The adaptive capacity of marine calcifiers to ocean acidification (OA) is a topic of great interest to evolutionary biologists and ecologists. Previous studies have provided evidence to suggest that larval resilience to high pCO­₂ seawater for these species is a trait with a genetic basis and variability in natural populations. To date, however, it remains unclear how the selective effects of OA occur within the context of complex genetic interactions underpinning larval development in many of the most vulnerable taxa. Here we evaluated phenotypic and genetic changes during larval development of Pacific oysters (Crassostrea gigas) reared in ambient (~ 400 µatm) and high (~ 1600 µatm) pCO₂ conditions, both in domesticated and naturalized ‘wild’ oysters from the Pacific Northwest, USA. Using pooled DNA samples, we determined changes in allele frequencies across larval development, from early “D-stage” larvae to metamorphosed juveniles (spat), in both groups and environments. Domesticated larvae had ~ 26% fewer loci with changing allele frequencies across developmental stages and < 50% as many loci affected by acidified culture conditions, compared to larvae from wild brood stock. Functional enrichment analyses of genetic markers with significant changes in allele frequency revealed that the structure and function of cellular membranes were disproportionately affected by high pCO₂ conditions in both groups. These results indicate the potential for a rapid adaptive response of oyster populations to OA conditions; however, underlying genetic changes associated with larval development differ between these wild and domesticated oyster stocks and influence their adaptive responses to OA conditions.

Pooled samples of oyster larvae  (n=200-3000) were collected at 2 and 22 days post fertilization.  DNA was extracted in bulk, converted to 2bRAD libraries (BCGI enzyme) and sequenced on an Illumina Hiseq (SE 50bp reads).   Samples represent two oyster populations (MBP or Wild) from the Pacific Northwest USA.  Larvae from each population was reared in ambient (~400 pCO2) and acidified (~1600 pCO2) conditions from fertilization to settlement (22 days post fertilization). 

FASTQ file labeling is as follows:  M= MBP, W=Wild, A= ambient pCO2, O= simulated OA (high pCO2), D2/22= days 2 or 22 post fertilization.  Numbers following group designation (e.g. 'MA') denote biological replicate (n=5 each group).  For example: 'WA2_D22*.fastq' denotes 'Wild, Ambient, rep 2, Day 22'.  Another example: 'MO3_D2*.fastq' refers to 'MBP larvae, in OA conditions, from day 2'.

The CSV file contains all 1288 curated SNPs and read counts (A/B allele) for each replicate.

Please see manuscript for experimental setup.