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Population differentiation may arise because of random genetic drift and FST may be influenced by unequal sample sizes.
Because FST may be influenced by unequal sample sizes, we limited our search for genes of interest to the nine high FST regions that also had significant deviations from expected heterozygosity in Thoroughbred.
Because these estimates of species richness per habitat are biased by unequal sample sizes (point counts per habitat), we also carried out rarefaction analysis to interpolate estimated species richness to equal sample sizes.
To allow for a reduction in power caused by unequal sample sizes among clusters, the target sample size has been set to 3000 (an average of 250 per cluster).
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There are no evidences that heterogeneous levels of genetic variability were produced by unequal sample size for each population through Pearson's correlation test between diversity indices and sample size (r = 0.082 and P = 0.790 for numbers of haplotypes, r = -0.02 and P = 0.996 for haplotype diversity, and r = 0.141 and P = 0.645 for nucleotide diversity, respectively).
The distribution of shared and private potential paralogs among populations and species was further examined by controlling for unequal sample sizes, by randomly sampling four individuals (the smallest sample size) per locality.
Estimates of π in each 10-kb window were corrected for unequal sample sizes by multiplying by a factor of n/(n − 1) (Nei 1987).
Differences between treatments were tested with one-way ANOVA, followed by post hoc Tukey test for unequal sample sizes (Unequal N HSD test).
Additionally, the power to detect moderators might have been decreased by the relatively small sample size, unequal sample sizes across groups (e.g. male vs. female), and possibly heterogeneous error variance [ 51].
Analysis was performed by one way ANOVA followed by an adjusted Dunnett's post hoc test for unequal sample sizes.
Non-parametric statistical tests were applied because of frequent non-normality of data sets (tested by the Shapiro-Wilk normality test), or small or unequal sample sizes.
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