Data from: Foraging-induced craniofacial plasticity is associated with an early, robust, and dynamic transcriptional response
Data files
Mar 24, 2024 version files 81.36 KB
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cichlid_timeseries_expression_compiled_all.csv
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Linkages_residuals_timeseries_compiled.csv
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README.md
Abstract
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.
README: 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