DOI: 10.5061/dryad.mpg4f4qxx
title: The genetic basis of coordinated plasticity across functional units in a Lake Malawi cichlid mapping population

description: Adaptive radiations are often stereotypical, as populations repeatedly
 specialize along conserved environmental axes. Phenotypic plasticity may
 be similarly stereotypical, as individuals respond to environmental cues.
 These parallel patterns of variation, which are often consistent across
 traits, have led researchers to propose that plasticity can facilitate
 predictable patterns of evolution along environmental gradients. This
 “flexible stem” model of evolution raises questions about the genetic
 nature of plasticity, including: How complex is the genetic basis for
 plasticity? Is plasticity across traits mediated by many distinct loci, or
 few “global” regulators? To address these questions, we reared a hybrid
 cichlid mapping population on alternate diet regimes mimicking an
 important environmental axis. We show that plasticity across an array of
 ecologically relevant traits is generally morphologically integrated, such
 that traits respond in a coordinated manner, especially those with
 overlapping function. Our genetic data are more ambiguous. While our
 mapping experiment provides little evidence for global genetic regulators
 of plasticity, these data do contain a genetic signal for the integration
 of plasticity across traits. Overall, our data suggest a compromise
 between genetic modularity, whereby plasticity may evolve independently
 across traits, and low-level but widespread genetic integration,
 establishing the potential for plasticity to experience coordinated
 evolution.
description: Full methods can be found in the article in Evolution. In brief,
 we used a hybrid mapping cross of cichlid fish to assess the genetic basis
 of diet-induced plasticity. F3 hybrid animals resulting from a cross
 between a <em>Labeotropheus fuelliborni</em> female and a
 <em>Tropheops </em>sp. "redcheek" male were split
 into two diet treatments. These hybrids were then sacrificed, dissected,
 & analyzed for a variety of phenotypic traits, including both
 linear & geometric morphometrics. Continuous traits resulting from
 the geometric morphometric analyses were subjected to a canonical variates
 analysis, which produced an axis arraying individuals from more plastic
 animals at each extreme, to less plastic animals near the origin. These
 values were then used as the basis for a series of QTL analyses aimed at
 linking plasticity to its underlying genetic basis. Finally, both the
 trait values and the genetic associations were used in two separate
 network analyses to determine whether plasticity was correlated across the
 body at either the morphological or genetic level. For
 each trait, I have provided two TPS files - one with the unadjusted
 landmark coordinates (named: "Trait X.tps"), and one with the
 allometry-adjusted landmark coordinates (named: "Trait X SL
 Corr.tps"). I also include the file with the standard length values
 for each individual ("SL.csv") - these were used in the size
 standardizations. I have also provided the files used in the network
 analyses based on shape ("Shape Scores for Network
 Analysis.csv") and genetics ("LOD Scores for Network
 Analysis.csv"). These provide the shape scores for each individual
 for each trait and the LOD scores at every position sampled along the
 genome for each individual for each trait, respectively. Finally, I have
 provided the QTL map with all 21 phenotypes that were mapped ("QTL
 Map with Traits.csv").