PMC

The study system. Illustration of the T. cristinae study system, with individuals of each insect ecotype shown on the left and drawings of the host plants that they are adapted to on the right. Illustrations courtesy of R. Marín.

Phenotypic divergence of T. cristinae between host plant species in the field experiment. Each bar represents the difference between hosts within a paired block in the proportion of individuals that are striped (proportion striped on Adenostoma minus the proportion striped on Ceanothus). Increases in divergence between release and recapture in the predicted direction were observed for four of the five paired blocks and were statistically significant overall (t = −2.95, d.f. = 4, P = 0.021, paired t-test).

Genetic variability at the onset of the experiment. (a) Distribution of minor allele frequencies at the onset of the experiment within one experimental population (1A). Similar distributions were seen in all populations (Table S3). (b) Levels of linkage disequilibrium (LD, estimated using Δ, text for details) within each experimental population at the onset of the experiment (> 17 billion pairwise comparisons per population, bars depict means and error bars 5% and 95% quantiles). Results are shown for mean LD for single-nucleotide polymorphism (SNP) pairs on the same vs. different genotyping-by-sequencing contigs and the maximum LD between SNPs. The diagram above the bars depicts the general results is schematic form (horizontal grey lines denote genotype-by-sequencing (GBS) contigs and vertical grey lines denote SNPs): specifically it illustrates that although LD was generally higher for SNP pairs on the same vs. different GBS contigs, maximum LD tended to occur between SNPs on different contigs.

Variation in selection index across the genome. Results are shown for parallel divergence across the five populations on Ceanothus (results on the other host were comparable). (a) Correlogram of genomic autocorrelation of selection index values across the genome, at different physical distances. Genomic autocorrelation is near zero (dashed red line) at distances >100 bp. ‘Inf’ represents loci on different scaffolds. (b) The genomic distribution of selection index values along two size-matched scaffolds in the T. cristinae whole-genome assembly. The top panel depicts a scaffold with one exceptional change locus, whereas the bottom panel depicts a scaffold with no exceptional change loci. This is the maximum difference observed for size-matched scaffolds. (c) The genomic distribution of selection index values along the longest scaffold in the T. cristinae whole-genome assembly. High and low parameter estimates are widely distributed, with pronounced local increases and decreases in parameter values (SI for statistics considering numerous scaffolds).

Genomic change in the field experiment. (a) Observed allele frequency changes for each experimental population and treatment (C = Ceanothus, A = Adenostoma). Bars represent means and error bars the 97.5% upper quantile. Grey circles are maximum change. (b) Fixation of alleles as a function of minor allele frequency. Results are depicted for one experimental population (1A), but were similar among experimental populations (Table S4 for details). (c) Numbers of loci with ‘exceptional change’. Bars and numbers above them indicate observed numbers of exceptional change loci. The numbers expected given the number of comparisons made under a null model of genome-wide drift are depicted by the error bars (mean, 2.5%, 97.5% quantiles). (d) Selection coefficients and 95% credible intervals for the 129 loci exhibiting exceptional parallel change in the populations transplanted to Ceanothus (for comparable results on Adenostoma see Fig. S3).

Study species and site, experimental design and predictions. (a) Schematic representation of how selection acting on phenotypic traits affecting fitness can affect allele frequency change in the genome, either directly or via correlations among loci. (b) The source population on Adenostoma fasciculatum at 775 m used to found the experiment is depicted in the left of the diagram. In the experiment, individuals were transplanted from the source population to five paired blocks that contained a single plant individual of the native host Adenostoma and one of the novel host species Ceanothus (illustration credit: Rosa Marín). Different bushes were also at different elevations as indicated. (c) A photo depicting the location of the founding population (orange oval) and the experimental field site (grey oval). (d) Null distributions of allele frequency change between release and recapture at individual loci in the absence of selection. A typical locus is depicted as well as one with exceptional change inconsistent with neutral expectations.