Population genomics of the basket cockle Clinocardium nuttallii in the southern Salish Sea: Assessing genetic risks of stock enhancement for a culturally important marine bivalve.

Coastal Indigenous communities that rely on subsistence harvests are uniquely vulnerable to declines in nearshore species. The basket cockle Clinocardium nuttallii is among the favored foods of Indigenous people along the northwest Pacific coast of North America, yet localized declines in their abundance have led to interest in stock enhancement efforts. We used a population genomics approach to examine potential risks associated with stock enhancement of C. nuttallii in the southern Salish Sea, a large inland estuary that includes Puget Sound. More than 8000 single nucleotide polymorphisms across 349 individuals at 12 locations were assembled de novo using restriction site-associated DNA sequencing. Results indicated that C. nuttallii within the southern Salish Sea were distinct from those along the outer Pacific coast (F ST = 0.021-0.025). Within the southern Salish Sea, C. nuttallii populations appear to be well-connected despite numerous potential impediments to gene flow; Hood Canal, which experiences the lowest flushing rates of all Puget Sound sub-basins, was a minor exception to this strong connectivity. We found evidence of isolation by distance within the southern Salish Sea, but the slope of this relationship was shallow, and F ST values were low (F ST = 0.001-0.004). Meanwhile, outlier analyses did not support the hypothesis that southern Salish Sea sub-populations are locally adapted. Estimates of effective population size had no upper bound, suggesting potentially very high adaptive capacity in C. nuttallii, but also making it difficult to assess potential reductions in effective population size resulting from stock enhancement. We present several strategies to augment cockle populations for subsistence harvest that would limit risk to the genetic diversity of wild cockle populations.

Quantifying rates of evolutionary adaptation in response to ocean acidification.

The global acidification of the earth's oceans is predicted to impact biodiversity via physiological effects impacting growth, survival, reproduction, and immunology, leading to changes in species abundances and global distributions. However, the degree to which these changes will play out critically depends on the evolutionary rate at which populations will respond to natural selection imposed by ocean acidification, which remains largely unquantified. Here we measure the potential for an evolutionary response to ocean acidification in larval development rate in two coastal invertebrates using a full-factorial breeding design. We show that the sea urchin species Strongylocentrotus franciscanus has vastly greater levels of phenotypic and genetic variation for larval size in future CO(2) conditions compared to the mussel species Mytilus trossulus. Using these measures we demonstrate that S. franciscanus may have faster evolutionary responses within 50 years of the onset of predicted year-2100 CO(2) conditions despite having lower population turnover rates. Our comparisons suggest that information on genetic variation, phenotypic variation, and key demographic parameters, may lend valuable insight into relative evolutionary potentials across a large number of species.

Response to technical comment on `meta-analysis reveals negative yet variable effects of ocean acidification on marine organisms'.

It has been proposed that crustaceans should be excluded from a comparison of biological responses to ocean acidification among organisms with different calcium carbonate (CaCO3 ) forms in their calcified structures. We re-analysed our data without crustaceans and found high variation in organismal responses within CaCO3 categories. We conclude that the CaCO3 polymorph alone does not predict sensitivity, and a consideration of functional differences among organisms is necessary for predicting variation in response to acidification.

Meta-analysis reveals negative yet variable effects of ocean acidification on marine organisms.

Ocean acidification is a pervasive stressor that could affect many marine organisms and cause profound ecological shifts. A variety of biological responses to ocean acidification have been measured across a range of taxa, but this information exists as case studies and has not been synthesized into meaningful comparisons amongst response variables and functional groups. We used meta-analytic techniques to explore the biological responses to ocean acidification, and found negative effects on survival, calcification, growth and reproduction. However, there was significant variation in the sensitivity of marine organisms. Calcifying organisms generally exhibited larger negative responses than non-calcifying organisms across numerous response variables, with the exception of crustaceans, which calcify but were not negatively affected. Calcification responses varied significantly amongst organisms using different mineral forms of calcium carbonate. Organisms using one of the more soluble forms of calcium carbonate (high-magnesium calcite) can be more resilient to ocean acidification than less soluble forms (calcite and aragonite). Additionally, there was variation in the sensitivities of different developmental stages, but this variation was dependent on the taxonomic group. Our analyses suggest that the biological effects of ocean acidification are generally large and negative, but the variation in sensitivity amongst organisms has important implications for ecosystem responses.