The timing and strength of wind-driven coastal upwelling along the eastern margins of major ocean basins regulate the productivity of critical fisheries and marine ecosystems by bringing deep and nutrient-rich waters to the sunlit surface, where photosynthesis can occur. How coastal upwelling regimes might change in a warming climate is therefore a question of vital importance. Although enhanced land-ocean differential heating due to greenhouse warming has been proposed to intensify coastal upwelling by strengthening alongshore winds, analyses of observations and previous climate models have provided little consensus on historical and projected trends in coastal upwelling. Here we show that there are strong and consistent changes in the timing, intensity and spatial heterogeneity of coastal upwelling in response to future warming in most Eastern Boundary Upwelling Systems (EBUSs). An ensemble of climate models shows that by the end of the twenty-first century the upwelling season will start earlier, end later and become more intense at high but not low latitudes. This projected increase in upwelling intensity and duration at high latitudes will result in a substantial reduction of the existing latitudinal variation in coastal upwelling. These patterns are consistent across three of the four EBUSs (Canary, Benguela and Humboldt, but not California). The lack of upwelling intensification and greater uncertainty associated with the California EBUS may reflect regional controls associated with the atmospheric response to climate change. Given the strong linkages between upwelling and marine ecosystems, the projected changes in the intensity, timing and spatial structure of coastal upwelling may influence the geographical distribution of marine biodiversity.

The near-term progression of ocean acidification (OA) is projected to bring about sharp changes in the chemistry of coastal upwelling ecosystems. The distribution of OA exposure across these early-impact systems, however, is highly uncertain and limits our understanding of whether and how spatial management actions can be deployed to ameliorate future impacts. Through a novel coastal OA observing network, we have uncovered a remarkably persistent spatial mosaic in the penetration of acidified waters into ecologically-important nearshore habitats across 1,000 km of the California Current Large Marine Ecosystem. In the most severe exposure hotspots, suboptimal conditions for calcifying organisms encompassed up to 56% of the summer season, and were accompanied by some of the lowest and most variable pH environments known for the surface ocean. Persistent refuge areas were also found, highlighting new opportunities for local adaptation to address the global challenge of OA in productive coastal systems.

8Ecosystems are shaped by processes occurring and interacting over multiple and temporal spatial 9 scales. Theory suggests such complexity can be simplified by focusing on processes sharing the 10 same scale as the pattern of interest. This scale-dependent approach to studying communities has 11 been challenged by multi-scale meta-ecosystem theory, which recognizes that systems are 12 interconnected by the movement of "ecological subsidies" and suggests that cross-scale 13 feedbacks between local and regional processes can be equally important for understanding 14 community structure. We reconcile these two perspectives by developing and testing a 15 hierarchical meta-ecosystem model. The model predicts local community responses to 16 connectivity over multiple oceanographic spatial scales, defined as macro-(100s km), meso-17 (10s km) and local-scales (100s m). It assumes that local communities occur in distinct regions 18 and that connectivity effects are strongest among local sites. Predictions are that if macro-scale 19 processes dominate, then regardless of meso-scale differences, (1) local communities will be 20 similar, and (2) even more so with increased connectivity. With dominance of meso-scale (i.e., 21 regional) processes (3) local structure will be similar within but distinct between regions, and (4) 22 with increased connectivity similar both within and among regions. With dominance of local-23 scale processes (5) local communities will differ both within and among regions, and (6) with 24 increased connectivity be similar within but not between regions. We tested the model by 25 evaluating rocky intertidal community structure patterns to variation in ecological subsidies and 26 environmental conditions at 13 sites spanning 725 km of the northern California Current System. 27External factors operating at meso-and local-scales had strong effects, explaining 52% and 27% 28 of the variance, respectively, in community structure. Sessile invertebrate and predator 29 dominance was associated with weaker upwelling, higher phytoplankton abundance and higher 30 Rocky intertidal meta-ecosystem ecology 3 recruitment and the opposite was true for macrophyte dominance. Overall, our results support the 31 theory that meta-ecosystems are organized hierarchically, with environmental processes 32 dominating at meso-to macro-scales and ecological processes playing a more important role at 33 local scales, but with important bidirectional cross-scale interactions. 34

Synchrony has fundamental but conflicting implications for the persistence and stability of food webs at local and regional scales. In a constant environment, compensatory dynamics between species can maintain food web stability, but factors that synchronize population fluctuations within and between communities are expected to be destabilizing. We studied the dynamics of a food web in a metacommunity to determine how environmental variability and dispersal affect stability by altering compensatory dynamics and average species abundance. When dispersal rate is high, weak correlated environmental fluctuations promote food web stability by reducing the amplitude of compensatory dynamics. However, when dispersal rate is low, weak environmental fluctuations reduce food web stability by inducing intraspecific synchrony across communities. Irrespective of dispersal rate, strong environmental fluctuations disrupt compensatory dynamics and decrease stability by inducing intermittent correlated fluctuations between consumers in local food webs, which reduce both total consumer abundance and predator abundance. Strong correlated environmental fluctuations lead to (i) spatially asynchronous and highly correlated local consumer dynamics when dispersal is low and (ii) spatially synchronous but intermediate local consumer correlation when dispersal is high. By controlling intraspecific synchrony, dispersal mediates the capacity of strong environmental fluctuations to disrupt compensatory dynamics at both local and metacommunity scales.

Determining the relative importance of local and regional processes for the distribution of population abundance is a fundamental but contentious issue in ecology. In marine systems, classical theory holds that the influence of demographic processes and dispersal is confined to local populations whereas the environment controls regional patterns of abundance. Here, we use spatial synchrony to compare the distribution of population abundance of the dominant mussel Mytilus californianus observed along the West Coast of the United States to that predicted by dynamical models undergoing different dispersal and environmental treatments to infer the relative influence of local and regional processes. We reveal synchronized fluctuations in the abundance of mussel populations across a whole continent despite limited larval dispersal and strong environmental forcing. We show that dispersal among neighboring populations interacts with local demographic processes to generate characteristic patterns of spatial synchrony that can govern the dynamic distribution of mussel abundance over 1,800 km of coastline. Our study emphasizes the importance of dispersal and local dynamics for the distribution of abundance at the continental scale. It further highlights potential limits to the use of "climate envelope" models for predicting the response of large-scale ecosystems to global climate change.dispersal | environmental variability | metapopulation | synchrony | cross-scale interactions S ynchronized fluctuations in abundance among spatially segregated populations are common in nature and can be used to quantify and understand the distribution of abundance in space and time (1). Synchrony can be induced by local intrinsic processes such as dispersal among populations and strong interactions with mobile predators or regional extrinsic processes such as spatially correlated environmental variability (1). Although these processes are well known, identifying their relative contribution to patterns of synchrony remains a challenge (1). Recent work has shown that when the processes that contribute to synchrony can be studied in isolation, be it via natural barriers to dispersal among populations (2, 3) or experimental manipulation (4), synchrony patterns can be ascribed to their underlying cause. However, when intrinsic and extrinsic causes of synchrony co-occur, as is the case in most systems, assigning synchrony patterns to any specific causal process becomes onerous (1). Here, we show that in marine populations experiencing both intrinsic and extrinsic sources of synchrony, the shape of spatial synchrony patterns can be used to infer the cause of synchrony and explain the regional distribution of abundance.Marine population theory has relied mostly on the environment to explain the regional (>1,000 km) dynamics of populations. This focus is motivated by the lengthy pelagic larval stage commonly found in marine organisms, during which the larvae can be transported over large distances by strong nearshore currents (5). The potential fo...

Understanding spatiotemporal variation in environmental conditions is important to determine how climate change will impact ecological communities. The spatial and temporal autocorrelation of temperature can have strong impacts on community structure and persistence by increasing the duration and the magnitude of unfavorable conditions in sink populations and disrupting spatial rescue effects by synchronizing spatially segregated populations. Although increases in spatial and temporal autocorrelation of temperature have been documented in historical data, little is known about how climate change will impact these trends. We examined daily air temperature data from 21 General Circulation Models under the business-as-usual carbon emission scenario to quantify patterns of spatial and temporal autocorrelation between 1871 and 2099. Although both spatial and temporal autocorrelation increased over time, there was significant regional variation in the temporal autocorrelation trends. Additionally, we found a consistent breakpoint in the relationship between spatial autocorrelation and time around the year 2030, indicating an acceleration in the rate of increase of the spatial autocorrelation over the second half of the 21st century. Overall, our results suggest that ecological populations might experience elevated extinction risk under climate change because increased spatial and temporal autocorrelation of temperature is expected to erode both spatial and temporal refugia.

Summary1. There is growing recognition that linking patterns to their underlying processes in interconnected and dynamic ecological systems requires data sampled at multiple spatial and temporal scales. 2. However, spatially explicit and temporally resolved data sets can be difficult to analyze using classical statistical methods because the data are typically autocorrelated and thus violate the assumption of independence. 3. Here, we describe the synchrony package for the R programming environment, which provides modern parametric and nonparametric methods for (i) quantifying temporal and spatial patterns of auto-and cross-correlated variability in univariate, bivariate, and multivariate data sets, and (ii) assessing their statistical significance via Monte Carlo randomizations. 4. We illustrate how the methods included in the package can be used to investigate the causes of spatial and temporal variability in ecological systems through a series of examples, and discuss the assumptions and caveats of each statistical procedure in order to provide a practical guide for their application in the real world.

Eastern boundary current systems are among the most productive and lucrative ecosystems on Earth because they benefit from upwelling currents. Upwelling currents subsidize the base of the coastal food web by bringing deep, cold and nutrient-rich water to the surface. As upwelling is driven by large-scale atmospheric patterns, global climate change has the potential to affect a wide range of significant ecological processes through changes in water chemistry, water temperature, and the transport processes that influence species dispersal and recruitment. We examined longterm trends in the frequency, duration, and strength of continuous upwelling events for the Oregon and California regions of the California Current System in the eastern Pacific Ocean. We then associated event-scale upwelling with up to 21 years of barnacle and mussel recruitment, and water temperature data measured at rocky intertidal field sites along the Oregon coast. Our analyses suggest that upwelling events are changing in ways that are consistent with climate change predictions: upwelling events are becoming less frequent, stronger, and longer in duration. In addition, upwelling events have a quasi-instantaneous and cumulative effect on rocky intertidal water temperatures, with longer events leading to colder temperatures. Longer, more persistent upwelling events were negatively associated with barnacle recruitment but positively associated with mussel recruitment. However, since barnacles facilitate mussel recruitment by providing attachment sites, increased upwelling persistence could have indirect negative impacts on mussel populations. Overall, our results indicate that changes in coastal upwelling that are consistent with climate change predictions are altering the tempo and the mode of environmental forcing in near-shore ecosystems, with potentially severe and discontinuous ramifications for ecosystem structure and functioning.