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USGS2021

Recovering individual-level spatial inference from aggregated binary data

Binary regression models are commonly used in disciplines such as epidemiology and ecology to determine how spatial covariates influence individuals. In many studies, binary data are shared in a spatially aggregated form to protect privacy. For example, rather than reporting the location and result for each individual that was tested for a disease, researchers may report that a disease was detected or not detected within geopolitical units. Often, the spatial aggregation process obscures the values of response variables, spatial covariates, and locations of each individual, which makes recovering individual-level inference difficult. We show that applying a series of transformations, including a change of support, to a bivariate point process model allows researchers to recover individual-level inference for spatial covariates from spatially aggregated binary data. The series of transformations preserves the convenient interpretation of desirable binary regression models that are commonly applied to individual-level data. Using a simulation experiment, we compare the performance of our proposed method under varying types of spatial aggregation against the performance of standard approaches using the original individual-level data. We illustrate our method by modeling individual-level probability of infection using a data set that has been aggregated to protect an at-risk and endangered species of bats. Our simulation experiment and data illustration demonstrate the utility of the proposed method when access to original non-aggregated data is impractical or prohibited.

Northeast and Midwest United States↗

USGS2024

Hyperspectral Image Transects during Transient Events in Rivers (HITTER): Framework development and application to a tracer experiment on the Missouri River, USA

Rivers convey a broad range of materials, such as sediment, nutrients, and contaminants. Much of this transport can occur during or immediately after an episodic, pulsed event like a flood or an oil spill. Understanding the flow processes that influence the motion of these substances is important for managing water resources and conserving aquatic ecosystems. This study introduces a new remote sensing framework for characterizing dynamic phenomena at the scale of a channel cross-section: Hyperspectral Image Transects during Transient Events in Rivers (HITTER). We present a workflow that uses repeated hyperspectral scan lines acquired from a hovering uncrewed aircraft system (UAS) to quantify how a water attribute of interest varies laterally across the river and evolves over time. Data from a tracer experiment on the Missouri River are used to illustrate the components of the end-to-end processing chain we used to quantify the passage of a visible dye. The framework is intended to be flexible and could be applied in a number of different contexts. The results of this initial proof-of-concept investigation suggest that HITTER could potentially provide insight regarding the dispersion of a range of materials in rivers, which would facilitate ecological and geomorphic studies and help inform management.

Remote Sensing↗

USGS2011

Structural and functional effects of herbicides on non-target organisms in aquatic ecosystems with an emphasis on atrazine

Herbicide use has increased dramatically around the world over the past 6 decades (Gianessi and Reigner, 2007). Few herbicides were in use in the 1950s. However, by 2001 approximately 1.14 billion kilograms of herbicides were applied globally for the control of undesireable vegetation in agricultural, silvicultural, lawncare, aquacultural, and irrigation/recreational water management activities (Kiely et al., 2004). Twenty-eight percent of the total mass of herbicides is applied in the United States, with the remaining 72 percent being applied elsewhere around the globe (Kiely et al., 2004). Herbicides represent 36% of global pesticide use, followed by insecticides (25%), fungicides (10%) and other chemical classes (Kiely et al., 2004). Agricultural production accounts for approximately 90% of herbicide use in the U.S. (Kiely et al., 2004). Gianessi and Reigner (2007) indicated that herbicides are routinely used on more than 90% of the area designated for large commercial crops including corn, soybeans, cotton, sugar beets, peanuts, and rice. Increased farm mechanization, technological advancements in production of inexpensive sources of inorganic nitrogen fertilizer (e.g., anhydrous ammonia), and conversion of forest, grassland, and wetland habitats to cropland has led to a tremendous increase in global food production over the past half-century. Herbicides have augmented advances in large-scale agricultural systems and have largely replaced mechanical and hand-weeding control mechanisms (Gianessi and Reigner, 2007). The wide-spread use of herbicides in agriculture has resulted in frequent chemical detections in surface and groundwaters (Gilliom, 2007). The majority of herbicides used are highly water soluble and are therefore prone to runoff from terrestrial environments. In additon, spray drift and atmospheric deposition can contribute to herbicide contamination of aquatic environments. Lastly, selected herbicides are deliberately applied to aquatic environments for controlling nuisance aquatic vegetation. Although aquatic herbicide exposure has been widely documented, these exposures are not necessarily related to adverse non-target ecological effects on natural communities in aquatic environments. This chapter evaluates the potential for effects of herbicides on the structure and function of aquatic envrionments at the population, community, and ecosystem levels of biological organization. In this manuscript I examine several critical aspects of the subject matter area: primary herbicides in use and chemical modes of action; the regulatory process used for registration and risk assessment of herbicides; data regarding non-target risks and the relative sensitivity of aquatic plants, inveretebrates, and fish to herbicides; and emerging areas of science regarding the potential for endocrine-disrupting effects of herbicides on aquatic vertebrates. Much of the focus of this paper is on atrazine due to the extensive database which exists regarding its fate and effects.

Book chapter↗

USGS1998

International impact research and management

To be sustainable, ecotourism requires the protection of natural environments and processes both from development and operation of the tourism infrastructure, and from the activities of ecotourists within protected areas. This book chapter reviews the international literature on the study of visitor or recreation-related resource impacts with special reference to ecotourism. Four case examples are presented to characterize the geographic scope, focus, and principal findings of this recreation ecology literature and its relevance to ecotourism management. Case examples include the Cairngorms National Nature Reserve, Scotland; the Great Barrier Reef, Australia; the Central American tropics; and wildlife viewing in Kenya?s protected areas. Implications for the management of international protected areas and ecotourism resources are discussed.

Book chapter↗

USGS2016

A geological perspective on the degradation and conservation of western Atlantic coral reefs

Continuing coral-reef degradation in the western Atlantic is resulting in loss of ecological and geologic functions of reefs. With the goal of assisting resource managers and stewards of reefs in setting and measuring progress toward realistic goals for coral-reef conservation and restoration, we examined reef degradation in this region from a geological perspective. The importance of ecosystem services provided by coral reefs—as breakwaters that dissipate wave energy and protect shorelines and as providers of habitat for innumerable species—cannot be overstated. However, the few coral species responsible for reef building in the western Atlantic during the last approximately 1.5 million years are not thriving in the 21st century. These species are highly sensitive to abrupt temperature extremes, prone to disease infection, and have low sexual reproductive potential. Their vulnerability and the low functional redundancy of branching corals have led to the low resilience of western Atlantic reef ecosystems. The decrease in live coral cover over the last 50 years highlights the need for study of relict (senescent) reefs, which, from the perspective of coastline protection and habitat structure, may be just as important to conserve as the living coral veneer. Research is needed to characterize the geological processes of bioerosion, reef cementation, and sediment transport as they relate to modern-day changes in reef elevation. For example, although parrotfish remove nuisance macroalgae, possibly promoting coral recruitment, they will not save Atlantic reefs from geological degradation. In fact, these fish are quickly nibbling away significant quantities of Holocene reef framework. The question of how different biota covering dead reefs affect framework resistance to biological and physical erosion needs to be addressed. Monitoring and managing reefs with respect to physical resilience, in addition to ecological resilience, could optimize the expenditure of resources in conserving Atlantic reefs and the services they provide.

Conservation Biology↗

USGS2013

Seasonal climate variation and caribou availability: Modeling sequential movement using satellite-relocation data

Livelihood systems that depend on mobile resources must constantly adapt to change. For people living in permanent settlements, environmental changes that affect the distribution of a migratory species may reduce the availability of a primary food source, with the potential to destabilize the regional social-ecological system. Food security for Arctic indigenous peoples harvesting barren ground caribou ( Rangifer tarandus granti ) depends on movement patterns of migratory herds. Quantitative assessments of physical, ecological, and social effects on caribou distribution have proven difficult because of the significant interannual variability in seasonal caribou movement patterns. We developed and evaluated a modeling approach for simulating the distribution of a migratory herd throughout its annual cycle over a multiyear period. Beginning with spatial and temporal scales developed in previous studies of the Porcupine Caribou Herd of Canada and Alaska, we used satellite collar locations to compute and analyze season-by-season probabilities of movement of animals between habitat zones under two alternative weather conditions for each season. We then built a set of transition matrices from these movement probabilities, and simulated the sequence of movements across the landscape as a Markov process driven by externally imposed seasonal weather states. Statistical tests showed that the predicted distributions of caribou were consistent with observed distributions, and significantly correlated with subsistence harvest levels for three user communities. Our approach could be applied to other caribou herds and could be adapted for simulating the distribution of other ungulates and species with similarly large interannual variability in the use of their range.

Alaska, Yukon Territory↗

USGS2004

Seafloor habitat mapping and classification in Glacier Bay, Alaska: Phase 1 & 2 1996-2004

Glacier Bay is a diverse fjord ecosystem with multiple sills, numerous tidewater glaciers and a highly complex oceanographic system. The Bay was completely glaciated prior to the 1700’s and subsequently experienced the fastest glacial retreat recorded in historical times. Currently, some of the highest sedimentation rates ever observed occur in the Bay, along with rapid uplift (up to 2.5 cm/year) due to a combination of plate tectonics and isostatic rebound. Glacier Bay is the second deepest fjord in Alaska, with depths over 500 meters. This variety of physical processes and bathymetry creates many diverse habitats within a relatively small area (1,255 km 2 ). Habitat can be defined as the locality, including resources and environmental conditions, occupied by a species or population of organisms (Morrison et al 1992). Mapping and characterization of benthic habitat is crucial to an understanding of marine species and can serve a variety of purposes including: understanding species distributions and improving stock assessments, designing special management areas and marine protected areas, monitoring and protecting important habitats, and assessing habitat change due to natural or human impacts. In 1996, Congress recognized the importance of understanding benthic habitat for fisheries management by reauthorizing the Magnuson-Stevens Fishery Conservation and Management Act and amending it with the Sustainable Fisheries Act (SFA). This amendment emphasizes the importance of habitat protection to healthy fisheries and requires identification of essential fish habitat in management decisions. Recently, the National Park Service’s Ocean Stewardship Strategy identified the creation of benthic habitat maps and sediment maps as crucial components to complete basic ocean park resource inventories (Davis 2003). Glacier Bay National Park managers currently have very limited knowledge about the bathymetry, sediment types, and various marine habitats of ecological importance in the Park. Ocean floor bathymetry and sediment type are the building blocks of marine communities. Bottom type and shape affects the kinds of benthic communities that develop in a particular environment as well as the oceanographic conditions that communities are subject to. Accurate mapping of the ocean floor is essential for park manager’s understanding of existing marine communities and will be important in assessing human induced changes (e.g., vessel traffic and commercial fishing), biological change (e.g., rapid sea otter recolonization), and geological processes of change (e.g., deglaciation). Information on animal-habitat relationships, particularly within a marine reserve framework, will be valuable to agencies making decisions about critical habitats, marine reserve design, as well as fishery management. Identification and mapping of benthic habitat provides National Park Service mangers with tools to increase the effectiveness of resource management. The primary objective of this project is to investigate the geological characteristics of the biological habitats of halibut, Dungeness crab, king crab, and Tanner crab within Glacier Bay National Park. Additionally, habitat classification of shallow water regions of Glacier Bay will provide crucial information on the relationship between benthic habitat features and the abundance of benthic prey items for a variety of marine predators, including sea ducks, the rapidly increasing population of sea otters, and other marine mammals.

Alaska↗

USGS2017

Mechanisms of nitrogen deposition effects on temperate forest lichens and trees

We review the mechanisms of deleterious nitrogen (N) deposition impacts on temperate forests, with a particular focus on trees and lichens. Elevated anthropogenic N deposition to forests has varied effects on individual organisms depending on characteristics both of the N inputs (form, timing, amount) and of the organisms (ecology, physiology) involved. Improved mechanistic knowledge of these effects can aid in developing robust predictions of how organisms respond to either increases or decreases in N deposition. Rising N levels affect forests in micro- and macroscopic ways from physiological responses at the cellular, tissue, and organism levels to influencing individual species and entire communities and ecosystems. A synthesis of these processes forms the basis for the overarching themes of this paper, which focuses on N effects at different levels of biological organization in temperate forests. For lichens, the mechanisms of direct effects of N are relatively well known at cellular, organismal, and community levels, though interactions of N with other stressors merit further research. For trees, effects of N deposition are better understood for N as an acidifying agent than as a nutrient; in both cases, the impacts can reflect direct effects on short time scales and indirect effects mediated through long-term soil and belowground changes. There are many gaps on fundamental N use and cycling in ecosystems, and we highlight the most critical gaps for understanding potential deleterious effects of N deposition. For lichens, these gaps include both how N affects specific metabolic pathways and how N is metabolized. For trees, these gaps include understanding the direct effects of N deposition onto forest canopies, the sensitivity of different tree species and mycorrhizal symbionts to N, the influence of soil properties, and the reversibility of N and acidification effects on plants and soils. Continued study of how these N response mechanisms interact with one another, and with other dimensions of global change, remains essential for predicting ongoing changes in lichen and tree populations across North American temperate forests.

Ecosphere↗

USGS2005

Surface elevation dynamics in a regenerating mangrove forest at Homebush Bay, Australia

Following the dieback of an interior portion of a mangrove forest at Homebush Bay, Australia, surface elevation tables and feldspar marker horizons were installed in the impacted, intermediate and control forest to measure vertical accretion, elevation change, and shallow subsidence. The objectives of the study were to determine current vertical accretion and elevation change rates as a guide to understanding mangrove dieback, ascertain the factors controlling surface elevation change, and investigate the sustainability of the mangrove forest under estimated sea-level rise conditions. The study demonstrates that the influences on surface dynamics are more complex than soil accretion and soil autocompaction alone. During strong vegetative regrowth in the impacted forest, surface elevation increase exceeded vertical accretion apparently as a result of belowground biomass production. In addition, surface elevation in all forest zones was correlated with total monthly rainfall during a severe El Niño event, highlighting the importance of rainfall to groundwater recharge and surface elevation. Surface elevation increase for all zones exceeded the 85-year sea level trend for Sydney Harbour. Since mean sea-level also decreased during the El Niño event, the decrease in surface elevation did not translate to an increase in inundation frequency or influence the sustainability of the mangrove forest. These findings indicate that subsurface soil processes such as organic matter accumulation and groundwater flux can significantly influence mangrove surface elevation, and contribute to the long-term sustainability of mangrove systems under a scenario of rising sea levels.

Homebush Bay↗

USGS2013

Reconciling resource utilization and resource selection functions

Summary: 1. Analyses based on utilization distributions (UDs) have been ubiquitous in animal space use studies, largely because they are computationally straightforward and relatively easy to employ. Conventional applications of resource utilization functions (RUFs) suggest that estimates of UDs can be used as response variables in a regression involving spatial covariates of interest. 2. It has been claimed that contemporary implementations of RUFs can yield inference about resource selection, although to our knowledge, an explicit connection has not been described. 3. We explore the relationships between RUFs and resource selection functions from a hueristic and simulation perspective. We investigate several sources of potential bias in the estimation of resource selection coefficients using RUFs (e.g. the spatial covariance modelling that is often used in RUF analyses). 4. Our findings illustrate that RUFs can, in fact, serve as approximations to RSFs and are capable of providing inference about resource selection, but only with some modification and under specific circumstances. 5. Using real telemetry data as an example, we provide guidance on which methods for estimating resource selection may be more appropriate and in which situations. In general, if telemetry data are assumed to arise as a point process, then RSF methods may be preferable to RUFs; however, modified RUFs may provide less biased parameter estimates when the data are subject to location error.

Journal of Animal Ecology↗

USGS2009

Guiding concepts for park and wilderness stewardship in an era of global environmental change

The major challenge to stewardship of protected areas is to decide where, when, and how to intervene in physical and biological processes, to conserve what we value in these places. To make such decisions, planners and managers must articulate more clearly the purposes of parks, what is valued, and what needs to be sustained. A key aim for conservation today is the maintenance and restoration of biodiversity, but a broader range of values are also likely to be considered important, including ecological integrity, resilience, historical fidelity (ie the ecosystem appears and functions much as it did in the past), and autonomy of nature. Until recently, the concept of “naturalness” was the guiding principle when making conservation‐related decisions in park and wilderness ecosystems. However, this concept is multifaceted and often means different things to different people, including notions of historical fidelity and autonomy from human influence. Achieving the goal of nature conservation intended for such areas requires a clear articulation of management objectives, which must be geared to the realities of the rapid environmental changes currently underway. We advocate a pluralistic approach that incorporates a suite of guiding principles, including historical fidelity, autonomy of nature, ecological integrity, and resilience, as well as managing with humility. The relative importance of these guiding principles will vary, depending on management goals and ecological conditions.

Frontiers in Ecology and the Environment↗

USGS2008

Characteristics of mangrove swamps managed for mosquito control in eastern Florida, USA

Manipulations of the vegetation and hydrology of wetlands for mosquito control are common worldwide, but these modifications may affect vital ecosystem processes. To control mosquitoes in mangrove swamps in eastern Florida, managers have used rotational impoundment management (RIM) as an alternative to the worldwide practice of mosquito ditching. Levees surround RIM swamps, and water is pumped into the impoundment during the summer, a season when natural swamps have low water levels. In the New World, these mosquito-managed swamps resemble the mixed basin type of mangrove swamp (based on PCA analysis). An assessment was made of RIM, natural (control), and breached-RIM (restored) swamps in eastern Florida to compare their structural complexities, soil development, and resistance to invasion. Regarding structural complexity, dominant species composition differed between these swamps; the red mangrove Rhizophora mangle occurred at a higher relative density in RIM and breached-RIM swamps, and the black mangrove Avicennia germinans had a higher relative density in natural swamps. Tree density and canopy cover were higher and tree height lower in RIM swamps than in natural and breached-RIM swamps. Soil organic matter in RIM swamps was twice that in natural or breached-RIM swamps. RIM swamps had a lower resistance to invasion by the Brazilian pepper tree Schinus terebinthifolius , which is likely attributable to the lower porewater salinity in RIM swamps. These characteristics may reflect differences in important ecosystem processes (primary production, trophic structure, nutrient cycling, decomposition). Comparative assessments of managed wetlands are vital for land managers, so that they can make informed decisions compatible with conservation objectives.

Florida↗

USGS2022

Functional wetland loss drives emerging risks to waterbird migration networks

Migratory waterbirds (i.e., shorebirds, wading birds, and waterfowl) rely on a diffuse continental network of wetland habitats to support annual life cycle needs. Emerging threats of climate and land-use change raise new concerns over the sustainability of these habitat networks as water scarcity triggers cascading ecological effects impacting wetland habitat availability. Here we use important waterbird regions in Oregon and California, United States, as a model system to examine patterns of landscape change impacting wetland habitat networks in western North America. Wetland hydrology and flooded agricultural habitats were monitored monthly from 1988 to 2020 using satellite imagery to quantify the timing and duration of inundation—a key delimiter of habitat niche values associated with waterbird use. Trends were binned by management practice and wetland hydroperiods (semi-permanent, seasonal, and temporary) to identify differences in their climate and land-use change sensitivity. Wetland results were assessed using 33 waterbird species to detect non-linear effects of network change across a diversity of life cycle and habitat needs. Pervasive loss of semi-permanent wetlands was an indicator of systemic functional decline. Shortened hydroperiods caused by excessive drying transitioned semi-permanent wetlands to seasonal and temporary hydrologies—a process that in part counterbalanced concurrent seasonal and temporary wetland losses. Expansion of seasonal and temporary wetlands associated with closed-basin lakes offset wetland declines on other public and private lands, including wildlife refuges. Diving ducks, black terns, and grebes exhibited the most significant risk of habitat decline due to semi-permanent wetland loss that overlapped important migration, breeding, molting, and wintering periods. Shorebirds and dabbling ducks were beneficiaries of stable agricultural practices and top-down processes of functional wetland declines that operated collectively to maintain habitat needs. Outcomes from this work provide a novel perspective of wetland ecosystem change affecting waterbirds and their migration networks. Understanding the complexity of these relationships will become increasingly important as water scarcity continues to restructure the timing and availability of wetland resources.

California, Nevada, Oregon↗

USGS2016

Variability of the carbonate chemistry in a shallow, seagrass-dominated ecosystem: implications for ocean acidification experiments

Open ocean observations have shown that increasing levels of anthropogenically derived atmospheric CO 2 are causing acidification of the world's oceans. Yet little is known about coastal acidification and studies are just beginning to characterise the carbonate chemistry of shallow, nearshore zones where many ecologically and economically important organisms occur. We characterised the carbonate chemistry of seawater within an area dominated by seagrass beds (Saint Joseph Bay, Florida) to determine the extent of variation in pH and p CO 2 over monthly and daily timescales. Distinct diel and seasonal fluctuations were observed at daily and monthly timescales respectively, indicating the influence of photosynthetic and respiratory processes on the local carbonate chemistry. Over the course of a year, the range in monthly values of pH (7.36-8.28), aragonite saturation state (0.65-5.63), and calculated pCO2 (195-2537 μatm) were significant. When sampled on a daily basis the range in pH (7.70-8.06), aragonite saturation state (1.86-3.85), and calculated p CO 2 (379-1019 μatm) also exhibited significant range and indicated variation between timescales. The results of this study have significant implications for the design of ocean acidification experiments where nearshore species are utilised and indicate that coastal species are experiencing far greater fluctuations in carbonate chemistry than previously thought.

Marine and Freshwater Research↗

USGS2015

Population connectivity of deep-sea corals

Identifying the scale of dispersal among habitats has been a challenge in marine ecology for decades (Grantham et al., 2003; Kinlan & Gaines, 2003; Hixon, 2011). Unlike terrestrial habitats in which barriers to dispersal may be obvious (e.g. mountain ranges, rivers), few absolute barriers to dispersal are recognizable in the sea. Additionally, most marine species have complex life cycles in which juveniles are more mobile than adults. As such, the dynamics of populations may involve processes in distant habitats that are coupled by a transport mechanism. Studies of population connectivity try to quantify the transport, or dispersal of individuals, among geographically separated populations. For benthic marine species, such as corals and demersal fishes, colonization of new populations occurs primarily by dispersal of larvae (Figure 1; Shank, 2010). Successful dispersal and recruitment, followed by maturation and reproduction of these new migrants ensures individuals contribute to the gene pool (Hedgecock, 2007). Thus, successful dispersal links and cohesively maintains spatially separated sub-populations. At shorter time scales (10-100s years), connectivity regulates community structure by influencing the genetic composition, diversity and demographic stability of the population, whereas at longer time scales (1000s years), geographic distributions are affected (McClain and Hardy, 2010). Alternatively, populations may become extinct or speciation may occur if connectivity ceases (Cowen et al., 2007). Therefore, the genetic exchange of individuals between populations is fundamental to the short-term resilience and long-term maintenance of the species. However, for the vast majority of marine species, population connectivity remains poorly understood.

NOAA Technical Memorandum↗

USGS2016

Richness, biomass, and nutrient content of a wetland macrophyte community affect soil nitrogen cycling in a diversity-ecosystem functioning experiment

The development of soil nitrogen (N) cycling in created wetlands promotes the maturation of multiple biogeochemical cycles necessary for ecosystem functioning. This development proceeds from gradual changes in soil physicochemical properties and influential characteristics of the plant community, such as competitive behavior, phenology, productivity, and nutrient composition. In the context of a 2-year diversity experiment in freshwater mesocosms (0, 1, 2, 3, or 4 richness levels), we assessed the direct and indirect impacts of three plant community characteristics – species richness, total biomass, and tissue N concentration – on three processes in the soil N cycle – soil net ammonification, net nitrification, and denitrification potentials. Species richness had a positive effect on net ammonification potential (NAP) through higher redox potentials and likely faster microbial respiration. All NAP rates were negative, however, due to immobilization and high rates of ammonium removal. Net nitrification was inhibited at higher species richness without mediation from the measured soil properties. Higher species richness also inhibited denitrification potential through increased redox potential and decreased nitrification. Both lower biomass and/or higher tissue ratios of carbon to nitrogen, characteristics indicative of the two annual plants, were shown to have stimulatory effects on all three soil N processes. The two mediating physicochemical links between the young macrophyte community and microbial N processes were soil redox potential and temperature. Our results suggest that early-successional annual plant communities play an important role in the development of ecosystem N multifunctionality in newly created wetland soils.

Ecological Engineering↗

USGS1999

Processes governing phytoplankton blooms in estuaries. II: The role of horizontal transport

The development and distribution of phytoplankton blooms in estuaries are functions of both local conditions (i.e. the production-loss balance for a water column at a particular spatial location) and large-scale horizontal transport. In this study, the second of a 2-paper series, we use a depth-averaged hydrodynamic-biological model to identify transport-related mechanisms impacting phytoplankton biomass accumulation and distribution on a system level. We chose South San Francisco Bay as a model domain, since its combination of a deep channel surrounded by broad shoals is typical of drowned-river estuaries. Five general mechanisms involving interaction of horizontal transport with variability in local conditions are discussed. Residual (on the order of days to weeks) transport mechanisms affecting bloom development and location include residence time/export, import, and the role of deep channel regions as conduits for mass transport. Interactions occurring on tidal time scales, i.e. on the order of hours) include the phasing of lateral oscillatory tidal flow relative to temporal changes in local net phytoplankton growth rates, as well as lateral sloshing of shoal-derived biomass into deep channel regions during ebb and back into shallow regions during flood tide. Based on these results, we conclude that: (1) while local conditions control whether a bloom is possible, the combination of transport and spatial-temporal variability in local conditions determines if and where a bloom will actually occur; (2) tidal-time-scale physical-biological interactions provide important mechanisms for bloom development and evolution. As a result of both subtidal and tidal-time-scale transport processes, peak biomass may not be observed where local conditions are most favorable to phytoplankton production, and inherently unproductive areas may be regions of high biomass accumulation.

Marine Ecology Progress Series↗

USGS2012

A general theory of multimetric indices and their properties

1. Stewardship of biological and ecological resources requires the ability to make integrative assessments of ecological integrity. One of the emerging methods for making such integrative assessments is multimetric indices (MMIs). These indices synthesize data, often from multiple levels of biological organization, with the goal of deriving a single index that reflects the overall effects of human disturbance. Despite the widespread use of MMIs, there is uncertainty about why this approach can be effective. An understanding of MMIs requires a quantitative theory that illustrates how the properties of candidate metrics relates to MMIs generated from those metrics. 2. We present the initial basis for such a theory by deriving the general mathematical characteristics of MMIs assembled from metrics. We then use the theory to derive quantitative answers to the following questions: Is there an optimal number of metrics to comprise an index? How does covariance among metrics affect the performance of the index derived from those metrics? And what are the criteria to decide whether a given metric will improve the performance of an index? 3. We find that the optimal number of metrics to be included in an index depends on the theoretical distribution of signal of the disturbance gradient contained in each metric. For example, if the rank-ordered parameters of a metric-disturbance regression can be described by a monotonically decreasing function, then an optimum number of metrics exists and can often be derived analytically. We derive the conditions by which adding a given metric can be expected to improve an index. 4. We find that the criterion defining such conditions depends nonlinearly of the signal of the disturbance gradient, the noise (error) of the metric and the correlation of the metric errors. Importantly, we find that correlation among metric errors increases the signal required for the metric to improve the index. 5. The theoretical framework presented in this study provides the basis for understanding the properties of MMIs. It can also be useful throughout the index construction process. Specifically, it can be used to aid understanding of the benefits and limitations of combining metrics into indices; it can inform selection/collection of candidate metrics; and it can be used directly as a decision aid in effective index construction.

Methods in Ecology and Evolution↗