DOI: 10.5061/dryad.0gb5mkm8f
title: Data from: Foraging-induced craniofacial plasticity is associated with an early, robust, and dynamic transcriptional response

description: Phenotypic plasticity is the ability of a single genotype to vary its
 phenotype in response to the environment. Plasticity of the skeletal
 system in response to mechanical input is widely studied, but the timing
 of its transcriptional regulation is not well-understood. Here we used the
 cichlid feeding apparatus to examine the transcriptional dynamics of
 skeletal plasticity over time. Using three closely related species that
 vary in their ability to remodel bone and a panel of 11 genes, including
 well studied skeletal differentiation markers and newly characterized
 environmentally sensitive genes, we examined plasticity at 1, 2, 4 and 8
 weeks following the onset of alternate foraging challenges. We found that
 the plastic species exhibited environment-specific bursts in gene
 expression at 1 week, followed by a sharp decline in levels, while the
 species with more limited plasticity exhibited consistently low levels of
 gene expression. This trend held across nearly all genes, suggesting that
 it is a hallmark of the larger plasticity regulatory network. We conclude
 that plasticity of the cichlid feeding apparatus is not the result of
 slowly accumulating gene expression difference over time, but rather is
 stimulated by early bursts of environment-specific gene expression
 followed by a return to homeostatic levels.
description: # Foraging-induced craniofacial plasticity is associated with an early,
 robust, and dynamic transcriptional response Below, please find a
 description of the folders/files used for this project. There are two main
 types of files/analyses used in this project: gene expression analysis via
 qPCR, and shape analysis. File: Linkages_residuals_timeseries_compiled.csv
 This csv contains the species (column 1), treatment (column 2), species by
 treatment (column 3), duration of treatment by week (column 4), species by
 treatment by week (column 5), and ID number (column 6) for each
 individual. In addition, linear measures of length were generated in
 ImageJ of the head (column 7, HL), fixed linkage (column 8, FL), input
 linkage (column 9, IL), coupler linkage (column 10, CL), and output
 linkage (column 11, OL). Residual values were calculated for each linkage
 length except the fixed link by head length (columns 12-14), but were not
 used in the dataset. The rest of the file contains statistical analysis
 results with a species between treatments for any given week in terms of
 linkage length, and also the differences in growth slopes between species
 across all timepoints or between treatments within a species. Data in this
 file were used to generate Figure 3. File:
 cichlid_timeseries_expression_compiled_all.csv This csv file contains
 deltaCt values for a panel of genes deemed important in plasticity,
 species differences, and bone shape/growth (columns 4-12), in addition to
 species (column 1), time in the experiment (column 2), and treatment
 (column 3) for each individual. Data in this file were used to generate
 Figure 2 and Figure S1. The data are also contained at
 github.com/tetra22e/timeseries2023 Any questions can be directed to Craig
 Albertson, [rcalbert@umass.edu](mailto:rcalbert@umass.e)