Quantifying the frequency of recombination as a function of the genetic divergence between donor and recipient DNA sequences.

(A) Schematic illustration showing the genetic divergence of 2 recombined fragments relative to the focal pair of genomes. The synonymous divergence of each detected transfer is computed and aggregated across all closely related pairs within a species. (B–E) Distribution of donor-recipient divergence for all detected transfers in 4 example species. Orange lines show the observed data, while the blue lines show a null expectation obtained by randomly drawing segments from the observed collection of genomes (Section 3.6 in S1 Text). Insets show the corresponding complementary cumulative distribution functions. For species with a strong clade structure (D and E), the average between-clade divergence is indicated by dashed vertical lines. (F) Differences between the observed and simulated divergence distributions for all of the species in Fig 3, summarized by the Kolmogorov–Smirnov (K-S) distance (inset). Solid bars indicate statistically significant differences (P−3; one-sided K-S test), while arrows indicate the example species in panels B–E. Together, these data show that many species exhibit only small differences between their observed and expected divergence distributions (K-S distance ≲0.1), even when their overall sequence divergence is comparable to counterexamples like D and E (Figs W and X in S1 Text). The data underlying this figure can be found in https://doi.org/10.5281/zenodo.10304481.