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Estuaries provide valuable habitat for the eastern oyster (Crassostrea virginica). Although salinity at a given location fluctuates regularly with tides, upbay and downbay salinity differences span a broad estuarine salinity gradient. Higher salinity habitats downbay support faster oyster growth, whereas lower salinities upbay act as a refuge from predation and disease but slows growth. Two experiments were performed to investigate the effect of salinity, postsettlement salinity changes, and shell morphology on juvenile oyster growth. One experiment used wild oyster spat collected from three distinct Delaware Bay salinity zones that were then transplanted into various salinity conditions in the laboratory, where growth was monitored. Transplanting into low salinity led to decreased growth compared with transplanting to higher salinity, and growth of oyster spat was overall highest for spat from the lowest salinity source. Growth did not differ among shell morphologies. A second experiment used hatchery reared larvae set in one of four different salinity conditions. Those spat were maintained in settlement salinities 22, 16, 10, and 6 for 2–3 wk postsettlement, then measured before fully factorial transfer into new salinity conditions with measurement 3 wk later. Lower final salinity treatments were associated with lower growth, lower initial salinity treatments were associated with faster final treatment growth, and final growth depended on the interaction between initial and final salinity. Therefore, in addition to the effects of acute salinity changes on growth, early postsettlement hyposalinity stress can generate compensatory juvenile oyster growth. As increased freshwater events due to climate change are expected in the Delaware Bay and regionally in the Northeast, these results indicate that nonlinear early life stress responses are important to quantify to better understand oyster stock resilience and plan management. 

Genome assembly can be challenging for species that are characterized by high amounts of polymorphism, heterozygosity, and large effective population sizes. High levels of heterozygosity can result in genome mis-assemblies and a larger than expected genome size due to the haplotig versions of a single locus being assembled as separate loci. Here, we describe the first chromosome-level genome for the eastern oyster, Crassostrea virginica. Publicly released and annotated in 2017, the assembly has a scaffold N50 of 54 mb and is over 97.3% complete based on BUSCO analysis. The genome assembly for the eastern oyster is a critical resource for foundational research into molluscan adaptation to a changing environment and for selective breeding for the aquaculture industry. Subsequent resequencing data suggested the presence of haplotigs in the original assembly, and we developed a post hoc method to break up chimeric contigs and mask haplotigs in published heterozygous genomes and evaluated improvements to the accuracy of downstream analysis. Masking haplotigs had a large impact on SNP discovery and estimates of nucleotide diversity and had more subtle and nuanced effects on estimates of heterozygosity, population structure analysis, and outlier detection. We show that haplotig masking can be a powerful tool for improving genomic inference, and we present an open, reproducible resource for the masking of haplotigs in any published genome. 

Complex life cycles, in which discrete life stages of the same organism differ in form or function and often occupy different ecological niches, are common in nature. Because stages share the same genome, selective effects on one stage may have cascading consequences through the entire life cycle. Theoretical and empirical studies have not yet generated clear predictions about how life cycle complexity will influence patterns of adaptation in response to rapidly changing environments or tested theoretical predictions for fitness trade-offs (or lack thereof) across life stages. We discuss complex life cycle evolution and outline three hypotheses—ontogenetic decoupling, antagonistic ontogenetic pleiotropy and synergistic ontogenetic pleiotropy—for how selection may operate on organisms with complex life cycles. We suggest a within-generation experimental design that promises significant insight into composite selection across life cycle stages. As part of this design, we conducted simulations to determine the power needed to detect selection across a life cycle using a population genetic framework. This analysis demonstrated that recently published studies reporting within-generation selection were underpowered to detect small allele frequency changes (approx. 0.1). The power analysis indicates challenging but attainable sampling requirements for many systems, though plants and marine invertebrates with high fecundity are excellent systems for exploring how organisms with complex life cycles may adapt to climate change.