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  1. Synopsis

    Understanding recent population trends is critical to quantifying species vulnerability and implementing effective management strategies. To evaluate the accuracy of genomic methods for quantifying recent declines (beginning <120 generations ago), we simulated genomic data using forward-time methods (SLiM) coupled with coalescent simulations (msprime) under a number of demographic scenarios. We evaluated both site frequency spectrum (SFS)-based methods (momi2, Stairway Plot) and methods that employ linkage disequilibrium information (NeEstimator, GONE) with a range of sampling schemes (contemporary-only samples, sampling two time points, and serial sampling) and data types (RAD-like data and whole-genome sequencing). GONE and momi2 performed best overall, with >80% power to detect severe declines with large sample sizes. Two-sample and serial sampling schemes could accurately reconstruct changes in population size, and serial sampling was particularly valuable for making accurate inferences when genotyping errors or minor allele frequency cutoffs distort the SFS or under model mis-specification. However, sampling only contemporary individuals provided reliable inferences about contemporary size and size change using either site frequency or linkage-based methods, especially when large sample sizes or whole genomes from contemporary populations were available. These findings provide a guide for researchers designing genomics studies to evaluate recent demographic declines.

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  2. Global policy goals for halting biodiversity loss and climate change depend on each other to be successful. Marine biodiversity and climate change are intertwined through foodwebs that cycle and transport carbon and contribute to carbon sequestration. Yet, biodiversity conservation and fisheries management seldom explicitly include ocean carbon transport and sequestration. In order to effectively manage and govern human activities that affect carbon cycling and sequestration, international biodiversity and climate agreements need to address both biodiversity and climate issues. International agreements that address issues for climate and biodiversity are best poised to facilitate the protection of ocean carbon with existing policies. The degree to which the main international biodiversity and climate agreements make reference to multiple issues has however not been documented. Here, we used a text mining analysis of over 2,700 binding and non-binding policy documents from ten global ocean-related agreements to identify keywords related to biodiversity, climate, and ocean carbon. While climate references were mostly siloed within climate agreements, biodiversity references were included in most agreements. Further, we found that six percent of policy documents (n=166) included ocean carbon keywords. In light of our results, we highlight opportunities to strengthen the protection of ocean carbon in upcoming negotiations of international agreements, and via area-based management, environmental impact assessment and strategic environmental assessment. 
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  3. The year 2021 marked the highest temperature and likely the lowest oxygen content for the oceans since human records began ( 1 , 2 ). These changes have put marine species on the front lines of climate change. For example, marine species’ geographical ranges are shifting faster and experiencing more contractions than those of terrestrial species ( 3 , 4 ). However, whether climate change poses an existential threat to ocean life has been less clear. Marine species are often considered to be more resilient to extinction than terrestrial ones, and human-caused global extinctions of marine species have been relatively rare ( 5 ). On page 524 of this issue, Penn and Deutsch ( 6 ) present extensive modeling to reveal that runaway climate change would put ocean life on track for a mass extinction rivaling the worst in Earth’s history. Furthermore, they reveal how keeping global warming below an increase of 2°C compared with preindustrial levels could largely prevent these outcomes. 
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  4. Obtaining dispersal estimates for a species is key to understanding local adaptation and population dynamics and to implementing conservation actions. Genetic isolation-by-distance (IBD) patterns can be used for estimating dispersal, and these patterns are especially useful for marine species in which few other methods are available. In this study, we genotyped coral reef fish (Amphiprion biaculeatus) at 16 microsatellite loci across eight sites across 210 km in the central Philippines to generate fine-scale estimates of dispersal. All sites except for one followed IBD patterns. Using IBD theory, we estimated a larval dispersal kernel spread of 8.9 km (95% confidence interval of 2.3–18.4 km). Genetic distance to the remaining site correlated strongly with the inverse probability of larval dispersal from an oceanographic model. Ocean currents were a better explanation for genetic distance at large spatial extents (sites greater than 150 km apart), while geographic distance remained the best explanation for spatial extents less than 150 km. Our study demonstrates the utility of combining IBD patterns with oceanographic simulations to understand connectivity in marine environments and to guide marine conservation strategies. 
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  5. Adaptive evolution is not just the stuff of geological history books—it is an ongoing process across ecosystems and can occur on a year-to-year time scale. However, in a world rapidly changing as the result of human activity, it can be challenging to differentiate which changes result from evolution rather than other mechanisms ( 1 ). On page 420 of this issue, Czorlich et al. ( 2 ) reveal a fascinating example that suggests that commercial fishing drove rapid evolutionary change in an Atlantic salmon population over the past 40 years. Their findings are surprising in two ways—that fishing for salmon drove evolution in the opposite direction from what one would typically expect, and that salmon evolution also was affected by fishing for other species in the ecosystem. 
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  6. Species ranges are shifting in response to climate change, but most predictions disregard food–web interactions and, in particular, if and how such interactions change through time. Predator–prey interactions could speed up species range shifts through enemy release or create lags through biotic resistance. Here, we developed a spatially explicit model of interacting species, each with a thermal niche and embedded in a size-structured food–web across a temperature gradient that was then exposed to warming. We also created counterfactual single species models to contrast and highlight the effect of trophic interactions on range shifts. We found that dynamic trophic interactions hampered species range shifts across 450 simulated food–webs with up to 200 species each over 200 years of warming. All species experiencing dynamic trophic interactions shifted more slowly than single-species models would predict. In addition, the trailing edges of larger bodied species ranges shifted especially slowly because of ecological subsidies from small shifting prey. Trophic interactions also reduced the numbers of locally novel species, novel interactions and productive species, thus maintaining historical community compositions for longer. Current forecasts ignoring dynamic food–web interactions and allometry may overestimate species' tendency to track climate change. 
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  7. Abstract

    Interest is growing in developing conservation strategies to restore and maintain coral reef ecosystems in the face of mounting anthropogenic stressors, particularly climate warming and associated mass bleaching events. One such approach is to propagate coral coloniesex situand transplant them to degraded reef areas to augment habitat for reef‐dependent fauna, prevent colonization from spatial competitors, and enhance coral reproductive output. In addition to such “demographic restoration” efforts, manipulating the thermal tolerance of outplanted colonies through assisted relocation, selective breeding, or genetic engineering is being considered for enhancing rates of evolutionary adaptation to warming. Although research into such “assisted evolution” strategies has been growing, their expected performance remains unclear. We evaluated the potential outcomes of demographic restoration and assisted evolution in climate change scenarios using an eco‐evolutionary simulation model. We found that supplementing reefs with pre‐existing genotypes (demographic restoration) offers little climate resilience benefits unless input levels are large and maintained for centuries. Supplementation with thermally resistant colonies was successful at improving coral cover at lower input levels, but only if maintained for at least a century. Overall, we found that, although demographic restoration and assisted evolution have the potential to improve long‐term coral cover, both approaches had a limited impact in preventing severe declines under climate change scenarios. Conversely, with sufficient natural genetic variance and time, corals could readily adapt to warming temperatures, suggesting that restoration approaches focused on building genetic variance may outperform those based solely on introducing heat‐tolerant genotypes.

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