Computational protocol: Unexpectedly Low Rangewide Population Genetic Structure of the Imperiled Eastern Box Turtle Terrapene c. carolina

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Protocol publication

[…] To test for the presence of null alleles and large allelic dropout, we used Microchecker (version 2.2.3; ). To assess how well our dataset and each population met Hardy-Weinberg equilibrium (HWE) assumptions, we used the web version of Genepop (version 4.0.10; ) to test for a significant deficit of heterozygotes using an exact method with default parameters. We used a Markov chain Monte Carlo (MCMC) method to assess significant deviations from HWE. We quantified deviations from Hardy-Weinberg equilibrium (HWE) by estimating F IS in Genepop with 10,000 iterations. [...] We evaluated rangewide isolation by distance by using a Mantel test performed in Alleles in Space (Ais, version 1.0; ) to determine whether a significant correlation existed between pairwise matrices of Nei's genetic distances and geographic distances matrices. We log10-transformed the geographic distance matrix to meet the assumption of normality and used 1,000 randomized replicates to assess significance. To estimate the geographic scale at which IBD may begin to operate, we also performed a complementary spatial autocorrelation analysis in Ais, using 10 classes of equal distance and 1,000 replicates to assess significance. […]

Pipeline specifications

Software tools Genepop, AIS
Application Population genetic analysis