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.
MATLAB Statistics for Gene Expression Data
This 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.xlsx
Code used for MATLAB
This file contains the code used to generate the data for the marine and freshwater stickleback contrasts.
MatlabCode_Contrasts.m
Normalized and Filtered Gene Expression Data
This 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.xlsx
LIMMA Supplemental Results
LIMMA 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.xlsx
LIMMA Targets File
This 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.txt
Transcript ID
This file contains a key for matching "Custxxx" microarray probenames with their respective Ensembl transcript ID.
transcriptID.xlsx
Feature Extraction Output for Microarray Slide No. 3
This 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.xlsx
Feature Extraction Output for Microarray Slide No. 6
This 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.xlsx
Feature Extraction Output for Microarray Slide No. 7
This 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.xlsx
Feature Extraction Output for Microarray Slide No. 8
This 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.xlsx
Feature Extraction Output for Microarray Slide No. 9
This 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.xlsx
Feature Extraction Output for Microarray Slide No. 10
This 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.xlsx
Summary of Significantly Enriched Gene Classes
This 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.xlsx
Hierarchical GO Graph, Marine 22 deg C, Biological Processes
Significantly enriched gene classes shown in hierarchical graph, for biological processes.
GO_marineall_22deg_biological.pdf
Hierarchical GO Graph, Marine 22 deg C, Molecular Processes
Significantly enriched gene classes shown in hierarchical graph, for molecular processes.
GO_marineall_22deg_molecular.pdf
Hierarchical GO Graph, Marine 22 deg C, Cellular Processes
Significantly enriched gene classes shown in hierarchical graph, for cellular processes.
GO_marineall_22deg_cellular.pdf
Hierarchical GO Graph, Marine 7 deg C, Molecular Processes
Significantly enriched gene classes shown in hierarchical graph, for molecular processes.
GO_marineall_7deg_molecular.pdf
Hierarchical GO Graph, Marine 7 deg C, Biological Processes
Significantly enriched gene classes shown in hierarchical graph, for biological processes.
GO_marineall_7deg_biological.pdf
Hierarchical GO Graph, Marine 7 deg C, Cellular Processes
Significantly enriched gene classes shown in hierarchical graph, for cellular processes.
GO_marineall_7deg_cellular.pdf
Hierarchical GO Graph, Freshwater 22 deg C, Biological Processes
Significantly enriched gene classes shown in hierarchical graph, for biological processes.
GO_fwall_22deg_biological.pdf
Hierarchical GO Graph, Freshwater 22 deg C, Cellular Processes
Significantly enriched gene classes shown in hierarchical graph, for cellular processes.
GO_fwall_22deg_cellular.pdf
Hierarchical GO Graph, Freshwater 22 deg C, Molecular Processes
Significantly enriched gene classes shown in hierarchical graph, for molecular processes.
GO_fwall_22deg_molecular.pdf
Hierarchical GO Graph, Freshwater 7 deg C, Biological Processes
Significantly enriched gene classes shown in hierarchical graph, for biological processes.
GO_fwall_7deg_biological.pdf
Hierarchical GO Graph, Freshwater 7 deg C, Cellular Processes
Significantly enriched gene classes shown in hierarchical graph, for cellular processes.
GO_fwall_7deg_cellular.pdf
Hierarchical GO Graph, Freshwater 7 deg C, Molecular Processes
Significantly enriched gene classes shown in hierarchical graph, for molecular processes.
GO_fwall_7deg_molecular.pdf