A few essential genetic loci distinguish Penstemon species with flowers adapted to pollination by bees or hummingbirds

Abstract

In the formation of species, adaptation by natural selection generates distinct combinations of traits that function well together. The maintenance of adaptive trait combinations in the face of gene flow depends on the strength and nature of selection acting on the underlying genetic loci. Floral pollination syndromes exemplify the evolution of trait combinations adaptive for particular pollinators. The North American wildflower genus Penstemon displays remarkable floral syndrome convergence, with at least 20 separate lineages that have evolved from ancestral bee pollination syndrome (wide blue-purple flowers that present a landing platform for bees and small amounts of nectar) to hummingbird pollination syndrome (bright red narrowly tubular flowers offering copious nectar). Related taxa that differ in floral syndrome offer an attractive opportunity to examine the genomic basis of complex trait divergence. In this study, we characterized genomic divergence among 229 individuals from a Penstemon species complex that includes both bee and hummingbird floral syndromes. Field plants are easily classified into species based on phenotypic differences and hybrids displaying intermediate floral syndromes are rare. Despite unambiguous phenotypic differences, genome-wide differentiation between species is minimal. Hummingbird-adapted populations are more genetically similar to nearby bee-adapted populations than to geographically distant hummingbird-adapted populations, in terms of genome-wide dXY. However, a small number of genetic loci are strongly differentiated between species. These approximately 20 "species-diagnostic loci," which appear to have nearly fixed differences between pollination syndromes, are sprinkled throughout the genome in high recombination regions. Several map closely to previously established floral trait quantitative trait loci (QTLs). The striking difference between the diagnostic loci and the genome as whole suggests strong selection to maintain distinct combinations of traits, but with sufficient gene flow to homogenize the genomic background. A surprisingly small number of alleles confer phenotypic differences that form the basis of species identity in this species complex.

Fig 1. Genetic relationships between sampled P. barbatus, P. neomexicanus, and P. virgatus populations based a matrix of average pairwise genetic distance between populations.

(A) Neighbor-joining tree. (B) Multidimensional scaling applied to the matrix. (C) Average pairwise genetic distance (d_XY) between populations as a function of geographic distance and summarized by contrast type. Red: pairwise contrasts between P. barbatus populations, green: pairwise contrasts between P. barbatus vs. bee-adapted populations. AZ: Arizona, CO: Colorado, NM: New Mexico, b: P. barbatus, n: P. neomexicanus, v: P. virgatus. Photographs by C.A.W. The data underlying this figure can be found in 10.5061/dryad.xpnvx0kmp.

Fig 2. SNP genotype associations with pollination syndrome, plotted according to the magnitude of the LRT statistic.

Points highlighted in red are outlier SNPs (difference in allele frequency > 0.9 and LRT > 100). (A) Genome-wide view, horizontal black bars at top of each panel indicate the 21 regions with highly differentiated SNPs, vertical colored lines indicate peak LOD positions for floral trait QTLs identified in a genetic cross between floral syndromes. (B) Insets show SNPs of interest near major QTLs, with colored shaded areas representing 1.5-LOD confidence intervals of QTLs for nectar volume and flower width. Circled SNPs correspond to SNPs cosegregating most strongly with floral syndrome. Tables show genotype counts in bee-adapted (blue) vs. hummingbird-adapted (red) individuals for circled SNPs. (C) Average d_XY in the vicinity of major floral trait QTLs, plotted in moving averages of ten 100-kb windows. Red trace: average pairwise d_XY between P. barbatus populations, green trace: average pairwise d_XY between P. barbatus vs. bee-adapted populations. Dotted lines indicate genome-wide average values. b: P. barbatus, n: P. neomexicanus, v: P. virgatus. The data underlying this figure can be found in 10.5061/dryad.xpnvx0kmp. LOD, logarithm of odds; LRT, likelihood ratio test; QTL, quantitative trait locus; SNP, single nucleotide polymorphism.