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

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, genomewide
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 genomewide dXY. However, a small number of genetic loci are strongly
differentiated between species. These ~ 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 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.