Genomic architecture and introgression shape a butterfly radiation

We used 20 de novo genome assemblies to probe the speciation history and architecture of gene flow in rapidly radiating Heliconius butterflies. Our tests to distinguish incomplete lineage sorting from introgression indicate that gene flow has obscured several ancient phylogenetic relationships in this group over large swathes of the genome. Introgressed loci are underrepresented in low-recombination and gene-rich regions, consistent with the purging of foreign alleles more tightly linked to incompatibility loci. Here, we identify a hitherto unknown inversion that traps a color pattern switch locus. We infer that this inversion was transferred between lineages by introgression and is convergent with a similar rearrangement in another part of the genus. These multiple de novo genome sequences enable improved understanding of the importance of introgression and selective processes in adaptive radiation.

Transitions from Single- to Multi-Locus Processes during Speciation with Gene Flow

During speciation-with-gene-flow, a transition from single-locus to multi-locus processes can occur, as strong coupling of multiple loci creates a barrier to gene flow. Testing predictions about such transitions with empirical data requires building upon past theoretical work and the continued development of quantitative approaches. We simulated genomes under several evolutionary scenarios of gene flow and divergent selection, extending previous work with the additions of neutral sites and coupling statistics. We used these simulations to investigate, in a preliminary way, if and how selected and neutral sites differ in the conditions they require for transitions during speciation. For the parameter combinations we explored, as the per-locus strength of selection grew and/or migration decreased, it became easier for selected sites to show divergence-and thus to rise in linkage disequilibrium (LD) with each other as a statistical consequence-farther in advance of the conditions under which neutral sites could diverge. Indeed, even very low rates of effective gene flow were sufficient to prevent differentiation at neutral sites. However, once strong enough, coupling among selected sites eventually reduced gene flow at neutral sites as well. To explore whether similar transitions might be detectable in empirical data, we used published genome resequencing data from three taxa of Heliconius butterflies. We found that fixation index ( F S T ) outliers and allele-frequency outliers exhibited stronger patterns of within-deme LD than the genomic background, as expected. The statistical characteristics of within-deme LD-likely indicative of the strength of coupling of barrier loci-varied between chromosomes and taxonomic comparisons. Qualitatively, the patterns we observed in the empirical data and in our simulations suggest that selection drives rapid genome-wide transitions to multi-locus coupling, illustrating how divergence and gene flow interact along the speciation continuum.

Diversification of the silverspot butterflies (Nymphalidae) in the Neotropics inferred from multi-locus DNA sequences

The tribe Heliconiini (Lepidoptera: Nymphalidae) is a diverse group of butterflies distributed throughout the Neotropics, which has been studied extensively, in particular the genus Heliconius. However, most of the other lineages, such as Dione, which are less diverse and considered basal within the group, have received little attention. Basic information, such as species limits and geographical distributions remain uncertain for this genus. Here we used multilocus DNA sequence data and the geographical distribution analysis across the entire range of Dione in the Neotropical region in order to make inferences on the evolutionary history of this poorly explored lineage. Bayesian time-tree reconstruction allows inferring two major diversification events in this tribe around 25mya. Lineages thought to be ancient, such as Dione and Agraulis, are as recent as Heliconius. Dione formed a monophyletic clade, sister to the genus Agraulis. Dione juno, D. glycera and D. moneta were reciprocally monophyletic and formed genetic clusters, with the first two more close related than each other in relation to the third. Divergence time estimates support the hypothesis that speciation in Dione coincided with both the rise of Passifloraceae (the host plants) and the uplift of the Andes. Since the sister species D. glycera and D. moneta are specialized feeders on passion-vine lineages that are endemic to areas located either within or adjacent to the Andes, we inferred that they co-speciated with their host plants during this vicariant event.