DOI: 10.5061/dryad.84b09
title: Data from: Molecular investigation of genetic assimilation during the rapid adaptive radiations of East African cichlid fishes

description: Adaptive radiations are characterized by adaptive diversification
 intertwined with rapid speciation within a lineage resulting in many
 ecologically specialized, phenotypically diverse species. It has been
 proposed that adaptive radiations can originate from ancestral lineages
 with pronounced phenotypic plasticity in adaptive traits, facilitating
 ecologically-driven phenotypic diversification that is ultimately fixed
 through genetic assimilation of gene regulatory regions. This study aimed
 to investigate how phenotypic plasticity is reflected in gene expression
 patterns in the trophic apparatus of several lineages of East African
 cichlid fishes, and whether the observed patterns support genetic
 assimilation. This investigation used a split brood experimental design to
 compare adaptive plasticity in species from within and outside of adaptive
 radiations. The plastic response was induced in the crushing pharyngeal
 jaws through feeding individuals either a hard or soft diet. We find that
 non-radiating, basal lineages show higher levels of adaptive morphological
 plasticity than the derived, radiated lineages, suggesting that these
 differences have become partially genetically fixed during the formation
 of the adaptive radiations. Two candidate genes that may have undergone
 genetic assimilation, gif and alas1 were identified, in addition to
 alterations in the wiring of LPJ patterning networks. Taken together, our
 results suggest that genetic assimilation may have dampened the
 inducibility of plasticity related genes during the adaptive radiations of
 East African cichlids, flattening the reaction norms and canalizing their
 feeding phenotypes, driving adaptation to progressively more narrow
 ecological niches.
description: Gunter2017_linearmorphometricsLinear, meristic and mass measurements of the lower pharyngeal jaws of various cichlid species, which are specified in column A. Individuals were fed one of of two experimental diets, either a soft diet (SD) or hard diet (HD), specified in column B. Standard length of each fish is recorded in mm in column E. Linear measurements are in mm, area is in mm squared and mass is in mg.Gunter2017_landmarksLandmarks of geometric morphometric measurements of the lower pharyngeal jaws of various cichlid species, as specified in tpsDig. Individuals were fed one of of two experimental diets, either a soft diet (SD) or hard diet (HD).Gunter2017_landmark_covarSLLandmarks of geometric morphometric measurements of the lower pharyngeal jaws of various cichlid species, as specified in tpsDig. Individuals were fed one of of two experimental diets, either a soft diet (SD) or hard diet (HD).slidersLandmarks of geometric morphometric measurements of the lower pharyngeal jaws of various cichlid species, as specified in tpsDig. Individuals were fed one of of two experimental diets, either a soft diet (SD) or hard diet (HD).Gunter2017_geneexpressionGene expression measurements of the lower pharyngeal jaws of various cichlid species, which are specified in column A. Individuals were fed one of of two experimental diets, either a soft diet (SD) or hard diet (HD), specified in column B. Standard length of each fish is recorded in mm in column E. Gene expression values are derived from qRT-PCR experiments using 13 candidate genes, with values scaled against 3 housekeeping genes and normalised.