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men12009-sup-0002-FigureS1-S2.pdfapplication/PDF113KFig. S1 Plot of point estimates (black lines) of cline parameter along all markers in the simulated genome (201 equally spaced loci on each of 10 chromosomes) from one representative replicate. Three introgression outlier loci are marked with + symbols (with qn = 0.05 and using the median as the posterior estimate of the inline image quantile; two of the + symbols overlap). We did not detect excess ancestry. Dashed vertical lines give the location of a pair of interacting loci that cause a Dobzhansky-Muller incompatibility and dotted vertical lines denote chromosome boundaries. Fig. S2 Histogram of the locus-specific error probabilities estimated from base alignment quality (A). Scatter-plots depict the relationship between hybrid index (B) or cline parameter a (C) estimated with and without incorporating sequence errors. The solid black lines denote a one to one relationship between parameter estimates.
men12009-sup-0001-TableS1-S7.pdfapplication/PDF1294KTable S1 Sample input data file format for the parental population allele counts with geno-types known. Table S2 Sample input data file format for the parental population allele counts with geno-types known. Table S3 Sample input data file format for the parental population allele counts with genotype uncertainty. Table S4 Sample input data file format for admixed population(s) allele counts with genotype uncertainty. Table S5 Sample input data file format for a genetic map, which is used with the linkage model. Table S6 Command line arguments that are used by bgc. Table S7 Command line arguments that are used by estpost.

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