Data from: We get by with a little help from our friends: shared adaptive variation provides a bridge to novel ecological specialists during adaptive radiation

Adaptive radiations involve astounding bursts of phenotypic, ecological,
and species diversity. However, the microevolutionary processes that
underlie the origins of these bursts are still poorly understood. We
report the discovery of an intermediate ‘wide-mouth’ scale-eating ecomorph
in a sympatric radiation of Cyprinodon pupfishes,
illuminating the transition from a widespread algae-eating generalist to a
novel microendemic scale-eating specialist. We first show that this
ecomorph occurs in sympatry with generalist C.
variegatus and scale-eating specialist C.
desquamator on San Salvador Island, Bahamas, but is genetically
differentiated, morphologically distinct, and often consumes
scales. We then compared the timing of selective sweeps on shared
and unique adaptive variants in trophic specialists to
characterize their adaptive walk. Shared adaptive regions swept
first in both the specialist desquamator and the
intermediate ‘wide-mouth’ ecomorph, followed by unique sweeps of
introgressed variation in ‘wide-mouth’ and de novo variation
in desquamator. The two scale-eating populations additionally
shared 9% of their hard selective sweeps with molluscivores C.
brontotheroides, despite no single common ancestor among
specialists. Our work provides a new microevolutionary framework
for investigating how major ecological transitions occur
and illustrates how both shared and unique genetic variation can provide a bridge for multiple species to access novel ecological niches.