Fig. 2: Evidence supporting the gap-filling model for the generation of single-copy Pack-TIRs.

a Distribution of Pack-TIRs classified by distance from their parental copies. The pie charts show the statistics for all species, western clawed frogs, and humans, respectively. Numbers of multicopy Pack-TIRs are highlighted in pink. For example, three out of five interchromosomal Pack-TIRs are multicopy in western clawed frogs. b Histogram of intrachromosomal Pack-TIRs in terms of distance to their parental copies. The dashed curve shows the lowess fitting result. c Distribution of Pack-TIRs classified by the presence of microhomology at two breakpoints. The sidebar shows the histogram of the microhomology length. d Distribution of Pack-TIRs with respect to the microhomology presence at breakpoints. Single-copy Pack-TIRs close or far from parental copies and multicopy Pack-TIRs are separately counted. e A comparative view of a demo Pack-TIR in gibbons (case #144 in Supplementary Data 1). To simplify, in addition to gibbons, only four phylogenetically representative primates are shown. The figure convention follows Fig. 1d except that the microhomology is marked in orange. Note that the left TSD was mutated from TA to CA in the ancestor of humans and monkeys. f Proportion of each gap (n = 281 samples) relative to the corresponding consensus TE. The distribution is shown as a violin plot: the box indicates the median (middle line) and the interquartile range (IQR, box limits); outliers are beyond 1.5 times IQR; and the violin curve indicates the probability density of the data. g Cumulative density distribution of the observed and simulated relative positions of breakpoints to consensus TEs. Values closer to 0.5 at X-axis indicate positions closer to the middle of the TEs, whereas values close to 0 indicate positions closer to the terminals. The two-sided Kolmogorov-Smirnov test was used to calculate the P-value.