Evolutionary and acclimatory shifts in gene expression of Eurytemora affinis copepods reared in saline and freshwater conditions during laboratory experiments from 2011-2014

To explore mechanisms of freshwater adaptation and distinguish between adaptive (evolutionary) and acclimatory (plastic) responses to salinity change, we examined genome‐wide patterns of gene expression between ancestral saline and derived freshwater populations of the Eurytemora affinis species complex, reared under two different common‐garden conditions (0 vs. 15 PSU). These data include the RNA-seq Illumina short paired end reads (101 base pairs) of 10 freshwater and 12 saline copepods Eurytemora affinis samples. The freshwater copepod samples were collected in Lake Michigan (Racine Harbor), while the saline copepods were collected in Baie de L'Isle Verte, St. Lawrence marsh, Quebec, Canada. These data have important implications for our understanding of the evolutionary and physiological mechanisms of range expansions by some of the most widespread invaders in aquatic habitats.