A region of the sex chromosome associated with population differences in diapause induction contains highly divergent alleles at clock genes

On the origin of an insular hybrid butterfly lineage

A new species can form through hybridization between species. Hybrid speciation in animals has been intensely debated, partly because hard evidence for the process has been difficult to obtain. Here, we report the discovery of a European hybrid butterfly lineage, a finding that can be considered surprising given the intense and long-term study of European butterflies. The lineage we describe is mainly inhabiting an island in the Baltic Sea and was previously designated as a subspecies (horkei) of one of the parental species (Aricia artaxerxes). By analyzing whole-genome resequencing data and developing a novel cluster analysis based on historical recombination events (Fisher junctions), we determine that horkei originated by hybridization between the nonsister species A. artaxerxes and A. agestis. This hybridization event occurred approximately 54,000 years ago, predating the last glaciation of the current distribution range. Horkei must therefore have persisted long enough to be able to colonize its current range, despite that this area lies between the current distributions of the parental species. The hybrid origin, the maintenance of genomic integrity across times of dramatic climate change, and the expression of a combination of parental traits suggest that horkei could be in the process of hybrid speciation.

Repeated evolution of photoperiodic plasticity by different genetic architectures during recurrent colonizations in a butterfly

In cases of recurrent colonizations of similar habitats from the same base population, it is commonly expected that repeated phenotypic adaptation is caused by parallel changes in genetic variation. However, it is becoming increasingly clear that similar phenotypic variation may also evolve by alternative genetic pathways. Here, we explore the repeated evolution of photoperiodic plasticity for diapause induction across Swedish populations of the speckled wood butterfly, Pararge aegeria. This species has colonized Scandinavia at least twice, and population genomic results show that one of the candidate regions associated with spatial variation in photoperiodism is situated on the Z-chromosome. Here, we assay hybrid crosses between several populations that differ in photoperiodic plasticity for sex-linked inheritance of the photoperiodic reaction norm. We find that while a cross between more distantly related populations from the two different colonization events shows strong sex-dependent inheritance of photoperiodic plasticity, a cross between two more closely related populations within the oldest colonization range shows no such effect. We conclude that the genotype-phenotype map for photoperiodic plasticity varies across these populations and that similar local phenotypic adaptation has evolved during recurrent colonization events by partly non-parallel genetic changes.

A supergene controls facultative diapause in the crop pest Helicoverpa armigera

Many insect species, including the economically important pest Helicoverpa armigera, avoid unfavorable conditions by suspending development. This form of phenotypic plasticity-facultative diapause-is a complex trait, though its evolution and intricate genetic architecture remain poorly understood. To investigate how such a polygenic trait could be locally adapted, we explore its genetic architecture. We map a large-effect diapause-associated locus to the Z chromosome by crossing high- and low-latitude populations. By generating multiple chromosome-scale assemblies, we identify an ∼5.93-Mb chromosomal inversion that constitutes the locus. Within this inversion, 33 genes harbor divergent non-synonymous mutations, notably including three circadian rhythm genes: Period, Clock, and Cycle. CRISPR-Cas9 knockout experiments confirm that each gene is independently essential for pupal diapause. Thus, a diapause supergene arose within H. armigera via a Z chromosome inversion, enabling local climatic adaptation in this economically important crop pest.

Testing for variation in photoperiodic plasticity in a butterfly: Inconsistent effects of circadian genes between geographic scales

The genetic components of the circadian clock have been implicated as involved in photoperiodic regulation of winter diapause across various insect groups, thereby contributing to adaptation to adverse seasonal conditions. So far, the effects of within-population variation in these genes have not been well explored. Here, we present an experimental test of the effects of within-population variation at two circadian genes, timeless and period, on photoperiodic responses in the butterfly Pararge aegeria. While nonsynonymous candidate SNPs in both of these genes have previously shown to be associated with diapause induction on a between-population level, in the present experiment no such effect was found on a within-population level. In trying to reconcile these results, we examine sequence data, revealing considerable, previously unknown protein-level variation at both timeless and period across Scandinavian populations, including variants unique to the population studied here. Hence, we hypothesize that these variants may counteract the previously observed diapause-averting effect of the candidate SNPs, possibly explaining the difference in results between the experiments. Whatever the cause, these results highlight how the effects of candidate SNPs may sometimes vary across genetic backgrounds, which complicates evolutionary interpretations of geographic patterns of genetic variation.

A time course analysis through diapause reveals dynamic temporal patterns of microRNAs associated with endocrine regulation in the butterfly Pieris napi

Organisms inhabiting highly seasonal environments must cope with a wide range of environmentally induced challenges. Many seasonal challenges require extensive physiological modification to survive. In winter, to survive extreme cold and limited resources, insects commonly enter diapause, which is an endogenously derived dormant state associated with minimized cellular processes and low energetic expenditure. Due to the high degree of complexity involved in diapause, substantial cellular regulation is required, of which our understanding primarily derives from the transcriptome via messenger RNA expression dynamics. Here we aim to advance our understanding of diapause by investigating microRNA (miRNA) expression in diapausing and direct developing pupae of the butterfly Pieris napi. We identified coordinated patterns of miRNA expression throughout diapause in both head and abdomen tissues of pupae, and via miRNA target identification, found several expression patterns to be enriched for relevant diapause-related physiological processes. We also identified two candidate miRNAs, miR-14-5p and miR-2a-3p, that are likely involved in diapause progression through their activity in the ecdysone pathway, a critical regulator of diapause termination. miR-14-5p targets phantom, a gene in the ecdysone synthesis pathway, and is upregulated early in diapause. miR-2a-3p has been found to be expressed in response to ecdysone, and is upregulated during diapause termination. Together, the expression patterns of these two miRNAs match our current understanding of the timing of hormonal regulation of diapause in P. napi and provide interesting candidates to further explore the mechanistic role of microRNAs in diapause regulation.

Genetic constraints in genes exhibiting splicing plasticity in facultative diapause

Phenotypic plasticity is produced and maintained by processes regulating the transcriptome. While differential gene expression is among the most important of these processes, relatively little is known about other sources of transcriptional variation. Previous work suggests that alternative splicing plays an extensive and functionally unique role in transcriptional plasticity, though plastically spliced genes may be more constrained than the remainder of expressed genes. In this study, we explore the relationship between expression and splicing plasticity, along with the genetic diversity in those genes, in an ecologically consequential polyphenism: facultative diapause. Using 96 samples spread over two tissues and 10 timepoints, we compare the extent of differential splicing and expression between diapausing and direct developing pupae of the butterfly Pieris napi. Splicing differs strongly between diapausing and direct developing trajectories but alters a smaller and functionally unique set of genes compared to differential expression. We further test the hypothesis that among these expressed loci, plastically spliced genes are likely to experience the strongest purifying selection to maintain seasonally plastic phenotypes. Genes with unique transcriptional changes through diapause consistently had the lowest nucleotide diversity, and this effect was consistently stronger among genes that were differentially spliced compared to those with just differential expression through diapause. Further, the strength of negative selection was higher in the population expressing diapause every generation. Our results suggest that maintenance of the molecular mechanisms involved in diapause progression, including post-transcriptional modifications, are highly conserved and likely to experience genetic constraints, especially in northern populations of P. napi.

Moths passing in the night: Phenological and genomic divergences within a forest pest complex

Temporal separation of reproductive timing can contribute to species diversification both through allochronic speciation and later reinforcement of species boundaries. Such phenological differences are an enigmatic component of evolutionary divergence between two major forest defoliator species of the spruce budworm complex: Choristoneura fumiferana and C. occidentalis. While these species interbreed freely in laboratory settings, natural hybridization rates have not been reliably quantified due to their indistinguishable morphology. To assess whether temporal isolation is contributing to reproductive isolation, we collected adult individuals throughout their expected zone of sympatry in western Canada at 10-day intervals over two successive years, assigning taxonomic identities using thousands of single nucleotide polymorphisms. We found unexpectedly broad sympatry between C. fumiferana and C. occidentalis biennis and substantial overlap of regional flight periods. However, flight period divergence was much more apparent on a location-by-location basis, highlighting the importance of considering spatial scale in these analyses. Phenological comparisons were further complicated by the biennial life cycle of C. o. biennis, the main subspecies of C. occidentalis in the region, and the occasional occurrence of the annually breeding subspecies C. o. occidentalis. Nonetheless, we demonstrate that biennialism is not a likely contributor to reproductive isolation within the species complex. Overall, interspecific F1 hybrids comprised 2.9% of sequenced individuals, confirming the genomic distinctiveness of C. fumiferana and C. occidentalis, while also showing incomplete reproductive isolation of lineages. Finally, we used F ST-based outlier and genotype-environment association analyses to identify several genomic regions under putative divergent selection. These regions were disproportionately located on the Z linkage region of C. fumiferana, and contained genes, particularly antifreeze proteins, that are likely to be associated with overwintering success and diapause. In addition to temporal isolation, we conclude that other mechanisms, including ecologically mediated selection, are contributing to evolutionary divergence within the spruce budworm species complex.

Local adaptation of life cycles in a butterfly is associated with variation in several circadian clock genes

Many insects exhibit geographical variation in voltinism, the number of generations produced per year. This includes high-latitude species in previously glaciated areas, meaning that divergent selection on life cycle traits has taken place during or shortly after recent colonization. Here, we use a population genomics approach to compare a set of nine Scandinavian populations of the butterfly Pararge aegeria that differ in life cycle traits (diapause thresholds and voltinism) along both north-south and east-west clines. Using a de novo-assembled genome, we reconstruct colonization histories and demographic relationships. Based on the inferred population structure, we then scan the genome for candidate loci showing signs of divergent selection potentially associated with population differences in life cycle traits. The identified candidate genes include a number of components of the insect circadian clock (timeless, timeless2, period, cryptochrome and clockwork orange). Most notably, the gene timeless, which has previously been experimentally linked to life cycle regulation in P. aegeria, is here found to contain a novel 97-amino acid deletion unique to, and fixed in, a single population. These results add to a growing body of research framing circadian gene variation as a potential mechanism for generating local adaptation of life cycles.

The Genome of the Margined White Butterfly (Pieris macdunnoughii): Sex Chromosome Insights and the Power of Polishing with PoolSeq Data

We report a chromosome-level assembly for Pieris macdunnoughii, a North American butterfly whose involvement in an evolutionary trap imposed by an invasive Eurasian mustard has made it an emerging model system for studying maladaptation in plant-insect interactions. Assembled using nearly 100× coverage of Oxford Nanopore long reads, the contig-level assembly comprised 106 contigs totaling 316,549,294 bases, with an N50 of 5.2 Mb. We polished the assembly with PoolSeq Illumina short-read data, demonstrating for the first time the comparable performance of individual and pooled short reads as polishing data sets. Extensive synteny between the reported contig-level assembly and a published, chromosome-level assembly of the European butterfly Pieris napi allowed us to generate a pseudochromosomal assembly of 47 contigs, placing 91.1% of our 317 Mb genome into a chromosomal framework. Additionally, we found support for a Z chromosome arrangement in P. napi, showing that the fusion event leading to this rearrangement predates the split between European and North American lineages of Pieris butterflies. This genome assembly and its functional annotation lay the groundwork for future research into the genetic basis of adaptive and maladaptive egg-laying behavior by P. macdunnoughii, contributing to our understanding of the susceptibility and responses of insects to evolutionary traps.