Genome divergence, lineage-specific sequence distribution, and historical demography of H. melpomene, H. erato, and H. charithonia from Panama and Puerto Rico. (A) Phylogenetic relations, genome sizes, and approximate divergence times. Colored lines indicate branches investigated in panel D. (B) Inference of historical effective population size changes using pairwise sequentially Markovian coalescent (PSMC) analysis. The PSMC estimates are scaled using a generation time of 0.25 yr and a mutation rate of 2 × 10−9. Note that the H. charithonia genome was obtained from the Puerto Rican population. (C) Venn diagrams represent homologous and nonhomologous (lineage-specific) genomic sequences (excluding Ns). Between the two pseudohaplotypes of the H. charithonia genome, we observed a total of 72.7 Mb of sequence identified as indel. Of these indels, 63.1 Mb (86.8%) were lineage-specific to H. charithonia, whereas 9.6 Mb (13.2%) were present in the H. erato genome. Consistent with divergence times, the H. charithonia genome comprised 43.5% (175.2 Mb; compared with the ∼6 Myr divergent H. erato) to 62.7% (252.3 Mb; compared with the ∼11 Myr divergent H. melpomene) of lineage-specific sequence resulting from structural variants (SVs). H. erato had 39.0% (151.2 Mb) lineage-specific sequences compared with H. charithonia and 58.0% (222.1 Mb) lineage-specific sequences compared with H. melpomene. H. melpomene had 34.5% (95.0 Mb) lineage-specific genomic sequence compared with H. erato and H. charithonia. (D) Length distribution of lineage-specific sequences. Colored histograms show the frequency of SVs for different phylogenetic comparisons (as indicated in panel A). The black line shows the frequency distribution of lineage-specific SVs that were characterized as transposable elements (TEs). Between the two H. charithonia haplotypes, indels had an average and median length of 13.5 and 2 bp. The average and median length was 34.2 and 4 bp for lineage-specific H. charithonia sequences relative to H. erato and 45.6 and 6 bp relative to H. melpomene.
