Rising atmospheric carbon dioxide (CO 2 ) conditions are driving unprecedented changes in seawater chemistry, resulting in reduced pH and carbonate ion concentrations in the Earth's oceans. This ocean acidification has negative but variable impacts on individual performance in many marine species. However, little is known about the adaptive capacity of species to respond to an acidified ocean, and, as a result, predictions regarding future ecosystem responses remain incomplete. Here we demonstrate that ocean acidification generates striking patterns of genome-wide selection in purple sea urchins (Strongylocentrotus purpuratus) cultured under different CO 2 levels. We examined genetic change at 19,493 loci in larvae from seven adult populations cultured under realistic future CO 2 levels. Although larval development and morphology showed little response to elevated CO 2 , we found substantial allelic change in 40 functional classes of proteins involving hundreds of loci. Pronounced genetic changes, including excess amino acid replacements, were detected in all populations and occurred in genes for biomineralization, lipid metabolism, and ion homeostasis-gene classes that build skeletons and interact in pH regulation. Such genetic change represents a neglected and important impact of ocean acidification that may influence populations that show few outward signs of response to acidification. Our results demonstrate the capacity for rapid evolution in the face of ocean acidification and show that standing genetic variation could be a reservoir of resilience to climate change in this coastal upwelling ecosystem. However, effective response to strong natural selection demands large population sizes and may be limited in species impacted by other environmental stressors.experimental evolution | population genomics | RNA sequencing | adaptation | environmental mosaic A ccelerating increases in ocean CO 2 concentrations and accompanying declines in pH are expected this century (1, 2), particularly in the California Current System (3). The negative impacts of ocean acidification have been seen in a broad range of species (4-8) and are predicted to lead to future populations of individuals with low growth, reproduction, or survival. However, the capacity of marine populations to adapt to these changes is unknown (9, 10), and, as a result, there may be circumstances in which natural selection could result in populations of individuals with better-than-expected fitness under acidified conditions. Until recently, the tools to scan for standing genetic variation with adaptive potential in the face of climate change have not been broadly available. Here we combine sequencing across the transcriptome of the purple sea urchin Strongylocentrotus purpuratus, growth measurements under experimental acidification, and tests of frequency shifts in 19,493 polymorphisms during development. We detect the widespread occurrence of genetic variation to tolerate ocean acidification.Rapid evolution in changing environments is likely to depend ...

SUMMARYAnthropogenic CO 2 is reducing the pH and altering the carbonate chemistry of seawater, with repercussions for marine organisms and ecosystems. Current research suggests that calcification will decrease in many species, but compelling evidence of impaired functional performance of calcium carbonate structures is sparse, particularly in key species. Here we demonstrate that ocean acidification markedly degrades the mechanical integrity of larval shells in the mussel Mytilus californianus, a critical community member on rocky shores throughout the northeastern Pacific. Larvae cultured in seawater containing CO 2 concentrations expected by the year 2100 (540 or 970ppm) precipitated weaker, thinner and smaller shells than individuals raised under presentday seawater conditions (380ppm), and also exhibited lower tissue mass. Under a scenario where mussel larvae exposed to different CO 2 levels develop at similar rates, these trends suggest a suite of potential consequences, including an exacerbated vulnerability of new settlers to crushing and drilling attacks by predators; poorer larval condition, causing increased energetic stress during metamorphosis; and greater risks from desiccation at low tide due to shifts in shell area to body mass ratios. Under an alternative scenario where responses derive exclusively from slowed development, with impacted individuals reaching identical milestones in shell strength and size by settlement, a lengthened larval phase could increase exposure to high planktonic mortality rates. In either case, because early life stages operate as population bottlenecks, driving general patterns of distribution and abundance, the ecological success of this vital species may be tied to how ocean acidification proceeds in coming decades.Key words: biomineralization, early survivorship, environmental change, form and function, shell properties. THE JOURNAL OF EXPERIMENTAL BIOLOGY Impaired larval shell integrityPotential tradeoffs among calcification and other physiological responses are likewise poorly understood (Hofmann and Todgham, 2010). Most marine calcifiers can increase fluid pH and carbonate ion concentration at the site of crystal nucleation, which enables synthesis of shells and/or skeletons even when external seawater parameters are thermodynamically unfavorable for the formation of CaCO 3 (Cohen and Holcomb, 2009). Maintenance of local conditions that differ from those of surrounding waters, however, often depends on active ion transport that is energetically costly (Palmer, 1992; Cohen and Holcomb, 2009). Whether OA-induced energetic expenditures require that organisms differentially prioritize certain physiological processes is largely unknown (Widdicomb and Spicer, 2008). In shell-forming species, for instance, it is unclear whether decreased growth arises from somatic resources being redirected to fortify the shell or as a direct consequence of acidified seawater. If OA reduces both growth and shell integrity, it is uncertain which might be degraded more strongly.Such que...

Human activities have led to widespread ecological decline; however, the severity of degradation is spatially heterogeneous due to some locations resisting, escaping, or rebounding from disturbances. We developed a framework for identifying oases within coral reef regions using long‐term monitoring data. We calculated standardised estimates of coral cover (z‐scores) to distinguish sites that deviated positively from regional means. We also used the coefficient of variation (CV) of coral cover to quantify how oases varied temporally, and to distinguish among types of oases. We estimated “coral calcification capacity” (CCC), a measure of the coral community's ability to produce calcium carbonate structures and tested for an association between this metric and z‐scores of coral cover. We illustrated our z‐score approach within a modelling framework by extracting z‐scores and CVs from simulated data based on four generalized trajectories of coral cover. We then applied the approach to time‐series data from long‐term reef monitoring programmes in four focal regions in the Pacific (the main Hawaiian Islands and Mo'orea, French Polynesia) and western Atlantic (the Florida Keys and St. John, US Virgin Islands). Among the 123 sites analysed, 38 had positive z‐scores for median coral cover and were categorised as oases. Synthesis and applications. Our framework provides ecosystem managers with a valuable tool for conservation by identifying “oases” within degraded areas. By evaluating trajectories of change in state (e.g., coral cover) among oases, our approach may help in identifying the mechanisms responsible for spatial variability in ecosystem condition. Increased mechanistic understanding can guide whether management of a particular location should emphasise protection, mitigation or restoration. Analysis of the empirical data suggest that the majority of our coral reef oases originated by either escaping or resisting disturbances, although some sites showed a high capacity for recovery, while others were candidates for restoration. Finally, our measure of reef condition (i.e., median z‐scores of coral cover) correlated positively with coral calcification capacity suggesting that our approach identified oases that are also exceptional for one critical component of ecological function.

The decline in abundance of scleractinian corals over the past three decades in the Caribbean has raised the possibility that other important benthic taxa, such as octocorals, are also changing in abundance. We used photoquadrats taken over 20 yr from reefs (7-9 m depth) at six sites on the south coast of St. John, US Virgin Islands, to test the hypothesis that octocorals have changed in abundance since 1992. Octocorals were counted in 0.25 m 2 photoquadrats at 2-to 3-yr intervals and identified to genus or family. Overall, there was variation over time in population density of octocorals (pooled among taxa, and also separately for Antillogorgia spp., Gorgonia spp., and plexaurids) at each site, and densities remained unchanged or increased over 20 yr; where increases in density occurred, the effects were accentuated after 2002. The local-scale analysis was expanded to the Caribbean (including the Florida Keys) by compiling data for octocoral densities from 31 studies for reefs at B25 m depth between 1968 and 2013. At this scale, analyses were limited by the paucity of historical data, and despite a weak trend of higher octocoral densities in recent decades, statistically, there was no change in octocoral abundance over time. Together with data from the whole Caribbean, the present analysis suggests that octocorals have not experienced a decadal-scale decline in population density, which has occurred for many scleractinian corals.

An extensive body of work suggests that altered marine carbonate chemistry can negatively influence marine invertebrates, but few studies have examined how effects are moderated and persist in the natural environment. A particularly important question is whether impacts initiated in early life might be exacerbated or attenuated over time in the presence or absence of other stressors in the field. We reared Olympia oyster (Ostrea lurida) larvae in laboratory cultures under control and elevated seawater pCO2 concentrations, quantified settlement success and size at metamorphosis, then outplanted juveniles to Tomales Bay, California, in the mid intertidal zone where emersion and temperature stress were higher, and in the low intertidal zone where conditions were more benign. We tracked survival and growth of outplanted juveniles for 4 months, halfway to reproductive age. Survival to metamorphosis in the laboratory was strongly affected by larval exposure to elevated pCO2 conditions. Survival of juvenile outplants was reduced dramatically at mid shore compared to low shore levels regardless of the pCO2 level that oysters experienced as larvae. However, juveniles that were exposed to elevated pCO2 as larvae grew less than control individuals, representing a larval carry-over effect. Although juveniles grew less at mid shore than low shore levels, there was no evidence of an interaction between the larval carry-over effect and shore level, suggesting little modulation of acidification impacts by emersion or temperature stress. Importantly, the carry-over effects of larval exposure to ocean acidification remained unabated 4 months later with no evidence of compensatory growth, even under benign conditions. This latter result points to the potential for extended consequences of brief exposures to altered seawater chemistry with potential consequences for population dynamics.