DOI: 10.5061/dryad.tqjq2bvxc
title: Magnitude and predictability of pH fluctuations shape plastic responses to ocean acidification

description: Phenotypic plasticity is expected to facilitate the persistence of natural
 populations as global change progresses. The attributes of fluctuating
 environments that favor the evolution of plasticity have received
 extensive theoretical investigation, yet empirical validation of these
 findings is still in its infancy. Here, we combine high-resolution
 environmental data with a laboratory-based experiment to explore the
 influence of habitat pH fluctuation dynamics on the plasticity of gene
 expression in two populations of the Mediterranean mussel, Mytilus
 galloprovincialis. We linked differences in the magnitude and
 predictability of pH fluctuations in two habitats to population-specific
 gene expression profiles in ambient and stressful pH treatments. The
 results presented demonstrate population-based differentiation in gene
 expression plasticity, whereby mussels native to a habitat exhibiting a
 large magnitude of pH fluctuations with low predictability display reduced
 phenotypic plasticity between experimentally imposed pH treatments. This
 work validates recent theoretical findings on evolution in fluctuating
 environments using an ecologically important marine bivalve, and suggests
 that populations inhabiting regions exposed to unpredictably fluctuating
 selection pressures may exhibit reduced plasticity as global change
 progresses.
description: For a full description of the methods, please see the associated
 manuscript for this Dryad submission. Breifly, one year
 of high-frequency pH and temperature monitoring was conducted at a coastal
 and lagoon habitat in the Northwest Mediterranean Sea (the Bay of
 Villefranche: 43.682<sup>o</sup>N,
 7.319<sup>o</sup> E and Thau
 Lagoon: 43.4158<sup>o</sup>N,
 3.6888<sup>o</sup>E). Resident mussels at each site were
 collected and reared in labortory common garden conditions for six weeks,
 after which a 5 day acclimation to two pH treatments (benign pH - 8.1;
 stressful pH - 7.75) was conducted. At the end of the acclimation
 peirod, total RNA was extracted from gill tissue samples,  and gene
 expression profiling was carried out using 3’ mRNA sequencing. All
 resulting raw and processed data files are included here. 
  
description: TranscriptCounts.csv – Transcript count data for all coastal and
 lagoon mussels reared in either benign or stressful pH conditions. Each
 row corresponds to a gene, while each column corresponds to the observed
 transcript count for each individual at that gene. Transcript counts were
 computed from the sequencing data using custom Perl script written by
 Misha Matz (available at
 https://github.com/z0on/tag-based_RNAseq). CountsID.csv
 – Identifying information for the individuals in the transcript counts
 matrix. Specifically, each row contains pertinent information for
 corresponding column of the transcript counts file, including source
 population and treatment information.
 SupplementaryFile1.csv – File containing gene expression data for
 the coastal population’s response to stressful pH conditions. Columns
 correspond to: reference contig ID (as identified in reference
 transcriptome provided by Moreira et al. 2015), transcript ID
 (corresponding to row number of counts matrix), log2-fold change, and raw
 p-value for each gene. Log2-fold-change values were computed using the
 DeSEQ2 software developed by Love <em>et al</em>. (2015)
 (doi:10.1186/s13059-014-0550-8). SupplementaryFile2.csv
 – File containing gene expression data for the lagoon population’s
 response to stressful pH conditions. Columns correspond to: reference
 contig ID (as identified in reference transcriptome provided by Moreira et
 al. 2015), transcript ID (corresponding to row number of counts matrix),
 log2-fold change, and raw p-value for each gene. Log2-fold-change values
 were computed using the DeSEQ2 software developed by Love <em>et
 al</em>. (2015) (doi:10.1186/s13059-014-0550-8).
 SupplementaryFile3.csv – File containing gene expression data for
 population differentiation in the benign pH treatment. Columns correspond
 to: reference contig ID (as identified in reference transcriptome provided
 by Moreira et al. 2015), transcript ID (corresponding to row number of
 counts matrix), log2-fold change, and raw p-value for each
 gene. Log2-fold-change values were computed using the DeSEQ2 software
 developed by Love <em>et al</em>. (2015)
 (doi:10.1186/s13059-014-0550-8). SupplementaryFile4.csv
 – File containing gene expression data for population differentiation in
 the stressful pH treatment. Columns correspond to: reference contig ID (as
 identified in reference transcriptome provided by Moreira et al. 2015),
 transcript ID (corresponding to row number of counts matrix), log2-fold
 change, and raw p-value for each gene. Log2-fold-change values were
 computed using the DeSEQ2 software developed by Love <em>et
 al</em>. (2015) (doi:10.1186/s13059-014-0550-8).
 SupplementaryFile5.csv – File containing temperature and pH data
 as measured by SeaFET pH sensor at hourly intervals from the coastal
 habitat. SupplementaryFile6.csv – File containing raw
 SeaFET pH sensor readings, as well as sensor-collected pH and
 temperature data at 20 minute intervals from the lagoon habitat.