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Oyster reef restoration in the Northern Gulf of Mexico: effect of artificial substrate and sge on nekton and benthic macroinvertebrate assemblage use

In the northern Gulf of Mexico (GOM), reefs built by eastern oysters, Crassostrea virginica, provide critical habitat within shallow estuaries, and recent efforts have focused on restoring reefs to benefit nekton and benthic macroinvertebrates. We compared nekton and benthic macroinvertebrate assemblages at historic, newly created (<5years) and old (>6years) shell and rock substrate reefs. Using crab traps, gill-nets, otter trawls, cast nets, and benthic macroinvertebrate collectors, 20 shallow reefs (<5m) in the northern GOM were sampled throughout the summer of 2011. We compared nekton and benthic assemblage abundance, diversity and composition across reef types. Except for benthic macroinvertebrate abundance, which was significantly higher on old rock reefs as compared to historic reefs, all reefs were similar to historic reefs, suggesting created reefs provide similar support of nekton and benthic assemblages as historic reefs. To determine refuge value of oyster structure for benthic macroinvertebrates compared to bare bottom, we tested preferences of juvenile crabs across depth and refuge complexity in the presence and absence of adult blue crabs (Callinectes sapidus). Juveniles were more likely to use deep water with predators present only when provided oyster structure. Provision of structural material to support and sustain development of benthic and mobile reef communities may be the most important factor in determining reef value to these assemblages, with biophysical characteristics related to reef location influencing assemblage patterns in areas with structure; if so, appropriately locating created reefs is critical.

Alabama, Florida, Louisiana, Mississippi, Texas↗

Supporting climate adaptation for rural Mekong River Basin communities in Thailand

Climate change impacts on large river basins, such as the Mekong River Basin (MRB), are complex due to shared governance and interconnected socioeconomic areas, making them highly vulnerable to change. The MRB, spanning six countries including Thailand, is crucial for the food and economic security of > 60 million people. However, in 2021, Thailand was ranked as the 9th highest risk country affected by climate change. To integrate climate adaptation in Thailand's MRB, we examined the effects of climate change on rapidly developing farmer and fisher communities in northeastern Thailand and explored feasible adaptation options. Using an interdisciplinary approach that included literature review, participatory action methods, and the resist-accept-direct (RAD) framework, we found that climate change is projected to increase temperatures, precipitation, extreme events, erosion, and water clarity, while decreasing heavy sediment transport. These changes negatively impact agriculture, fisheries, human health, and tourism. We identified several adaptation strategies across environmental, ecological, and human health categories to accommodate local needs, such as preventing habitat degradation (e.g., from dams and deforestation), providing fish refuge and passage, and supporting technical capacity. Community-driven adaptation planning and implementation are essential for supporting global sustainable development in a changing climate.

Mitigation and Adaptation Strategies for Global Ch↗

Food-web structure in canyon and slope-associated fauna revealed by stable isotopes

Food webs and associated trophic linkages among organisms are central themes in ecology that provide insight into the structure and function of ecosystems. In the deep sea, food webs rely on particulate flux raining from surface waters for energy (Klages et al. 2003), except for chemosynthetic communities, which rely on in situ production via chemosynthesis (Van Dover 2007). In general, the deep sea is a food limited environment because only a small percentage of organic carbon produced in surface waters settles to the seafloor (Gage and Tyler 1991, Klages et al. 2003, De La Rocha and Passow 2007). In contrast, relative to more quiescent slope environments, canyons can experience dynamic flow and turbulence. Internal tides can enhance turbulent mixing near the canyon seafloor leading to resuspension of sediments. Channeling of organic matter in deepsea canyons can enhance benthic productivity leading to high biodiversity (Vetter and Dayton 1998, 1999) and trophic complexity (Stefanescu et al. 1994, Cartes and Sorbe 1999). Thus, there may be a decoupling between the benthic-productivity relationships in canyon environments where food limitation may not be a driving factor influencing community structure. However, there have been only a few studies, often limited in depth range and spatial scale, that have examined the trophic pathways of deepsea canyons relative to adjacent slope environments (Duineveld et al. 2001, Fanelli et al. 2009, Cartes et al. 2010, Jeffreys et al. 2011).

OCS Study↗

A hierarchical model for estimating the spatial distribution and abundance of animals detected by continuous-time recorders

Motivation Several spatial capture-recapture (SCR) models have been developed to estimate animal abundance by analyzing the detections of individuals in a spatial array of traps. Most of these models do not use the actual dates and times of detection, even though this information is readily available when using continuous-time recorders, such as microphones or motion-activated cameras. Instead most SCR models either partition the period of trap operation into a set of subjectively chosen discrete intervals and ignore multiple detections of the same individual within each interval, or they simply use the frequency of detections during the period of trap operation and ignore the observed times of detection. Both practices make inefficient use of potentially important information in the data. Model and data analysis We developed a hierarchical SCR model to estimate the spatial distribution and abundance of animals detected with continuous-time recorders. Our model includes two kinds of point processes: a spatial process to specify the distribution of latent activity centers of individuals within the region of sampling and a temporal process to specify temporal patterns in the detections of individuals. We illustrated this SCR model by analyzing spatial and temporal patterns evident in the camera-trap detections of tigers living in and around the Nagarahole Tiger Reserve in India. We also conducted a simulation study to examine the performance of our model when analyzing data sets of greater complexity than the tiger data. Benefits Our approach provides three important benefits: First, it exploits all of the information in SCR data obtained using continuous-time recorders. Second, it is sufficiently versatile to allow the effects of both space use and behavior of animals to be specified as functions of covariates that vary over space and time. Third, it allows both the spatial distribution and abundance of individuals to be estimated, effectively providing a species distribution model, even in cases where spatial covariates of abundance are unknown or unavailable. We illustrated these benefits in the analysis of our data, which allowed us to quantify differences between nocturnal and diurnal activities of tigers and to estimate their spatial distribution and abundance across the study area. Our continuous-time SCR model allows an analyst to specify many of the ecological processes thought to be involved in the distribution, movement, and behavior of animals detected in a spatial trapping array of continuous-time recorders. We plan to extend this model to estimate the population dynamics of animals detected during multiple years of SCR surveys.

Western Ghats, Nagarahole Tiger Reserve↗

The use of discontinuities and functional groups to assess relative resilience in complex systems

It is evident when the resilience of a system has been exceeded and the system qualitatively changed. However, it is not clear how to measure resilience in a system prior to the demonstration that the capacity for resilient response has been exceeded. We argue that self-organizing human and natural systems are structured by a relatively small set of processes operating across scales in time and space. These structuring processes should generate a discontinuous distribution of structures and frequencies, where discontinuities mark the transition from one scale to another. Resilience is not driven by the identity of elements of a system, but rather by the functions those elements provide, and their distribution within and across scales. A self-organizing system that is resilient should maintain patterns of function within and across scales despite the turnover of specific elements (for example, species, cities). However, the loss of functions, or a decrease in functional representation at certain scales will decrease system resilience. It follows that some distributions of function should be more resilient than others. We propose that the determination of discontinuities, and the quantification of function both within and across scales, produce relative measures of resilience in ecological and other systems. We describe a set of methods to assess the relative resilience of a system based upon the determination of discontinuities and the quantification of the distribution of functions in relation to those discontinuities. ?? 2005 Springer Science+Business Media, Inc.

Ecosystems↗

Expression plasticity regulates intraspecific variation in the acclimatization potential of a reef-building coral

Phenotypic plasticity is an important ecological and evolutionary response for organisms experiencing environmental change, but the ubiquity of this capacity within coral species and across symbiont communities is unknown. We exposed ten genotypes of the reef-building coral Montipora capitata with divergent symbiont communities to four thermal pre-exposure profiles and quantified gene expression before stress testing 4 months later. Here we show two pre-exposure profiles significantly enhance thermal tolerance despite broadly different expression patterns and substantial variation in acclimatization potential based on coral genotype. There was no relationship between a genotype’s basal thermal sensitivity and ability to acquire heat tolerance, including in corals harboring naturally tolerant symbionts, which illustrates the potential for additive improvements in coral response to climate change. These results represent durable improvements from short-term stress hardening of reef-building corals and substantial cryptic complexity in the capacity for plasticity.

Nature Communications↗

Spatiotemporal interactions facilitate sympatry in a diverse mammalian community

Understanding mechanisms underlying coexistence among potential competitors, and between predators and prey, is a persistent challenge in community ecology. Using 6 years (2013–2018) of camera-trapping data and species interaction models, we investigated the spatiotemporal patterns of inter- and intra-guild interspecific interactions in a diverse terrestrial mammalian community in Pakke Wildlife Sanctuary and Tiger Reserve (PTR), Northeast India. We found no evidence of spatial interaction among apex predators (tiger Panthera tigris , leopard Panthera pardus , and dhole Cuon alpinus ). However, dholes temporally separated themselves from tigers and leopards. Among small carnivores, marbled cat ( Pardofelis marmorata ) and leopard cat ( Prionailurus bengalensis ) exhibited temporal separation, whereas leopard cat overlapped spatially and temporally with other small carnivores. Herbivores exhibited neither spatial nor temporal separation with each other. All apex predators exhibited diel activity and space-use patterns to overlap with their preferred prey. Our results suggest that the assembly of the diverse mammalian community of PTR is a complex process, and coexistence among potential competitors, and predators and prey is likely facilitated by several mechanisms including spatial and temporal segregation, and potentially dietary separation.

Arunachal Pradesh↗

A new remote sensing-based Carbon Sequestration Potential Index (CSPI): A tool to support land carbon management

Integrating remote sensing into assessments of carbon stocks and fluxes has advanced our understanding of how global change affects landscapes and our capacity to support decision making about forest management. However, there remains a lack of detailed and actionable analyses conducted across widely ranging environmental conditions that are appropriate for tactical planning. We used airborne laser scanning data and multi-source satellite imagery to estimate forest aboveground carbon density and gross primary production, and to map forest cover across the main Hawaiian Islands. We used these measures to develop the Carbon Sequestration Potential Index (CSPI), which identifies where the potential for carbon sequestration following afforestation would be highest within a complex landscape of 304 management units. Variation in CSPI was high across islands and between ecosystems, with low values for cool, dry and largely intact forest systems and high values for warm, wet and largely non-forested systems. The CSPI provided a rapid, spatially-explicit and actionable assessment of Hawaiian forest reserves, which can help stewardship agencies contribute to state carbon neutrality goals through climate-smart and science-driven prescriptions that encompass conservation to restoration.

Hawaii↗

Broad-scale predictors of canada lynx occurrence in eastern North America

The Canada lynx (Lynx canadensis) is listed as a threatened species throughout the southern extent of its geographic range in the United States. Most research on lynx has been conducted in the western United States and Canada; little is known about the ecology of lynx in eastern North America. To fill critical knowledge gaps about this species, we modeled and mapped lynx occurrence using habitat and weather data from 7 eastern states and 3 Canadian provinces. Annual snowfall, road density, bobcat (L. rufus) harvest, deciduous forest, and coniferous forest were compared at 1,150 lynx locations and 1,288 random locations. Nineteen a priori models were developed using the information-theoretic approach, and logistic regression models were ranked using Akaike's Information Criterion (AIC) and by our ability to correctly classify reserved data (Kappa). Annual snowfall and deciduous forest predicted lynx presence and absence for a reserved dataset (n = 278) with 94% accuracy. A map of the probability of lynx occurrence throughout the region revealed that 92% of the potential habitat (i.e., >50% probability of occurrence) was concentrated in a relatively contiguous complex encompassing northern Maine, New Brunswick, and the Gaspe?? peninsula of Quebec. Most of the remaining potential habitat (5%) was on northern Cape Breton Island in Nova Scotia. Potential habitat in New Hampshire, Vermont, and New York was small (1,252 km2), fragmented, and isolated (>200 km) from known lynx populations. When federally listed as threatened in the contiguous United States in 2000, inadequate regulations on federal lands were cited as the primary threat to Canada lynx. However, the majority of potential lynx habitat in the eastern United States is on private lands and continuous with potential habitat in Canada. Therefore, lynx conservation in eastern North America will need to develop partnerships across national, state, and provincial boundaries as well as with private landowners.

Journal of Wildlife Management↗

Resilience to stress and disturbance, and resistance to Bromus tectorum L. invasion in cold desert shrublands of western North America

Alien grass invasions in arid and semi-arid ecosystems are resulting in grass–fire cycles and ecosystem-level transformations that severely diminish ecosystem services. Our capacity to address the rapid and complex changes occurring in these ecosystems can be enhanced by developing an understanding of the environmental factors and ecosystem attributes that determine resilience of native ecosystems to stress and disturbance, and resistance to invasion. Cold desert shrublands occur over strong environmental gradients and exhibit significant differences in resilience and resistance. They provide an excellent opportunity to increase our understanding of these concepts. Herein, we examine a series of linked questions about (a) ecosystem attributes that determine resilience and resistance along environmental gradients, (b) effects of disturbances like livestock grazing and altered fire regimes and of stressors like rapid climate change, rising CO 2 , and N deposition on resilience and resistance, and (c) interacting effects of resilience and resistance on ecosystems with different environmental conditions. We conclude by providing strategies for the use of resilience and resistance concepts in a management context. At ecological site scales, state and transition models are used to illustrate how differences in resilience and resistance influence potential alternative vegetation states, transitions among states, and thresholds. At landscape scales management strategies based on resilience and resistance—protection, prevention, restoration, and monitoring and adaptive management—are used to determine priority management areas and appropriate actions.

Ecosystems↗

Importance of a lake-wetland complex for a resilient Walleye fishery

Wetlands serve as unique habitats that can support high biodiversity. Large-scale loss of wetland habitats can threaten important linkages between lake and wetland habitats that could affect diversity and growth of aquatic organisms. In this study, we compare prey diversity and abundance as well as Walleye ( Sander vitreus ) diets and condition in a large glacial lake (Lake Kampeska, South Dakota) with a connected wetland to better understand seasonal changes in the benefits provided by each habitat. We examined seasonal differences (spring, summer, and fall) through two years (summer 2021 through fall 2022) between the habitats using prey fish catch per unit effort, richness, Shannon diversity, and Bray–Curtis dissimilarity as well as Walleye relative weight, percent of empty stomachs, diet weight, stomach fullness, diet energy, and diet taxa importance. The prey fish community was more diverse and abundant in the wetland, and Walleye consumed more prey (by weight) in the wetland during all seasons except spring. Wetland reconnection can be a tool for managers to improve water quality while providing seasonal habitat needs for fish. Additionally, the diversity of prey resources provided by wetlands, many of which are unique, support resilience in the face of ecological change. Protection of wetlands may be critical for maintaining healthy and resilient fisheries into the future.

South Dakota↗

Temporal shifts in top-down vs. bottom-up control of epiphytic algae in a seagrass ecosystem

In coastal marine food webs, small invertebrate herbivores (mesograzers) have long been hypothesized to occupy an important position facilitating dominance of habitat-forming macrophytes by grazing competitively superior epiphytic algae. Because of the difficulty of manipulating mesograzers in the field, however, their impacts on community organization have rarely been rigorously documented. Understanding mesograzer impacts has taken on increased urgency in seagrass systems due to declines in seagrasses globally, caused in part by widespread eutrophication favoring seagrass overgrowth by faster-growing algae. Using cage-free field experiments in two seasons (fall and summer), we present experimental confirmation that mesograzer reduction and nutrients can promote blooms of epiphytic algae growing on eelgrass ( Zostera marina ). In this study, nutrient additions increased epiphytes only in the fall following natural decline of mesograzers. In the summer, experimental mesograzer reduction stimulated a 447% increase in epiphytes, appearing to exacerbate seasonal dieback of eelgrass. Using structural equation modeling, we illuminate the temporal dynamics of complex interactions between macrophytes, mesograzers, and epiphytes in the summer experiment. An unexpected result emerged from investigating the interaction network: drift macroalgae indirectly reduced epiphytes by providing structure for mesograzers, suggesting that the net effect of macroalgae on seagrass depends on macroalgal density. Our results show that mesograzers can control proliferation of epiphytic algae, that top-down and bottom-up forcing are temporally variable, and that the presence of macroalgae can strengthen top-down control of epiphytic algae, potentially contributing to eelgrass persistence.

Ecology↗

Use of genetic data to infer population-specific ecological and phenotypic traits from mixed aggregations

Many applications in ecological genetics involve sampling individuals from a mixture of multiple biological populations and subsequently associating those individuals with the populations from which they arose. Analytical methods that assign individuals to their putative population of origin have utility in both basic and applied research, providing information about population-specific life history and habitat use, ecotoxins, pathogen and parasite loads, and many other non-genetic ecological, or phenotypic traits. Although the question is initially directed at the origin of individuals, in most cases the ultimate desire is to investigate the distribution of some trait among populations. Current practice is to assign individuals to a population of origin and study properties of the trait among individuals within population strata as if they constituted independent samples. It seemed that approach might bias population-specific trait inference. In this study we made trait inferences directly through modeling, bypassing individual assignment. We extended a Bayesian model for population mixture analysis to incorporate parameters for the phenotypic trait and compared its performance to that of individual assignment with a minimum probability threshold for assignment. The Bayesian mixture model outperformed individual assignment under some trait inference conditions. However, by discarding individuals whose origins are most uncertain, the individual assignment method provided a less complex analytical technique whose performance may be adequate for some common trait inference problems. Our results provide specific guidance for method selection under various genetic relationships among populations with different trait distributions.

PLoS ONE↗

Spatiotemporal dynamics of black-tailed prairie dog colonies affected by plague

Black-tailed prairie dogs (Cynomys ludovicianus) are a key component of the disturbance regime in semi-arid grasslands of central North America. Many studies have compared community and ecosystem characteristics on prairie dog colonies to grasslands without prairie dogs, but little is known about landscape-scale patterns of disturbance that prairie dog colony complexes may impose on grasslands over long time periods. We examined spatiotemporal dynamics in two prairie dog colony complexes in southeastern Colorado (Comanche) and northcentral Montana (Phillips County) that have been strongly influenced by plague, and compared them to a complex unaffected by plague in northwestern Nebraska (Oglala). Both plague-affected complexes exhibited substantial spatiotemporal variability in the area occupied during a decade, in contrast to the stability of colonies in the Oglala complex. However, the plague-affected complexes differed in spatial patterns of colony movement. Colonies in the Comanche complex in shortgrass steppe shifted locations over a decade. Only 10% of the area occupied in 1995 was still occupied by prairie dogs in 2006. In 2005 and 2006 respectively, 74 and 83% of the total area of the Comanche complex occurred in locations that were not occupied in 1995, and only 1% of the complex was occupied continuously over a decade. In contrast, prairie dogs in the Phillips County complex in mixed-grass prairie and sagebrush steppe primarily recolonized previously occupied areas after plague-induced colony declines. In Phillips County, 62% of the area occupied in 1993 was also occupied by prairie dogs in 2004, and 12% of the complex was occupied continuously over a decade. Our results indicate that plague accelerates spatiotemporal movement of prairie dog colonies, and have significant implications for landscape-scale effects of prairie dog disturbance on grassland composition and productivity. These findings highlight the need to combine landscape-scale measures of habitat suitability with long-term measures of colony locations to understand the role of plague-affected prairie dogs as a grassland disturbance process. ?? 2007 Springer Science+Business Media B.V.

Landscape Ecology↗

Rewilding the upper Klamath River Basin: Rapid recolonization of Chinook salmon following the world’s largest dam removal

Habitat fragmentation is a global driver of decline in biodiversity, yet evaluations of ecological response following re-connection remain rare. In 2024, four hydroelectric dams on the Klamath River were removed, reconnecting over 640 km of anadromous habitat and marking the largest dam removal project completed to date. We used a stationary high-resolution multi-beam imaging SONAR to quantify adult Chinook salmon ( Oncorhynchus tshawytscha ) passage into newly reopened reaches during the first two migratory seasons following dam removal. An estimated 7,742 (95% CI: 7,702–7,778) Chinook salmon migrated upstream in 2024 and 13,310 (95% CI: 12,876–13,733) in 2025, representing 18–19% of fish returning to the Klamath River Basin. Within this period, Chinook salmon recolonized 88% of their documented historical distribution, expanding into 345 km of reconnected habitats and reaching elevations of up to 1,250 m. Recolonization required fish to swim through dam removal sites, complex hydraulic corridors and engineered fishways, demonstrating the propensity for rapid recolonization at basin scale despite these challenges. These findings provide the first quantitative assessment of salmon response to the world’s largest dam removal and demonstrate how reconnection can catalyze large-scale recolonization in historically fragmented river networks.

California, Oregon↗

Final project memorandum: sea-level rise modeling handbook: resource guide for resource managers, engineers, and scientists

Coastal wetlands of the Southeastern United States are undergoing retreat and migration from increasing tidal inundation and saltwater intrusion attributed to climate variability and sea-level rise. Much of the literature describing potential sea-level rise projections and modeling predictions are found in peer-reviewed academic journals or government technical reports largely suited to reading by other Ph.D. scientists who are more familiar or engaged in the climate change debate. Various sea-level rise and coastal wetland models have been developed and applied of different designs and scales of spatial and temporal complexity for predicting habitat and environmental change that have not heretofore been synthesized to aid natural resource managers of their utility and limitations. Training sessions were conducted with Federal land managers with U.S. Fish and Wildlife Service, National Park Service, and NOAA National Estuarine Research Reserves as well as state partners and nongovernmental organizations across the northern Gulf Coast from Florida to Texas to educate and to evaluate user needs and understanding of concepts, data, and modeling tools for projecting sea-level rise and its impact on coastal habitats and wildlife. As a result, this handbook was constructed from these training and feedback sessions with coastal managers and biologists of published decision-support tools and simulation models for sea-level rise and climate change assessments. A simplified tabular context was developed listing the various kinds of decision-support tools and ecological models along with criteria to distinguish the source, scale, and quality of information input and geographic data sets, physical and biological constraints and relationships, datum characteristics of water and land elevation components, utility options for setting sea-level rise and climate change scenarios, and ease or difficulty of storing, displaying, or interpreting model output. The handbook is designed to be a primer to understanding sea-level rise and a practical synthesis of the current state of knowledge and modeling tools as a resource guide for DOl land management needs and facilitating Landscape Conservation Cooperative (LCC) research and conservation initiatives.

Conference Paper↗

Vegetative and geomorphic complexity at tributary junctions on the Colorado and Dolores Rivers: a blueprint for riparian restoration

Context Habitat complexity in rivers is linked to dynamic fluvial conditions acting at various spatial scales. On regulated rivers in the western United States, tributaries are regions of high energy and disturbance, providing important resource inputs for riparian ecosystems. Objectives This study investigated spatial patterns and extents of tributary influence on riparian habitat complexity in the near channel zone along regulated reaches of the Colorado (> 200 km) and Dolores Rivers (~ 300 km) in the western United States. Because tributary confluences are regions of increased dynamism, we hypothesized that: (1) geomorphic and land cover complexity would be greatest close to tributary junctions and decrease with distance from tributaries; and (2) patterns in complexity would vary across different sized spatial units. Methods Using a combination of remote sensing and spatial analysis, we classified fluvial features and land cover classes to investigate patterns longitudinally at 10-, 25-, and 100-m spatial units in the near channel zone of two regulated rivers. Results Using change point analysis and randomization tests, we detected shifts in riparian habitat complexity closer to tributary junctions. Patterns varied across 10-, 25-, and 100-m spatial units in the near channel zone, with significance (p ≤ 0.05) recorded for 10- and 25-m spatial units. Conclusions Tributary junctions deliver critical resource inputs on regulated systems, providing for increased geomorphic and land cover diversity upstream and downstream of tributaries. We found that patterns of response were non-linear and discontinuous, varying across spatial units and potentially influenced by the degree of mainstem flow regulation.

Colorado, Utah↗

Seagrass impact on sediment exchange between tidal flats and salt Marsh, and the sediment budget of shallow bays

Seagrasses are marine flowering plants that strongly impact their physical and biological surroundings and are therefore frequently referred to as ecological engineers. The effect of seagrasses on coastal bay resilience and sediment transport dynamics is understudied. Here we use six historical maps of seagrass distribution in Barnegat Bay, USA, to investigate the role of these vegetated surfaces on the sediment storage capacity of shallow bays. Analyses are carried out by means of the Coupled-Ocean-Atmosphere-Wave-Sediment Transport (COAWST) numerical modeling framework. Results show that a decline in the extent of seagrass meadows reduces the sediment mass potentially stored within bay systems. The presence of seagrass reduces shear stress values across the entire bay, including unvegetated areas, and promotes sediment deposition on tidal flats. On the other hand, the presence of seagrasses decreases suspended sediment concentrations, which in turn reduces the delivery of sediment to marsh platforms. Results highlight the relevance of seagrasses for the long-term survival of coastal ecosystems, and the complex dynamics regulating the interaction between subtidal and intertidal landscapes.

New Jersey↗