Lack of genotype‐by‐environment interaction suggests limited potential for evolutionary changes in plasticity in the eastern oyster,Crassostrea virginica

Abstract

Eastern oysters in the northern Gulf of Mexico are facing rapid environmental changes and can respond to this change via plasticity or evolution. Plasticity can act as an immediate buffer against environmental change, but this buffering could impact the organism's ability to evolve in subsequent generations. While plasticity and evolution are not mutually exclusive, the relative contribution and interaction between them remains unclear. In this study, we investigate the roles of plastic and evolved responses to environmental variation and Perkinsus marinus infection in Crassostrea virginica by using a common garden experiment with 80 oysters from six families outplanted at two field sites naturally differing in salinity. We use growth data, P. marinus infection intensities, 3′ RNA sequencing (TagSeq) and low‐coverage whole‐genome sequencing to identify the effect of genotype, environment and genotype‐by‐environment interaction on the oyster's response to site. As one of first studies to characterize the joint effects of genotype and environment on transcriptomic and morphological profiles in a natural setting, we demonstrate that C. virginica has a highly plastic response to environment and that this response is parallel among genotypes. We also find that genes responding to genotype have distinct and opposing profiles compared to genes responding to environment with regard to expression levels, Ka/Ks ratios and nucleotide diversity. Our findings suggest that C. virginica may be able to buffer the immediate impacts of future environmental changes by altering gene expression and physiology, but the lack of genetic variation in plasticity suggests limited capacity for evolved responses.

Differential DNA methylation across environments has no effect on gene expression in the eastern oyster

“…These differences were shown to be statistically significant using a Kruskal–Wallis Rank Sum test ( p ‐value <0.05) as described by Sirovy et al. (2021).…”

“…Differential gene expression was analysed and described by Sirovy et al. (2021), these methods are briefly summarized here. We filtered the gene list using the (filterByExpr) function and normalized the remaining reads using the trimmed mean of M‐values (TMM) normalization method (Robinson & Oshlack, 2010).…”

“…Sequencing reads were trimmed of adapter sequences using Trimmomatic (version 0.39; Bolger et al., 2014) and base pairs with quality scores below 30 were removed (Sirovy et al., 2021). The trimmed reads were mapped to the C .…”

“…high freshwater input-LUMCON vs. low freshwater input-Grand Isle) influenced the growth rate and dermo infection intensities leading to more growth but more infection in Grand Isle (Figure 1). These differences were shown to be statistically significant using a Kruskal-Wallis Rank Sum test (p-value <0.05) as described by Sirovy et al (2021).…”

“…In this study, we used a family‐based approach, with 80 oysters from six full‐sib families reared in two sites with differing salinity conditions for 14 months. These oysters were part of a larger study, where we observed effects of outplant site on growth rates, infection load ( Perkinsus marinus parasites) and global gene expression patterns (Figure 1; Sirovy et al., 2021). Our approach in this study allowed us to test the plasticity of DNA methylation and its association with changes in gene expression in response to variation in the abiotic environment.…”