figure S4. Summary results from the DAPC that did not use a priori group assignments are displayed. (A) Bayesian information criterion (BIC) steadily increases as the number of clusters (K) increases in the model (we selected the K value with the lowest BIC). (B) For each group, a density histogram is displayed to ease in the visualization of how individuals cluster along discriminant function one. (C) Additionally, individual assignment probabilities for each lek complex are displayed in a bar graph, with a priori lek and lek complex designations displayed above (results from DAPC analyses utilizing a priori group assignments are depicted in Fig.¬†3 of the main text). Figure S5. Results from PCA using the entire SNP dataset (panels A, D, G) were compared to subsets of data with the top 2¬†% (B, E, H) and top 3¬†% of FST (C, E, I) outliers removed. Any loci that were in the top 2 or 3¬†% of the FST distribution for any pairwise lek comparison were removed to create the subsets. Panels (A), (B), and (C) display scatterplots of PC1 and PC2, with symbols representing lek means and segments drawn from the means to individual scores. Panels (D), (E), and (G) depict the Procrustes correlation between the first two PCs and a standardized geographic matrix. Panels (G), (H), and (I) show the results of a regression with latitude predicting PC1. (PDF 2601 kb

    Input file for entropy analysis

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    Genotype likelihoods (simplified from VCF) at 11,221 SNPs for 2785 individual Catostomus fish. This file was used for analyses of hybridization

    Full VCF file

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    All variant sites initially identified for analysis of hybridization. This VCF was produced using samtools and bcftools, and contains information for 2785 Catostomus individuals

    Mvitellinus_draft_genome

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    This file contains the first draft assembly of the M. vitellinus genome. This file will be embargoed until a paper containing a full description of this and 49 other avian genomes is published, most likely in early 2013

    manacus_snpcnt

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    This file contains information on the number of reads representing each of two SNP states in each individual manakin across 59,100 loci. The file is organized by locus. For further details on how this file was generated, see the manuscript
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