DOI: 10.5061/dryad.871c7
title: Data from: Phenotypic and transcriptomic responses to salinity stress across genetically and geographically divergent Tigriopus californicus populations

description: Species inhabiting the North American west coast intertidal must tolerate
 an extremely variable environment, with large fluctuations in both
 temperature and salinity. Uncovering the mechanisms for this tolerance is
 key to understanding species’ persistence. We tested for differences in
 salinity tolerance between populations of Tigriopus californicus copepods
 from locations in northern (Bodega Reserve) and southern (San Diego)
 California known to differ in temperature, precipitation, and humidity. We
 also tested for differences between populations in their transcriptomic
 responses to salinity. Although these two populations have ~20% mtDNA
 sequence divergence and differ strongly in other phenotypic traits, we
 observed similarities in their phenotypic and transcriptomic responses to
 low and high salinity stress. Salinity significantly affected respiration
 rate (increased under low salinity and reduced under high salinity) but we
 found no significant effect of population on respiration or a population
 by salinity interaction. Under high salinity, there was no population
 difference in knockdown response but northern copepods had a smaller
 knockdown under low salinity stress, corroborating previous results for T.
 californicus. Northern and southern populations had a similar
 transcriptomic response to salinity based on a principle components
 analysis, although differential gene expression under high salinity stress
 was three times lower in the northern population compared to the southern
 population. Transcripts differentially regulated under salinity stress
 were enriched for ‘amino acid transport' and ‘ion transport’
 annotation categories, supporting previous work demonstrating that the
 accumulation of free amino acids is important for osmotic regulation in T.
 californicus.
description: READMEREADME file describing
 files associated with this project01-tig_filter_orthogroups_for_both_popsThis script filters the Orthogroups_All.txt file and pulls out the orthogroups that appear in both the northern and southern copepod populationsBD_transcriptomeThe transcriptome from the San Diego copepod population originally published in Kelly et al. 2017 DOI: 10.1111/1365-2435.12725BD_transcriptome.pepThe translated San Diego transcriptomeboth_pops_count_matrix_orthogroupsthe count matrix at the orthogroup level for both the northern and southern populationscount_matrix_BR_genesThe count matrix at the gene level for the Bodega Reserve populationcount_matrix_SD_genesThe count matrix at the gene level for the San Diego populationCount_orthosScript that sums the counts of reads mapped to all genes within an orthogroupfull_count_matrix_orthogroupsThe count matrix at the orthogroup level for orthogroups present in both populationsNorth_high_vs_midDESeq2 differential gene expression results for the north 60psu vs north 35psu exposureNorth_low_vs_midDESeq2 differential gene expression results for the north 15psu vs north 35psu exposureOrthogroups_AllAll the orthogroups inferred for the northern and southern copepod populations. Includes orthogroups that were present only in the north or only in the south population.Orthogroups_in_both_popsOrthogroups that were present in both the northern and southern populationsSA_transcriptomeThe transcriptome from the Salt Point (northern) copepod population originally published in Kelly et al. 2017 DOI: 10.1111/1365-2435.12725SA_transcriptome.pepThe translated Salt Point transcriptomesal_high_vs_midThe log p-value for orthogroups differentially expressed under high salinity stress. This file is used in the functional enrichment analysissal_low_vs_midThe log p-value for orthogroups differentially expressed under low salinity stress. This file is used in the functional enrichment analysisSouth_high_vs_midDESeq2 differential gene expression results for the south 60psu vs north 35psu exposureSouth_low_vs_midDESeq2 differential gene expression results for the south 15psu vs north 35psu exposuretig_ogs_with_gotermsList of gene ontology terms associated with the orthogroups that were present in both the northern and southern population