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.

Identifying the genomic changes that control morphological variation and understanding how they generate diversity is a major goal of evolutionary biology. In Heliconius butterflies, a small number of genes control the development of diverse wing color patterns. Here, we used full genome sequencing of individuals across the Heliconius erato radiation and closely related species to characterize genomic variation associated with wing pattern diversity. We show that variation around color pattern genes is highly modular, with narrow genomic intervals associated with specific differences in color and pattern. This modular architecture explains the diversity of color patterns and provides a flexible mechanism for rapid morphological diversification.

We here pioneer a low-cost assembly strategy for 20 Heliconiini genomes to characterize the evolutionary history of the rapidly radiating genus Heliconius. A bifurcating tree provides a poor fit to the data, and we therefore explore a reticulate phylogeny for Heliconius. We probe the genomic architecture of gene flow, and develop a new method to distinguish incomplete lineage sorting from introgression. We find that most loci with non-canonical histories arose through introgression, and are strongly underrepresented in regions of low recombination and high gene density. This is expected if introgressed alleles are more likely to be purged in such regions due to tighter linkage with incompatibility loci. Finally, we identify a hitherto unrecognized inversion, and show it is a convergent structural rearrangement that captures a known color pattern switch locus within the genus. Our multi-genome assembly approach enables an improved understanding of adaptive radiation.

BackgroundAlthough hybridization is thought to be relatively rare in animals, the raw genetic material introduced via introgression may play an important role in fueling adaptation and adaptive radiation. The butterfly genus Heliconius is an excellent system to study hybridization and introgression but most studies have focused on closely related species such as H. cydno and H. melpomene. Here we characterize genome-wide patterns of introgression between H. besckei, the only species with a red and yellow banded ‘postman’ wing pattern in the tiger-striped silvaniform clade, and co-mimetic H. melpomene nanna.ResultsWe find a pronounced signature of putative introgression from H. melpomene into H. besckei in the genomic region upstream of the gene optix, known to control red wing patterning, suggesting adaptive introgression of wing pattern mimicry between these two distantly related species. At least 39 additional genomic regions show signals of introgression as strong or stronger than this mimicry locus. Gene flow has been on-going, with evidence of gene exchange at multiple time points, and bidirectional, moving from the melpomene to the silvaniform clade and vice versa. The history of gene exchange has also been complex, with contributions from multiple silvaniform species in addition to H. besckei. We also detect a signature of ancient introgression of the entire Z chromosome between the silvaniform and melpomene/cydno clades.ConclusionsOur study provides a genome-wide portrait of introgression between distantly related butterfly species. We further propose a comprehensive and efficient workflow for gene flow identification in genomic data sets.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-0889-0) contains supplementary material, which is available to authorized users.

Natural selection leaves distinct signatures in the genome that can reveal the targets and history of adaptive evolution. By analysing high-coverage genome sequence data from 4 major colour pattern loci sampled from nearly 600 individuals in 53 populations, we show pervasive selection on wing patterns in the Heliconius adaptive radiation. The strongest signatures correspond to loci with the greatest phenotypic effects, consistent with visual selection by predators, and are found in colour patterns with geographically restricted distributions. These recent sweeps are similar between co-mimics and indicate colour pattern turnover events despite strong stabilising selection. Using simulations, we compare sweep signatures expected under classic hard sweeps with those resulting from adaptive introgression, an important aspect of mimicry evolution in Heliconius butterflies. Simulated recipient populations show a distinct 'volcano' pattern with peaks of increased genetic diversity around the selected target, characteristic of sweeps of introgressed variation and consistent with diversity patterns found in some populations. Our genomic data reveal a surprisingly dynamic history of colour pattern selection and co-evolution in this adaptive radiation.

ABSTRACT. External morphology of the immature stages of neotropical heliconians: IV. Dryas iulia alcionea (Lepidoptera, Nymphalidae, Heliconiinae). The external features of egg, larva and pupa of Dryas iulia alcionea (Cramer, 1779) are described and illustrated.

Adult body size, a key life history component, varies strongly within and between Heliconius erato phyllis (Lepidoptera: Nymphalidae) populations. In the present study, we determined whether seasonal variation in adult body size is temperature related and/or determined by seasonal changes of host plants (Passifloraceae) used by the larval stage. A population of H. erato phyllis located in a Eucalyptus plantation (Barba Negra Forest, Barra do Ribeiro County, Rio Grande do Sul State, Brazil) was sampled every 45 days from March 1997 to October 1998 to quantify seasonal variation in adult body size and use of larval host plants. In the laboratory, the effects of the following factors on adult body size were quantified: (i) host plant species ( Passiflora misera or Passiflora suberosa ); (ii) food quantity consumed by larvae (experimentally manipulated for each passion vine species); (iii) winter and summer temperatures (15 and 25 Њ C, respectively); and (iv) the interaction between host plant species and temperature. Adults emerging during summer were larger than those emerging in other seasons. Female butterflies oviposited selectively on P. misera even when the dominant passion vine was P. suberosa . They only switched from using P. misera to P. suberosa during later autumn and winter, when P. misera vines were completely defoliated. The laboratory feeding trials with both passion vines showed a strong positive association between food quantity consumed by larvae and adult size. They also confirmed that adults are larger when their larvae are reared on P. misera than on P. suberosa . Temperature during larval development had no effect on H. erato phyllis adult size. Thus, seasonal variation of H. erato phyllis adult size in a given place is primarily determined by the availability and quality of host plant species used by the larval stage.

ABSTRACT. External morphology of the immature stages of neotropical heliconians: V. Agraulis vanillae maculosa (Lepidoptera, Nymphalidae, Heliconiinae). The external features of egg, larva and pupa of Agraulis vanillae maculosa (Stichel, [1908]) are described and illustrated, based upon light and scanning electron microscopy.