Adaptation to distinct habitats is maintained by contrasting selection at different life stages in sunflower ecotypes

Inversions contribute disproportionately to parallel genomic divergence in dune sunflowers

The probability of parallel genetic evolution is a function of the strength of selection and constraints imposed by genetic architecture. Inversions capture locally adapted alleles and suppress recombination between them, which limits the range of adaptive responses. In addition, the combined phenotypic effect of alleles within inversions is likely to be greater than that of individual alleles; this should further increase the contributions of inversions to parallel evolution. We tested the hypothesis that inversions contribute disproportionately to parallel genetic evolution in independent dune ecotypes of Helianthus petiolaris. We analysed habitat data and identified variables underlying parallel habitat shifts. Genotype-environment association analyses of these variables indicated parallel responses of inversions to shared selective pressures. We also confirmed larger seed size across the dunes and performed quantitative trait locus mapping with multiple crosses. Quantitative trait loci shared between locations fell into inversions more than expected by chance. We used whole-genome sequencing data to identify selective sweeps in the dune ecotypes and found that the majority of shared swept regions were found within inversions. Phylogenetic analyses of shared regions indicated that within inversions, the same allele typically was found in the dune habitat at both sites. These results confirm predictions that inversions drive parallel divergence in the dune ecotypes.

Early Life History Divergence Mediates Elevational Adaptation in a Perennial Alpine Plant

Spatially divergent natural selection can drive adaptation to contrasting environments and thus the evolution of ecotypes. In perennial plants, selection shapes life history traits by acting on subsequent life stages, each contributing to fitness. While evidence of adaptation in perennial plants is common, the expression of life history traits is rarely characterized, limiting our understanding of their role in adaptive evolution. We conducted a multi-year reciprocal transplant experiment with seedlings from low and high elevation populations of the alpine carnation Dianthus carthusianorum to test for adaptation linked to contrasting climates and inferred specific contributions of early life stages to fitness. We assessed genotype by environment interactions in single fitness components, applied matrix population models to achieve an integrated estimate of fitness through population growth rates, and performed trade-off analyses to investigate the advantage of alternate life history traits across environments. We found evidence of genotype by environment interactions consistent with elevational adaptation at multiple stages of the early life cycle. Estimates of population growth rates corroborated a strong advantage of the local genotype. Early reproduction and survival are alternate major contributors to adaptation at low and high elevation, respectively, and are linked by trade-offs that underlie the evolution of divergent life history traits across environments. While these traits have a strong genetic basis, foreign populations express co-gradient plasticity, reflecting the adaptive strategy of the local populations. Our study reveals that selection associated to climate has driven the evolution of divergent life histories and the formation of elevational ecotypes. While the high energy environment and strong competition favor investment in early reproduction at low elevation, limiting resources favor a more conservative strategy relying on self-maintenance at high elevation. The co-gradient plasticity expressed by high-elevation populations may facilitate their persistence under warming climatic conditions.

Gene expression and alternative splicing contribute to adaptive divergence of ecotypes

Regulation of gene expression is a critical link between genotype and phenotype explaining substantial heritable variation within species. However, we are only beginning to understand the ways that specific gene regulatory mechanisms contribute to adaptive divergence of populations. In plants, the post-transcriptional regulatory mechanism of alternative splicing (AS) plays an important role in both development and abiotic stress response, making it a compelling potential target of natural selection. AS allows organisms to generate multiple different transcripts/proteins from a single gene and thus may provide a source of evolutionary novelty. Here, we examine whether variation in alternative splicing and gene expression levels might contribute to adaptation and incipient speciation of dune-adapted prairie sunflowers in Great Sand Dunes National Park, Colorado, USA. We conducted a common garden experiment to assess transcriptomic variation among ecotypes and analyzed differential expression, differential splicing, and gene coexpression. We show that individual genes are strongly differentiated for both transcript level and alternative isoform proportions, even when grown in a common environment, and that gene coexpression networks are disrupted between ecotypes. Furthermore, we examined how genome-wide patterns of sequence divergence correspond to divergence in transcript levels and isoform proportions and find evidence for both cis and trans-regulation. Together, our results emphasize that alternative splicing has been an underappreciated mechanism providing source material for natural selection at short evolutionary time scales.