Statistical Analyses
Descriptive statistics, a single factor analysis of variance (ANOVA), and a linear regression were calculated in Microsoft Excel v16.16.20 using the data analysis add in. The ANOVA was performed on the quality data (represented by the percentage of reads passing quality from prinseq) compared against the sample types.
The program MicroDrop v1.01 (Wang & Rosenberg, 2012) was run to evaluate the rates of allelic dropout within samples and across loci. The program was run twice, once on the genotypes called directly by CHIIMP based on the pooled data, and once on the genotypes determined by our best practices, shown in the ‘Manually Processed Genotypes’ column of Table 4. The program was run using the default parameters, and we did not enforce Hardy-Weinberg Equilibrium on our data due to the low number of alleles and samples. Individual replicates were not run on MicroDrop, as the program is designed to work on non-replicated datasets, although the pooled data had multiple replicates of each individual pooled prior to library preparation.