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Reduction of ecosystem connectivity has long-lasting impacts on food webs. Anadromous fish, which migrate from marine to freshwater ecosystems to complete reproduction, have seen their historically larger ecosystem role undercut by widespread riverine habitat fragmentation and other impacts mainly derived from anthropogenic sources. The result has been extensive extirpations and increased susceptibility to a suite of environmental factors that currently impede recovery. Under this present-day context of reduced productivity and connectivity, aggressive management actions and enforcement of catch limits including bycatch caps and complete moratoria on harvest have followed. What remains less understood are the implications of changes to food webs that co-occurred. What benefits restoration could provide in terms of ecosystem functioning in relation to economic costs associated with dam removal and remediation is unknown and can limit the scope and value of restoration activities. Here we employ, historical landscape-based biomass estimates of anadromous alosine for the first time in an ecosystem modeling of the Northeast US large marine ecosystem (LME), to evaluate the value of improving connectivity by measuring the increase in energy flow and population productivity. We compared a restored alosine model to a contemporary model, analyzing the impacts of the potential increase of connectivity between riverine and oceanic systems. There was the potential for a moderate biomass increase of piscivorous species with high economic value, including Atlantic cod, and for a major increase for species of conservation concern such as pelagic sharks, seabirds and marine mammals. Our study highlights the benefits of increased connectivity between freshwater and ocean ecosystems. We demonstrate the significant role anadromous forage fish could play in improving specific fisheries and overall ecosystem functioning, mainly through the diversification of species capable of transferring primary production to upper trophic levels, adding to benefits associated with their restoration.

Lost biomass of anadromous forage species resulting from the seventeenth to nineteenth century damming of waterways and from overharvest in the northeastern United States contributed to significant changes in coastal marine—terrestrial ecosystems. Historic alewife populations in Maine for the years 1600–1900 were assessed using analyses of nineteenth and twentieth century harvest records and waterway obstruction records dating to the 1600s. Obstructed spawning access in nine watersheds reduced the annual alewife productivity per watershed to 0%–16% of virgin estimates, equaling a cumulative lost fisheries production of 11 billion fish from 1750 to 1900. Including preharvest production, our estimates suggest a lost flux of anadromous forage fish increasing from 10 million fish per year in 1700 to 1.4 billion annually by 1850. Our results suggest a realignment of current restoration goals is needed to recognize oceanic and freshwater ecosystem interdependence and the gap between current targets and potential productivity.

Imminent development of offshore wind farms on the outer continental shelf of the United States has led to significant concerns for marine wildlife. The scarcity of empirical data regarding fish species that may utilize development sites, further compounded by the novelty of the technology and inherent difficulty of conducting offshore research, make identification and assessment of potential stressors to species of concern problematic. However, there is broad potential to mitigate putatively negative impacts to seasonal migrants during the exploration and construction phases. The goal of this study was to establish baseline information on endangered Atlantic Sturgeon in the New York Wind Energy Area (NY WEA), a future offshore development site. Passive acoustic transceivers equipped with acoustic release mechanisms were used to monitor the movements of tagged fish in the NY WEA from November 2016 through February 2018 and resulted in detections of 181 unique individuals throughout the site. Detections were highly seasonal and peaked from November through January. Conversely, fish were relatively uncommon or entirely absent during the summer months (July–September). Generalized additive models indicated that predictable transitions between coastal and offshore habitat were associated with long-term environmental cues and localized estuarine conditions, specifically the interaction between photoperiod and river temperature. These insights into the ecology of marine-resident Atlantic Sturgeon are crucial for both defining monitoring parameters and guiding threat assessments in offshore waters and represent an important initial step towards quantitatively evaluating Atlantic Sturgeon at a scale relevant to future development.

In contrast to freshwater fish it is presumed that marine fish are unlikely to spawn with close relatives due to the dilution effect of large breeding populations and their propensity for movement and reproductive mixing. Inbreeding is therefore not typically a focal concern of marine fish management. We measured the effective number of breeders in 6 New York estuaries for winter flounder (Pseudopleuronectes americanus), a formerly abundant fish, using 11 microsatellite markers (6-56 alleles per locus). The effective number of breeders for 1-2 years was remarkably small, with point estimates ranging from 65-289 individuals. Excess homozygosity was detected at 10 loci in all bays (FIS = 0.169-0.283) and individuals exhibited high average internal relatedness (IR; mean = 0.226). These both indicate that inbreeding is very common in all bays, after testing for and ruling out alternative explanations such as technical and sampling artifacts. This study demonstrates that even historically common marine fish can be prone to inbreeding, a factor that should be considered in fisheries management and conservation plans.

Extensive temporal and spatial monitoring data provide an opportunity to identify the drivers of ecosystem change and to understand spatial relationships useful to conservation and management. Such data can potentially overcome the considerable intrinsic variability present in sampling and justify the cost of sustained monitoring. In this study, the temporal and spatial structure and trends in the mobile invertebrate and fish assemblage of the Peconic Estuary were identified. Data were obtained primarily from a small mesh trawl survey conducted by the New York State Department of Environmental Conservation from 1987–2020 at 76 locations distributed throughout the system, supplemented by chlorophyll data and regional climate indices. A set of multivariate statistical tools, including K‐means cluster analysis, redundancy analysis, and multiscale ordination, were applied to the data set in a complementary way. Distinctly different drivers for temporal and spatial patterns were found. Abrupt community shifts on a decadal time scale occurred, including a regime shift in 1999–2000, and were driven by changes in regional climate factors as indexed by the unlagged and lagged Atlantic Multidecadal Oscillation and North Atlantic Oscillation. Spatially distinct habitats and assemblages were identified, separating eastern, inshore, and offshore regions of the system. These were differentiated by local conditions in bottom salinity, water depth and depth gradient, DO percent saturation, and water transparency. Each of these regions responded to the climate drivers in a similar way. Notably, annual bottom temperature and chlorophyll a were never found to be effective in explaining community variation. Overall, the results of this study suggest that, given the time lags in response, climate‐induced changes in the system can be anticipated by continued monitoring and that conservation and management actions can be applied system‐wide and not restricted to specific areas. A set of readily available multivariate tools was used in a complementary way to identify and better understand both the inter‐annual and spatial patterns in a fish and mobile invertebrate community in the Peconic Estuary. We found distinctly different drivers for temporal and spatial patterns, with temporal factors operating on a regional scale and spatial factors tied to local sampling conditions. Our findings have important implications suggesting that climate‐induced changes in a system can be anticipated by continued monitoring and that conservation and management actions can be applied system‐wide and not restricted to specific areas.

Temporal changes in occupancy of the Georges Bank (NE USA) fish and invertebrate community were examined and interpreted in the context of systems ecological theory of extinction debt (EDT). EDT posits that in a closed system with a mix of competitor and colonizer species and experiencing habitat fragmentation and loss, the competitor species will show a gradual decline in fitness (occupancy) eventually leading to their extinction (extirpation) over multiple generations. A corollary of this is a colonizer credit, where colonizer species occupancy may increase with fragmentation because the disturbance gives that life history a transient relative competitive advantage. We found that competitor species occupancy decreased in time concomitant with an increase in occupancy of colonizer species and this may be related to habitat fragmentation or loss owing to industrialized bottom trawl fishing. Mean species richness increased over time which suggests less specialization (decreased dominance) of the assemblage that may result from habitat homogenization. These analyses also showed that when abundance of species was decreased by fishing but eventually returned to previous levels, on average it had a lower occupancy than earlier in the series which could increase their vulnerability to depletion by fishing. Changing occupancy and diversity patterns of the community over time is consistent with EDT which can be exacerbated by direct impacts of fishery removals as well as climate change impacts on the fish community assemblage.

This study addresses the impact of spatial scale on explaining variance in benthic communities. In particular, the analysis estimated the fraction of community variation that occurred at a spatial scale smaller than the sampling interval (i.e., the geographic distance between samples). This estimate is important because it sets a limit on the amount of community variation that can be explained based on the spatial configuration of a study area and sampling design. Six benthic data sets were examined that consisted of faunal abundances, common environmental variables (water depth, grain size, and surficial percent cover), and sonar backscatter treated as a habitat proxy (categorical acoustic provinces). Redundancy analysis was coupled with spatial variograms generated by multiscale ordination to quantify the explained and residual variance at different spatial scales and within and between acoustic provinces. The amount of community variation below the sampling interval of the surveys (< 100 m) was estimated to be 36-59% of the total. Once adjusted for this small-scale variation, > 71% of the remaining variance was explained by the environmental and province variables. Furthermore, these variables effectively explained the spatial structure present in the infaunal community. Overall, no scale problems remained to compromise inferences, and unexplained infaunal community variation had no apparent spatial structure within the observational scale of the surveys (> 100 m), although small-scale gradients (< 100 m) below the observational scale may be present.

Marine protected areas (MPAs) have emerged as potentially important conservation tools for the conservation of biodiversity and mitigation of climate impacts. Among MPAs, a large percentage has been created with the implicit goal of protecting shark populations, including 17 shark sanctuaries which fully protect sharks throughout their jurisdiction. The Commonwealth of the Bahamas represents a long-term MPA for sharks, following the banning of commercial longlining in 1993 and subsequent designation as a shark sanctuary in 2011. Little is known, however, about the long-term behavior and space use of sharks within this protected area, particularly among reef-associated sharks for which the sanctuary presumably offers the most benefit. We used acoustic telemetry to advance our understanding of the ecology of such sharks, namely Caribbean reef sharks ( Carcharhinus perezi ) and tiger sharks ( Galeocerdo cuvier ), over two discrete islands (New Providence and Great Exuma) varying in human activity level, over 2 years. We evaluated which factors influenced the likelihood of detection of individuals, analyzed patterns of movement and occurrence, and identified variability in habitat selection among species and regions, using a dataset of 23 Caribbean reef sharks and 15 tiger sharks which were passively monitored in two arrays with a combined total of 13 acoustic receivers. Caribbean reef sharks had lower detection probabilities than tiger sharks, and exhibited relatively low habitat connectivity and high residency, while tiger sharks demonstrated wider roaming behavior across much greater space. Tiger sharks were associated with shallow seagrass habitats where available, but frequently transited between and connected different habitat types. Our data support the notion that large MPAs afford greater degrees of protection for highly resident species such as Caribbean reef sharks, yet still may provide substantial benefits for more migratory species such as tiger sharks. We discuss these findings within the context of species-habitat linkages, ecosystem services, and the establishment of future MPAs.

Abundance-–occupancy (A-–O) patterns were explored temporally and spatially for the Georges Bank finfish and shellfish community to evaluate long-term trends in the assemblage structure and to identify anthropogenic and environmental drivers impacting the ecosystem. Analyses were conducted for 32 species representing the assemblage from 1963 to 2006 using data from the National Marine Fisheries Service's annual autumn bottom trawl survey. For individual species, occupancy was considered the proportion of stations with at least one individual present, and abundance was estimated as the mean annual number of fish captured per station. Intraspecific relationships were estimated to provide information on utilization of space by a species. Multispecies interspecific relationships over all species for each year were fitted to estimate assemblage structural changes over the time series. Results indicated that the slopes and strengths of interspecific A-–O relationships significantly declined over the duration of the time series, and this decline was significantly related to groundfish landings. However, the rate of decline was not constant, and a breakpoint analysis of interspecific slopes indicated that 1973 was a period of \"“state\"” change. More importantly a jackknife-after-bootstrap analysis indicated that the early 1970s followed by the 1990s were periods of higher than average probability of significant break points. While it is difficult to determine causation, the results suggest that long-term impacts such as habitat fragmentation may be influencing the species assemblage structure in the Georges Bank ecosystem. Further, we used slopes from the intraspecific A-–O relationships to derive a measure of a species' potential risk of hyperstability, where catch rates remain high as the population declines. Combining this measure of the risk of hyperstability with resilience to exploitation provided a means to rank species risk of decline due to both demographics and the interaction of the behaviors of the species and fishing fleets.

The interspecific abundance-occupancy relationship (AOR) is a widely used tool that describes patterns of habitat utilization and, when evaluated over time, may be used to identify large-scale changes in community structure. Our primary goal for this research was to validate the utility of AORs as temporal indicators of community state. We used long-term survey data in four regions of the northwest Atlantic coastal shelf (NWACS) to estimate the diversity of spatial behaviors in each community, which we modeled with negative binomial (NB) distributions. NB parameters were used to generate time series data for simulated communities, from which AORs were then estimated and evaluated for temporal trends. We found that AORs from simulated communities were similar in year-to-year variation to empirical relationships. In order to further understand the role of spatial diversity in the generation of AOR trends, we did additional simulations where NB parameters were manually manipulated. In one instance, we ran simulations while holding species' parameters constant over time. This treatment effectively removed trends, suggesting that temporal change in community relationships was the result of genuine variation in intraspecific spatial use. In another set of simulations, we conducted a case study to evaluate the impact of a select group of schooling and spatially aggregating species on an especially rapid shift in AORs in the Gulf of Maine from 1973 to 1983. Removals of these species reduced the magnitudes of most trends, demonstrating their importance to observed community changes. This research directly links variation in AORs to distribution and density-related processes and provides a potentially powerful framework to identify community-level change and to test ecological and mechanistic hypotheses.