Fig. 5: D. miranda males show more de novo TE insertions than females.

a Schematic diagram of rationale behind TE insertion identification. b Computational pipeline implementing the strategy in a. The left panel outlines the mapping strategy to identify mate pairs at insertion junctions. The right panel outlines the filtering strategy to identify de novo TE insertions. See Supplementary Data 3 for summary of insertions filtered and identified for each library. c The numbers of de novo TE insertions identified in D. pseudooboscura embryos are plotted against the autosomal median coverages. Lines of best fit are shown for the male (blues) and female (reds) samples, separately. d The effect of library size is removed by regression of TE insertion numbers against library coverage and taking the residuals. Boxplot depicts the residuals of the regression binned by sex and developmental stages. P values are labeled above the comparisons (two-tailed Wilcoxon rank-sum test, no multiple testing correction). In the boxplots, whiskers delineate the minima and maxima of the distributions, the box delineates the 25th and 75th percentiles, and the centers mark the medians. e, f Same as c and d, but for D. miranda embryos. g The number of de novo insertions across all male D. miranda stage 7 embryos is plotted against the transcript abundance. Line of best fit is in red and R² of the regression and the significance of the correlation are shown. Only TEs with de novo insertions are plotted. h The observed and expected distribution of insertions across the chromosomes are depicted in females (top) and males (bottom). Source data are provided as a Source data file.