Robust quantification of fish early life CO2 sensitivities via serial experimentation.

Despite the remarkable expansion of laboratory studies, robust estimates of single species CO2 sensitivities remain largely elusive. We conducted a meta-analysis of 20 CO2 exposure experiments conducted over 6 years on offspring of wild Atlantic silversides (Menidia menidia) to robustly constrain CO2 effects on early life survival and growth. We conclude that early stages of this species are generally tolerant to CO2 levels of approximately 2000 µatm, likely because they already experience these conditions on diel to seasonal timescales. Still, high CO2 conditions measurably reduced fitness in this species by significantly decreasing average embryo survival (-9%) and embryo+larval survival (-13%). Survival traits had much larger coefficients of variation (greater than 30%) than larval length or growth (3-11%). CO2 sensitivities varied seasonally and were highest at the beginning and end of the species' spawning season (April-July), likely due to the combined effects of transgenerational plasticity and maternal provisioning. Our analyses suggest that serial experimentation is a powerful, yet underused tool for robustly estimating small but true CO2 effects in fish early life stages.

A comprehensive non-redundant reference transcriptome for the Atlantic silverside Menidia menidia.

The Atlantic silverside (Menidia menidia) has been the focus of extensive research efforts in ecology, evolutionary biology, and physiology over the past three decades, but lack of genomic resources has so far hindered examination of the molecular basis underlying the remarkable patterns of phenotypic variation described in this species. We here present the first reference transcriptome for M. menidia. We sought to capture a single representative sequence from as many genes as possible by first using a combination of Trinity and the CLC Genomics Workbench to de novo assemble contigs based on RNA-seq data from multiple individuals, tissue types, and life stages. To reduce redundancy, we passed the combined raw assemblies through a stringent filtering pipeline based both on sequence similarity to related species and computational predictions of transcript quality, condensing an initial set of >480,000 contigs to a final set of 20,998 representative contigs, amounting to a total length of 53.3 Mb. In this final assembly, 91% of the contigs were functionally annotated with putative gene function and gene ontology (GO) terms and/or InterProScan identifiers. The assembly contains complete or nearly complete copies of >95% of 248 highly conserved core genes present in low copy number across higher eukaryotes, and partial copies of another 3.8%, suggesting that our assembly provides relatively comprehensive coverage of the M. menidia transcriptome. The assembly provided here will be an important resource for future research.

A quantitative genetic approach to assess the evolutionary potential of a coastal marine fish to ocean acidification.

Assessing the potential of marine organisms to adapt genetically to increasing oceanic CO2 levels requires proxies such as heritability of fitness-related traits under ocean acidification (OA). We applied a quantitative genetic method to derive the first heritability estimate of survival under elevated CO2 conditions in a metazoan. Specifically, we reared offspring, selected from a wild coastal fish population (Atlantic silverside, Menidia menidia), at high CO2 conditions (∼2300 µatm) from fertilization to 15 days posthatch, which significantly reduced survival compared to controls. Perished and surviving offspring were quantitatively sampled and genotyped along with their parents, using eight polymorphic microsatellite loci, to reconstruct a parent-offspring pedigree and estimate variance components. Genetically related individuals were phenotypically more similar (i.e., survived similarly long at elevated CO2 conditions) than unrelated individuals, which translated into a significantly nonzero heritability (0.20 ± 0.07). The contribution of maternal effects was surprisingly small (0.05 ± 0.04) and nonsignificant. Survival among replicates was positively correlated with genetic diversity, particularly with observed heterozygosity. We conclude that early life survival of M. menidia under high CO2 levels has a significant additive genetic component that could elicit an evolutionary response to OA, depending on the strength and direction of future selection.