Butterfly genome reveals promiscuous exchange of mimicry adaptations among species

Abstract

The evolutionary importance of hybridization and introgression has long been debated. Hybrids are usually rare and unfit, but even infrequent hybridization can aid adaptation by transferring beneficial traits between species. Here we use genomic tools to investigate introgression in Heliconius, a rapidly radiating genus of neotropical butterflies widely used in studies of ecology, behaviour, mimicry and speciation. We sequenced the genome of Heliconius melpomene and compared it with other taxa to investigate chromosomal evolution in Lepidoptera and gene flow among multiple Heliconius species and races. Among 12,669 predicted genes, biologically important expansions of families of chemosensory and Hox genes are particularly noteworthy. Chromosomal organization has remained broadly conserved since the Cretaceous period, when butterflies split from the Bombyx (silkmoth) lineage. Using genomic resequencing, we show hybrid exchange of genes between three co-mimics, Heliconius melpomene, Heliconius timareta and Heliconius elevatus, especially at two genomic regions that control mimicry pattern. We infer that closely related Heliconius species exchange protective colour-pattern genes promiscuously, implying that hybridization has an important role in adaptive radiation.

Figure 1. Distribution, mimicry and phylogenetic relationships of sequenced taxa

a Phylogenetic relationship of sequenced species and subspecies in the ‘melpomene- silvaniform clade’ of Heliconius. H. elevatus falls in the ‘silvaniform’ clade, but its colour pattern mimics melpomene-timareta clade taxa. b Geographic distribution of ‘postman’ and ‘rayed’ H. melpomene races studied here (blue, yellow and purple), and the entire distribution of H. melpomene (grey). The H. timareta races investigated have limited distributions indicated by arrows (red) and mimic sympatric races of H. melpomene. H. elevatus and the other silvaniform species are distributed widely across the Amazon basin (Supplementary Information 22).

Figure 2. Comparative analysis of synteny and expansion of the chemosensory genes

a Maps of the 21 Heliconius chromosomes (above) and of the 28 Bombyx chromosomes (below in grey) based on positions of 6010 orthologue pairs demonstrate highly conserved synteny and a shared n=31 ancestor (Supplementary Information 8). Dotted lines within chromosomes indicate major chromosomal fusions. b Maximum likelihood tree showing expansion of the chemosensory protein genes (CSP) in two butterfly genomes.

Figure 3. Four-taxon ABBA-BABA test of introgression

a ABBA and BABA nucleotide sites employed in the test are derived (– – B –) in H. timareta, compared with the silvaniform outgroup (– – – A), but differ among H. melpomene amaryllis and H. melpomene aglaope (either ABBA or BABA). As this almost exclusively restricts attention to sites polymorphic in the ancestor of H. timareta and H. melpomene, equal numbers of ABBA and BABA sites are expected under a null hypothesis of no introgression, as depicted in the two gene genealogies. b Distribution among chromosomes of Patterson’s D-statistic ± s.e., which measures excess of ABBA vs. BABA sites, here for the comparison H. m. aglaope; H. m. amaryllis; H. timareta ssp. nov.; silvaniform. Chromosomes containing the two colour pattern regions (B/D red; N/Yb yellow) have the two highest D-statistics; the combinatorial probability of this occurring by chance is 0.005. The excess of ABBA sites (0 < D < 1) indicates introgression between sympatric H. timareta and H. melpomene amaryllis.

Figure 4. Evidence for adaptive introgression at the B/D mimicry locus

a Genetic divergence between H. melpomene races aglaope (rayed) and amaryllis (postman) across a hybrid zone in N.E. Peru. Divergence, F_ST, is measured along the B/D region (Supplementary Information 14). F_ST peaks in the region known to control red wing pattern elements between the genes kinesin and optix. b, c Distribution of fixed ABBA and BABA sites (see Fig. 4a) along B/D for two comparisons. Excesses of ABBA in b and BABA in c are highly significant (two-tailed Z-tests for D = 0; D = 0.90 ± 0.13, P = 5 × 10⁻¹⁴ and D = –0.91 ± 0.10, P = 9 × 10⁻²⁴ respectively), indicating introgression. d, e, f, Genealogical change along B/D investigated with maximum likelihood based on 50 kb windows. Three representative tree topologies are shown. Topology A, the species tree, is found within the white windows. In topologies B (dark green window) and C (light green windows) taxa group by colour pattern rather than species. Within striped windows H. melpomene and/or H. timareta are paraphyletic but the taxa do not group by colour pattern. Support is shown for nodes with > 50% bootstrap support (Supplementary Information 19).