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The difference between the null distribution and the true data set, which is highly enriched for a signature of social group, is shown using both histogram and quantile quantile plots in the new Figure 3 figure supplement 1. 2) Empirical validation of the procedure used to identify within social group socially structured species.
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In this procedure, positions of HDIs and LDIs and regions in-between were permuted simultaneously to compute the null distribution of the overlap between islands and genes.
The difference in likelihood scores between these runs comprised the null distribution against which the likelihood value from the harpy eagle dataset was tested.
(4) The hierarchical island model that identifies outlier loci by allowing the exchange of more migrants within groups than between groups while generating the null distribution of FST values to reduce the number of false positives, was also applied to the data set [ 80].
To determine the significance of the distance measures between breakpoints and features, the null distribution of distances from breakpoints to features was found by randomizing breakpoints through a circular permutation algorithm (fig. 2 A ). Specifically, S. cerevisiae chromosomes were randomly arranged in a circle.
A significant deviation between the observed value and the null distribution will indicate a model-misspecification problem.
In contrast, for each dataset, the false discovery rate is calculated relative to its permuted distribution, thereby controlling for differences in the null distribution between studies.
Whether KST was significantly different from zero was tested by permuting haplotypes between populations 100 times, giving the null distribution of pairwise KST values under the hypothesis of no difference between populations.
The null distribution is estimated by spline fitting [79] on the histogram, and the difference between the histogram fit (grey curve) and the null distribution (black curve) is used to give an estimate of the number of differentially expressed genes.
Sites under shifting selection were significantly associated with outliers both in extreme support and extreme rejection of the spurious nectar-feeding clade (Fig. 12B) relative to the null distribution of differences between alternative phylogenies (G-tests of goodness-of-fit for both CYTB and COX1 G2 = 59.182, P = 1.409E 13; for CYTB only G2 = 51.258, P = 7.402E 12).
In addition, the single-SNP P values showed no clear deviation from the null distribution, representing no association between SNPs and percentage density.
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