Genome-wide characterization of adaptation and speciation in tiger swallowtail butterflies using de novo transcriptome assemblies

Abstract

Hybrid speciation appears to be rare in animals, yet characterization of possible examples offers to shed light on the genomic consequences of this unique phenomenon, as well as more general processes such as the role of adaptation in speciation. Here, we first generate transcriptome assemblies for a putative hybrid butterfly species, Papilio appalachiensis, its parental species, P. glaucus and P. canadensis, and an outgroup, P. polytes. Then, we use these data to infer genome-wide patterns of introgression and genomic mosaicism using both phylogenetic and population genetic approaches. Our results reveal that there is little genetic divergence among all three of the focal species, but the subset of gene trees that strongly support a specific tree topology suggest widespread sharing of genetic variation between P. appalachiensis and both parental species, likely as a result of hybrid speciation. We also find evidence for substantial shared genetic variation between P. glaucus and P. canadensis, which may be due to gene flow or ancestral variation. Consistent with previous work, we show that P. applachiensis is more similar to P. canadensis at Z-linked genes and more similar to P. glaucus at mitochondrial genes. We also identify a variety of targets of adaptive evolution, which appear to be enriched for traits that are likely to be important in the evolution of this butterfly system, such as pigmentation, hormone sensitivity, developmental processes, and cuticle formation. Overall, our results provide a genome-wide portrait of divergence and introgression associated with adaptation and speciation in an iconic butterfly radiation.

Keywords: Papilio; adaptation; hybrid speciation; introgression; transcriptome.

Fig. 1.—

Distribution of conserved clusters among the four butterfly species. Conserved clusters were retrieved from predicted CDS data sets using Blat. A total of 3,961 clusters yielded a single sequence for each species and this set of conserved clusters was the core data set for subsequent analyses. Each species is depicted with images of female wing pattern phenotypes.

Fig. 2.—

Patterson’s D-statistic suggests widespread introgression between Papilio appalachiensis and the putative parental species. We calculated a transcriptome-wide D-statistic value for each of three tree topologies (A–C) and found evidence for significant introgression in comparisons with P. appalachiensis (D). Results suggest roughly equal introgression between appalachiensis/canadensis, compared with appalachiensis/glaucus (D₁, P = 0.715), but much more introgression between appalachiensis/canadensis and appalachiensis/glaucus, compared with glaucus/canadensis (D₂ and D₃, P < 0.01 for both).

Fig. 3.—

Genome-wide distribution and clustering of genes by tree topology. We mapped conserved clusters back to the genome of Heliconius melpomene (A and C) and Bombyx mori (B and D) and compared the chromosome-level distribution of clusters with a given tree topology with the null distribution given by all mapped clusters. The results of these tests are in table 6. (A, B) Tree topologies based on nucleotide alignments whereas (C) and (D) are based on peptide alignments.