DOI: 10.5061/dryad.5q65k
title: Data from: Gene expression plasticity evolves in response to colonization of freshwater lakes in threespine stickleback

description: Phenotypic plasticity is predicted to facilitate individual survival
 and/or evolve in response to novel environments. Plasticity that
 facilitates survival should both permit colonization and act as a buffer
 against further evolution, with contemporary and derived forms predicted
 to be similarly plastic for a suite of traits. On the other hand, given
 the importance of plasticity in maintaining internal homeostasis, derived
 populations that encounter greater environmental heterogeneity should
 evolve greater plasticity. We tested the evolutionary significance of
 phenotypic plasticity in coastal British Columbian postglacial populations
 of threespine stickleback (Gasterosteus aculeatus) that evolved under
 greater seasonal extremes in temperature after invading freshwater lakes
 from the sea. Two ancestral (contemporary marine) and two derived
 (contemporary freshwater) populations of stickleback were raised near
 their thermal tolerance extremes, 7°C and 22°C. Gene expression plasticity
 was estimated for more than 14 000 genes. Over five thousand genes were
 similarly plastic in marine and freshwater stickleback, but freshwater
 populations exhibited significantly more genes with plastic expression
 than marine populations. Furthermore, several of the loci shown to exhibit
 gene expression plasticity have been previously implicated in the adaptive
 evolution of freshwater populations, including a gene involved in
 mitochondrial regulation (PPARAa). Collectively, these data provide
 molecular evidence that highlights the importance of plasticity in
 colonization and adaptation to new environments.
description: MATLAB Statistics for
 Gene Expression DataThis file contains the
 results of the full model and the individual contrasts, for each of 14 208
 genes. The first six worksheets provide data from the full model: p-values
 for each gene for origin, temperature, population(origin), and the
 interaction term, q-values for the same, SSQ and degrees of freedom for
 the same, coefficients for each origin, temperature, population(origin),
 and interaction, and a summary of the significantly expressed genes for
 origin alone, temperature alone, both origin and temperature, and the
 interaction term, under p-value of 0.05 and q-values of 0.05 and 0.1.The
 remaining three worksheets contain a summary of the number of genes
 differentially expressed by temperature under the independent contrasts,
 including the total number, freshwater total, marine total, both marine
 and freshwater, only freshwater, and only marine, for p-value of 0.05 and
 q-values of 0.05 and 0.1. p-values and q-values for freshwater and marine
 contrasts follow.Matlab_GeneExpression_Filtered.xlsxCode used for MATLABThis file contains the code used to generate the data for the marine and freshwater stickleback contrasts.MatlabCode_Contrasts.mNormalized and Filtered Gene Expression DataThis file contains the LIMMA output for normalized and filtered microarray data. This data was then used in MATLAB. Each column contains a new microarray. Rows 1-7 provide descriptive data for each microarray, including population (Hoggan Lake freshwater, HLF; Cranby Lake freshwater, CLF; Oyster Lagoon marines, OLM; Little Campbell River marines, LCM), temperature (7 or 22 degrees C), Origin (marine, freshwater), the tank number the fish was raised in, sex of the fish, the microarray slide the microarray was on, and the microarray filename.Normalized_Filtered_GeneExpressionData.xlsxLIMMA Supplemental ResultsLIMMA output file using all 20 021 genes present on the microarray, as described in the supplemental information. Within-population contrasts were performed. Coefficients for all four populations, and associated t-statistics and p-values, along with F-statistics and p-values, are provided. Columns T,U,V,W: 0 = not significantly influenced by temperature; 1 = up-regulated at 22 degrees C; -1 = up-regulated at 7 degrees C. The microarray probe name and its associated Ensembl transcript ID follow.LIMMA_Results_SupplementalMaterials.xlsxLIMMA Targets FileThis text file contains information pertaining to each microarray (sex, population, temperature, tank, array number, array file name) used by LIMMA to Normalize the data for Matlab, or to provide supplemental results.targets.txtTranscript IDThis file contains a key for matching "Custxxx" microarray probenames with their respective Ensembl transcript ID.transcriptID.xlsxFeature Extraction Output for Microarray Slide No. 3This file contains the extracted data from all eight microarrays present on microarray slide number 3. For information on the output, see the Agilent Feature Extraction guide cited in text.MicroarrayNo3.xlsxFeature Extraction Output for Microarray Slide No. 6This file contains the extracted data from the seven microarrays present on microarray slide number 6 that passed quality control. For information on the output, see the Agilent Feature Extraction guide cited in text.MicroarrayNo6.xlsxFeature Extraction Output for Microarray Slide No. 7This file contains the extracted data from all eight microarrays present on microarray slide number 7. For information on the output, see the Agilent Feature Extraction guide cited in text.MicroarrayNo7.xlsxFeature Extraction Output for Microarray Slide No. 8This file contains the extracted data from all four microarrays present on microarray slide number 8. For information on the output, see the Agilent Feature Extraction guide cited in text.MicroarrayNo8.xlsxFeature Extraction Output for Microarray Slide No. 9This file contains the extracted data from all seven microarrays present on microarray slide number 9 that passed quality control. For information on the output, see the Agilent Feature Extraction guide cited in text.MicroarrayNo9.xlsxFeature Extraction Output for Microarray Slide No. 10This file contains the extracted data from all eight microarrays present on microarray slide number 10. For information on the output, see the Agilent Feature Extraction guide cited in text.MicroarrayNo10.xlsxSummary of Significantly Enriched Gene ClassesThis file contains the full list of enriched gene classes, and the members of each gene class. There are five worksheets: enriched gene classes in marine stickleback at 22 degrees C, enriched gene classes in marine stickleback at 7 degrees C, enriched gene classes in freshwater stickleback at 22 degrees C, enriched gene classes in freshwater stickleback at 7 degrees C, and a key that identifies probe number with Ensembl transcript ID.GO_summary.xlsxHierarchical GO Graph, Marine 22 deg C, Biological ProcessesSignificantly enriched gene classes shown in hierarchical graph, for biological processes.GO_marineall_22deg_biological.pdfHierarchical GO Graph, Marine 22 deg C, Molecular ProcessesSignificantly enriched gene classes shown in hierarchical graph, for molecular processes.GO_marineall_22deg_molecular.pdfHierarchical GO Graph, Marine 22 deg C, Cellular ProcessesSignificantly enriched gene classes shown in hierarchical graph, for cellular processes.GO_marineall_22deg_cellular.pdfHierarchical GO Graph, Marine 7 deg C, Molecular ProcessesSignificantly enriched gene classes shown in hierarchical graph, for molecular processes.GO_marineall_7deg_molecular.pdfHierarchical GO Graph, Marine 7 deg C, Biological ProcessesSignificantly enriched gene classes shown in hierarchical graph, for biological processes.GO_marineall_7deg_biological.pdfHierarchical GO Graph, Marine 7 deg C, Cellular ProcessesSignificantly enriched gene classes shown in hierarchical graph, for cellular processes.GO_marineall_7deg_cellular.pdfHierarchical GO Graph, Freshwater 22 deg C, Biological ProcessesSignificantly enriched gene classes shown in hierarchical graph, for biological processes.GO_fwall_22deg_biological.pdfHierarchical GO Graph, Freshwater 22 deg C, Cellular ProcessesSignificantly enriched gene classes shown in hierarchical graph, for cellular processes.GO_fwall_22deg_cellular.pdfHierarchical GO Graph, Freshwater 22 deg C, Molecular ProcessesSignificantly enriched gene classes shown in hierarchical graph, for molecular processes.GO_fwall_22deg_molecular.pdfHierarchical GO Graph, Freshwater 7 deg C, Biological ProcessesSignificantly enriched gene classes shown in hierarchical graph, for biological processes.GO_fwall_7deg_biological.pdfHierarchical GO Graph, Freshwater 7 deg C, Cellular ProcessesSignificantly enriched gene classes shown in hierarchical graph, for cellular processes.GO_fwall_7deg_cellular.pdfHierarchical GO Graph, Freshwater 7 deg C, Molecular ProcessesSignificantly enriched gene classes shown in hierarchical graph, for molecular processes.GO_fwall_7deg_molecular.pdf