Fig. 6: Examples of genomic regions suggestive of recombination events.

Schematic representation of three genomic segments (black bars) with recombination events (colored bars) inferred according to different methods implemented in RDP4 (ref. ⁷⁷). Each genomic segment was phased in four individuals (phased dataset 2, individuals L6-L9; see “Methods” section). The three shown segments were positioned on different contigs in the L1 diploid assembly. Numbers adjacent to the black bars indicate the coordinates of the segment start, end, and inferred breakpoints (ends of colored rectangles). Fragments delineated by boundaries of recombination events (dashed lines) were used to construct corresponding phylogenetic trees (connected with arrows to them). In phylogenies, haplotypes used by RDP4 to identify a recombination event are identified with colored shapes, with indices 1 and 2 designating the two haplotypes of a single individual. Trees were built using the maximum likelihood method in PhyML⁷⁴ under the GTR + G model with 1000 bootstrap replicates and midpoint-rooted. The bootstrap support values ≥50% are shown next to branches. Bootstrap support values are rounded to the nearest integer. Only those SNPs that satisfied all filtering criteria and were simultaneously phased in L6-L9 were used in the analysis. For further information on the shown segments and inferred recombination events (including RDP4 P values), see Supplementary Data 6 and “Methods” section. Haplotypes reconstructed for L6-L9 in these three segments are provided as Supplementary Data 7.