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Applied Geochemistry Special Issue on Environmental geochemistry of modern mining

Environmental geochemistry is an integral part of the mine-life cycle, particularly for modern mining. The critical importance of environmental geochemistry begins with pre-mining baseline characterization and the assessment of environmental risks related to mining, continues through active mining especially in water and waste management practices, and culminates in mine closure. The enhanced significance of environmental geochemistry to modern mining has arisen from an increased knowledge of the impacts that historical and active mining can have on the environment, and from new regulations meant to guard against these impacts. New regulations are commonly motivated by advances in the scientific understanding of the environmental impacts of past mining. The impacts can be physical, chemical, and biological in nature. The physical challenges typically fall within the purview of engineers, whereas the chemical and biological challenges typically require a multidisciplinary array of expertise including geologists, geochemists, hydrologists, microbiologists, and biologists. The modern mine-permitting process throughout most of the world now requires that potential risks be assessed prior to the start of mining. The strategies for this risk assessment include a thorough characterization of pre-mining baseline conditions and the identification of risks specifically related to the manner in which the ore will be mined and processed, how water and waste products will be managed, and what the final configuration of the post-mining landscape will be. In the Fall 2010, the Society of Economic Geologists held a short course in conjunction with the annual meeting of the Geological Society of America in Denver, Colorado (USA) to examine the environmental geochemistry of modern mining. The intent was to focus on issues that are pertinent to current and future mines, as opposed to abandoned mines, which have been the focus of numerous previous short courses. The geochemical challenges of current and future mines share similarities with abandoned mines, but differences also exist. Mining and ore processing techniques have changed; the environmental footprint of waste materials has changed; environmental protection has become a more integral part of the mine planning process; and most historical mining was done with limited regard for the environment. The 17 papers in this special issue evolved from the Society of Economic Geologists’ short course. The relevant geochemical processes encompass the source, transport, and fate of contaminants related to the life cycle of a mine. Contaminants include metals and other inorganic species derived from geologic sources such as ore and solid mine waste, and substances brought to the site for ore processing, such as cyanide to leach gold. Factors, such as mine-waste mineralogy, hydrologic setting, mine-drainage chemistry, and microbial activity, that affect the hydrochemical risks from mining are reviewed by Nordstrom et al. In another paper, Nordstrom discusses baseline characterization at mine sites in a regulatory framework, and emphasizes the influence of mineral deposits in producing naturally elevated concentrations of many trace elements in surface water and groundwater. Surface water quality in mineralized watersheds is influenced by a number of processes that act on daily (diel) cycles and can produce dramatic variations in trace element concentrations as described by Gammons et al. Pre-mining baseline characterization studies should strive to capture the magnitude of these diel variations. Desbarats et al., using a case study of mine drainage from a gold mine, illustrate how elements that commonly occur as negatively charged species (anions) in solution, such as arsenic as arsenate, behave in an opposite fashion than most metals, which occur as positively charged species (cations). Significant improvement in the understanding of factors that influence the toxicity of metals to aquatic organisms in surface water has highlighted the importance of aqueous chemistry, particularly dissolved organic carbon, as described by Smith et al. Stream sediment contamination is another important pathway for affecting aquatic organisms, as reviewed by Besser et al. Understanding and predicting environmental consequences from mining begins with knowing the mineralogy and mineral reactivity of the ore, the wastes, and of secondary minerals formed later. Jamieson et al. review the importance of mineralogical studies in mine planning and remediation. A number of types of site-specific studies are needed to identify environmental risks related to individual mines. Lapakko reviews the general framework of mine waste characterization studies that are integral to the mine planning process. Hageman et al. present a comparative study of several static tests commonly used to characterize mine waste. The mining and ore processing practices employed at a specific mine site will vary on the basis of the commodities being targeted, the geology of the deposit, the geometry of the deposit, and the mining and ore processing methods used. Thus, these factors, in addition to the waste management practices used, can result in a variety of end-member mine waste features, each of which has its own set of challenges. Open pit mines and underground mines require waste rock to be removed to access ore. Waste rock presents unique problems because the rock is commonly mineralized at sub-economic grades and has not been processed to remove potentially problematic minerals, such as pyrite. Amos et al. examine the salient aspects of the geochemistry of waste rock. Mill tailings – the waste material after ore minerals have been removed – are a volumetrically important solid waste at many mine sites. Their fine grain size and the options for their management make their behavior in the environment distinct from that of waste rock. Lindsay et al. describe some of these differences through three case-study examples. Subaqueous disposal of tailings is another option described by Moncur et al. Cyanide leaching for gold extraction is a common method throughout the world. Johnson describes environmental aspects of cyanidation. Uranium mining presents unique environmental challenges, particularly since in-situ recovery has seen widespread use. Campbell et al. review the environmental geochemistry of uranium mining and current research on bioremediation. Ore concentrates from many types of metal mining undergo a pyrometallurgical technique known as smelting to extract the metal. Slag is the result of smelting, and it may be an environmental liability or a valuable byproduct, as described by Piatak et al. Finally, the open pits that result from surface mining commonly reach below the water table. At the end of mining, these pits may fill to form lakes that become part of the legacy of the mine. Castendyk et al., in two papers, review theoretical aspects of the environmental limnology of pit lakes. They also describe approaches that have been used to model pit lake water balance, wall-rock contributions to pit lake chemistry, pit lake water quality, and limnological processes, such as vertical mixing, through the use of three case studies.

Applied Geochemistry

Development of aquaculture protocols and gonadal differentiation of green sunfish (Lepomis cyanellus)

We provide detailed rearing methods and describe green sunfish ( Lepomis cyanellus ) gonadal development and histological differentiation for both sexes. Developing in-depth aquaculture protocols and describing the gonadal differentiation of green sunfish could facilitate strategies to control nuisance populations, enhance stocking programs, and provide information for this species' use in bioassay trials or toxicology studies. Our methods resulted in consistent year-round production of green sunfish and allowed us to identify the timing of their gonadal differentiation through histological assessment. Our spawning methods provided year-round volitional spawns from green sunfish broodstock. Our rearing methods involved weaning larval green sunfish off live nauplii and onto only artificial diets by 37 days post-hatch (dph). Most of the offspring generation reached sexual maturity by 213 dph. Green sunfish are gonochoristic, with testes and ovaries differentiating directly from undifferentiated gonads. Ovaries begin to differentiate by 39 dph and testes begin to differentiate by 69 dph. This information can provide biologists consistent means to produce this Centrachid and understand their gonadal development.

Aquaculture

A decision-analytic approach to the optimal allocation of resources for endangered species consultation

The resources available to support conservation work, whether time or money, are limited. Decision makers need methods to help them identify the optimal allocation of limited resources to meet conservation goals, and decision analysis is uniquely suited to assist with the development of such methods. In recent years, a number of case studies have been described that examine optimal conservation decisions under fiscal constraints; here we develop methods to look at other types of constraints, including limited staff and regulatory deadlines. In the US, Section Seven consultation, an important component of protection under the federal Endangered Species Act, requires that federal agencies overseeing projects consult with federal biologists to avoid jeopardizing species. A benefit of consultation is negotiation of project modifications that lessen impacts on species, so staff time allocated to consultation supports conservation. However, some offices have experienced declining staff, potentially reducing the efficacy of consultation. This is true of the US Fish and Wildlife Service's Washington Fish and Wildlife Office (WFWO) and its consultation work on federally-threatened bull trout (Salvelinus confluentus). To improve effectiveness, WFWO managers needed a tool to help allocate this work to maximize conservation benefits. We used a decision-analytic approach to score projects based on the value of staff time investment, and then identified an optimal decision rule for how scored projects would be allocated across bins, where projects in different bins received different time investments. We found that, given current staff, the optimal decision rule placed 80% of informal consultations (those where expected effects are beneficial, insignificant, or discountable) in a short bin where they would be completed without negotiating changes. The remaining 20% would be placed in a long bin, warranting an investment of seven days, including time for negotiation. For formal consultations (those where expected effects are significant), 82% of projects would be placed in a long bin, with an average time investment of 15. days. The WFWO is using this decision-support tool to help allocate staff time. Because workload allocation decisions are iterative, we describe a monitoring plan designed to increase the tool's efficacy over time. This work has general application beyond Section Seven consultation, in that it provides a framework for efficient investment of staff time in conservation when such time is limited and when regulatory deadlines prevent an unconstrained approach. ?? 2010.

Biological Conservation

Diel biogeochemical processes in terrestrial waters

Many biogeochemical processes in rivers and lakes respond to the solar photocycle and produce persistent patterns of measureable phenomena that exhibit a day–night, or 24-h, cycle. Despite a large body of recent literature, the mechanisms responsible for these diel fluctuations are widely debated, with a growing consensus that combinations of physical, chemical, and biological processes are involved. These processes include streamflow variation, photosynthesis and respiration, plant assimilation, and reactions involving photochemistry, adsorption and desorption, and mineral precipitation and dissolution. Diel changes in streamflow and water properties such as temperature, pH, and dissolved oxygen concentration have been widely recognized, and recently, diel studies have focused more widely by considering other constituents such as dissolved and particulate trace metals, metalloids, rare earth elements, mercury, organic matter, dissolved inorganic carbon (DIC), and nutrients. The details of many diel processes are being studied using stable isotopes, which also can exhibit diel cycles in response to microbial metabolism, photosynthesis and respiration, or changes in phase, speciation, or redox state. In addition, secondary effects that diel cycles might have, for example, on biota or in the hyporheic zone are beginning to be considered. This special issue is composed primarily of papers presented at the topical session “Diurnal Biogeochemical Processes in Rivers, Lakes, and Shallow Groundwater” held at the annual meeting of the Geological Society of America in October 2009 in Portland, Oregon. This session was organized because many of the growing number of diel studies have addressed just a small part of the full range of diel cycling phenomena found in rivers and lakes. This limited focus is understandable because (1) fundamental aspects of many diel processes are poorly understood and require detailed study, (2) the interests and expertise of individual scientists typically do not encompass the wide diversity and range of processes that produce diel cycles, and (3) the logistics of making field measurements for 24-h periods has limited recognition and understanding of these important cycles. Thus, the topical session brought together hydrologists, biologists, geochemists, and ecologists to discuss field studies, laboratory experiments, theoretical modeling, and measurement techniques related to diel cycling. Hopefully with the cross-disciplinary synergy developed at the session as well as by this special issue, a more comprehensive understanding of the interrelationships between the diel processes will be developed. Needless to say, understanding diel processes is critical for regulatory agencies and the greater scientific community. And perhaps more importantly, expanded knowledge of biogeochemical cycling may lead to better predictions of how aquatic ecosystems might react to changing conditions of contaminant loading, eutrophication, climate change, drought, industrialization, development, and other variables.

Chemical Geology

A call to insect scientists: Challenges and opportunities of managing insect communities under climate change

As climate change moves insect systems into uncharted territory, more knowledge about insect dynamics and the factors that drive them could enable us to better manage and conserve insect communities. Climate change may also require us revisit insect management goals and strategies and lead to a new kind of scientific engagement in management decision-making. Here we make five key points about the role of insect science in aiding and crafting management decisions, and we illustrate those points with the monarch butterfly and the Karner blue butterfly, two species undergoing considerable change and facing new management dilemmas. Insect biology has a strong history of engagement in applied problems, and as the impacts of climate change increase, a reimagined ethic of entomology in service of broader society may emerge. We hope to motivate insect biologists to contribute time and effort toward solving the challenges of climate change.

Current Opinion in Insect Science

Transient population dynamics: Relations to life history and initial population state

Most environments are variable and disturbances (e.g., hurricanes, fires) can lead to substantial changes in a population's state (i.e., age, stage, or size distribution). In these situations, the long-term (i.e., asymptotic) measure of population growth rate (??1) may inaccurately represent population growth in the short-term. Thus, we calculated the short-term (i.e., transient) population growth rate and its sensitivity to changes in the life-cycle parameters for three bird and three mammal species with widely varying life histories. Further, we performed these calculations for initial population states that spanned the entire range of possibilities. Variation in a population's initial net reproductive value largely explained the variation in transient growth rates and their sensitivities to changes in life-cycle parameters (all AICc ??? 6.67 units better than the null model, all R2 ??? 0.55). Additionally, the transient fertility and adult survival sensitivities tended to increase with the initial net reproductive value of the population, whereas the sub-adult survival sensitivity decreased. Transient population dynamics of long-lived, slow reproducing species were more variable and more different than asymptotic dynamics than they were for short-lived, fast reproducing species. Because ??1 can be a biased estimate of the actual growth rate in the short-term (e.g., 19% difference), conservation and wildlife biologists should consider transient dynamics when developing management plans that could affect a population's state, or whenever population state could be unstable.

Ecological Modelling

Simulating detection-censored movement records for home range analysis planning

Home range estimation is an important analytical method; yet best practices for addressing the effects of spatial variation in detection probability on home range estimates remains elusive. We introduce the R package “DiagnoseHR,” simulation tools for assessing how variation in detection probability arising from landscape, animal behavior, and methodological processes affects home range inference. We demonstrate the utility of simulation methods for home range analysis planning by comparing bias arising from three home range estimation methods under multiple detection scenarios. We simulated correlated random walks in three landscapes that varied in detection probability and constructed home ranges from locations filtered through a range of sampling protocols. Home range estimates were less biased by reduced detection probability when sampling effort was increased, but the effects of sampling day distribution were marginal. Like others, we found that kernel density estimates were the least affected by variation in detection probability, while minimum convex polygons were most affected. Our results illustrate the value of quantifying uncertainty in home range estimates and suggest that field biologists working in conditions with low-detection may wish to weight sample-size greater than concerns about temporal autocorrelation when designing sampling protocols.

Article

Fisheries dependent and independent data inform a capture technique for an emerging invasive fish species in the mainstem Mississippi River; Black Carp Mylopharyngodon piceus

Black Carp Mylopharyngodon piceus were imported into the United States in the 1970s and 1980s for use in aquaculture; escape occurred and reported wild captures increased. Lacking species-specific capture methods, we assessed fisheries dependent incidental Black Carp catches for a common method, hoop nets, by kernel density analysis to identify an area of increased reporting and compare frequency of reports for water temperature, river stage, and capture date to identify seasonality. We then used fisheries independent effort to identify co-occurrence of species via non-metric multi-dimensional scaling and fit Black Carp catch and environmental covariates by generalized linear models to assess site-specific environmental covariates facilitating capture. The best approximating distribution was refitted for predictions and inference. The greatest density of fisheries dependent hoop net captures (39 %) was near the confluence of the Missouri and Mississippi rivers, primarily from July-September. Captures were characterized by median water temperature 26.7°C, river stage 5.02 m, and 223 day-of-year (DOY; mid-August). Ordination of fisheries independent catch identified similarity in environmental covariates of Smallmouth Buffalo Ictiobus bubalus and Black Carp. The probability of capturing ≥ 1 Black Carp increased with DOY, decreased with increasing current velocity, and increased with depth. Most captures occurred in outside bends (87 %) or side channels (12 %). Probability of Black Carp capture was low but increased in summer and early fall when stage is lower, facilitating reduced current velocity and access to deeper areas. Results may be validated beyond this river segment to test if site-specific hydrology or habitat characteristics facilitated increased commercial and biologist capture and for replication.

Illinois, Missouri

Evaluation of anal fin spines, otoliths, and scales for estimating age and back-calculated lengths of yellow perch in southern Green Bay

Southern Green Bay supports important fisheries for yellow perch Perca flavescens and valid estimates of age structure and growth are critical to effective management. Anal fin spines and scales are used by the Wisconsin Department of Natural Resources for age estimation, but these structures may provide lower precision and accuracy than otoliths. The primary objective of our assessment was to determine if age estimates, among-reader precision, and mean back-calculated total lengths (TLs) at age differed among scales, anal fin spines, and otoliths. Ages estimated from anal fin spines were more precise than scale ages, were as precise as otolith-based ages, and generally agreed with consensus ages estimated from sectioned otoliths. Relationships between TL and radii of calcified structures were linear for scales, anal spines, and otoliths along two different transects. Mean back-calculated TLs were generally similar between intercept-corrected direct proportion (ICDP) and linear regression (LR) models, but otolith-based direct proportion models (no intercept correction) generally provided higher back-calculated mean TLs at ages 1 and 2 than ICDP and LR models. Mean back-calculated TLs at age estimated from whole otoliths were higher than estimates for other structures; but differences among anal fin spines, scales, and sectioned otoliths were <10 mm. Our results suggest biologists have little to gain by switching to otoliths when assessing age structure and growth for this fast-growing yellow perch population with relatively few fish ≥age 6, but additional analyses are warranted for slower-growing perch populations in the Great Lakes where older fish are more common.

Wisconsin

Managing native and non-native sea lamprey ( Petromyzon marinus ) through anthropogenic change: A prospective assessment of key threats and uncertainties

Sea lamprey ( Petromyzon marinus ) is a species of conservation concern in their native range of the Atlantic coasts of Europe (Near Threatened to Critically Endangered) and North America (Secure to Critically Imperiled), and an invasive species of great economic and ecological concern in the Laurentian Great Lakes. Despite differences in life history strategy (anadromous natives vs adfluvial non-natives), the biology of sea lamprey is sufficiently similar to expect comparable responses to large-scale environmental change. We take a prospective look at the future (50 to 100 years) of sea lamprey management in an era of considerable environmental disturbance, and consider biological responses, management actions, and the future status of populations across the native and non-native ranges. Based on facilitated discussion by a diverse group of international experts, two major but poorly characterized classes of threats to sea lamprey were identified: climate change and socio-political issues. We discuss how climate induced changes affect growth, bioenergetics, and phenology of sea lamprey, and associated effects on control tactics (pesticides and barriers) and conservation. We consider tensions surrounding improving connectivity in the Great Lakes while controlling invasive sea lamprey, and discuss supplements and alternatives to pesticides and their wider effect, as well as the effects of new invasive species. To prevent the extirpation of native sea lamprey populations, or the re-expansion of non-native populations, we conclude with a call for new and ongoing dialogue and collaboration among all sea lamprey biologists and managers across the native and non-native range.

Journal of Great Lakes Research

Physically modeling operative temperatures and evaporation rates in amphibians

(1) We designed a physical model that simulates the thermal and evaporative properties of live Western toads ( Bufo boreas ). (2) In controlled tests, the model tracked the body temperature of live toads with an average error of 0.3&plusmn;0.03 &deg;C (test range=4&ndash;30 &deg;C). (3) It estimated the evaporative water loss of live toads with an average error of 0.35&ndash;0.65 g/h, or about 14% (test range=0.7&ndash;9 g/h). (4) Data collected with this physical model should provide an effective way for biologists to better understand habitat selection in toads and other amphibians.

Journal of Thermal Biology

Research is needed to inform environmental management of hydrothermally inactive and extinct polymetallic sulfide (PMS) deposits

Polymetallic sulfide (PMS) deposits produced at hydrothermal vents in the deep sea are of potential interest to miners. Hydrothermally active sulfide ecosystems are valued for the extraordinary chemosynthetic communities that they support. Many countries, including Canada, Portugal, and the United States, protect vent ecosystems in their Exclusive Economic Zones. When hydrothermal activity ceases temporarily (dormancy) or permanently (extinction), the habitat and associated ecosystem change dramatically. Until recently, so-called “inactive sulfide” habitats, either dormant or extinct, received little attention from biologists. However, the need for environmental management of deep-sea mining places new imperatives for building scientific understanding of the structure and function of inactive PMS deposits. This paper calls for actions of the scientific community and the emergent seabed mining industry to i) undertake fundamental ecological descriptions and study of ecosystem functions and services associated with hydrothermally inactive PMS deposits, ii) evaluate potential environmental risks to ecosystems of inactive PMS deposits through research, and iii) identify environmental management needs that may enable mining of inactive PMS deposits. Mining of some extinct PMS deposits may have reduced environmental risk compared to other seabed mining activities, but this must be validated through scientific research on a case-by-case basis.

Marine Policy

Hawai‘i forest review: Synthesizing the ecology, evolution, and conservation of a model system

As the most remote archipelago in the world, the Hawaiian Islands are home to a highly endemic and disharmonic biota that has fascinated biologists for centuries. Forests are the dominant terrestrial biome in Hawai‘i, spanning complex, heterogeneous climates across substrates that vary tremendously in age, soil structure, and nutrient availability. Species richness is low in Hawaiian forests compared to other tropical forests, as a consequence of dispersal limitation from continents and adaptive radiations in only some lineages, and forests are dominated by the widespread Metrosideros species complex. Low species richness provides a relatively tractable model system for studies of community assembly, local adaptation, and species interactions. Moreover, Hawaiian forests provide insights into predicted patterns of evolution on islands, revealing that while some evidence supports “island syndromes,” there are exceptions to them all. For example, Hawaiian plants are not as a whole less defended against herbivores, less dispersible, more conservative in resource use, or more slow-growing than their continental relatives. Clearly, more work is needed to understand the drivers, sources, and constraints on phenotypic variation among Hawaiian species, including both widespread and rare species, and to understand the role of this variation for ecological and evolutionary processes, which will further contribute to conservation of this unique biota. Today, Hawaiian forests are among the most threatened globally. Resource management failures – the proliferation of non-native species in particular – have led to devastating declines in native taxa and resulted in dominance by novel species assemblages. Conservation and restoration of Hawaiian forests now rely on managing threats including climate change, ongoing species introductions, novel pathogens, lost mutualists, and altered ecosystem dynamics through the use of diverse tools and strategies grounded in basic ecological, evolutionary, and biocultural principles. The future of Hawaiian forests thus depends on the synthesis of ecological and evolutionary research, which will continue to inform future conservation and restoration practices.

Hawaii

Practical application of disease resistance: A brook trout fishery selected for resistance to furunculosis

Selection is unwittingly influenced by nuances of fish culturists and adaptation of fish to intensive culture within artificial environments. When pathogens are present, susceptible individuals may be selectively eliminated from a population, accounting for inter-specific and intra-specific differences in susceptibility to disease. Biologists often intensify such selection to enhance resistance. Particularly important to this discourse is the selective breeding program initiated by the New York State Department of Environmental Conservation (Rome, NY, USA) to produce brown trout ( Salmo salar ) and brook trout ( Salvelinus fontinalis ) that are resistant to Aeromonas salmonicida . This program, specifically as it relates to brook trout, is reviewed throughout the current manuscript. In addition, we present a comparison between the performance of the Rome strain of brook trout to that of the Owhi strain of brook trout during a 17-month production cycle at the Ed Weed Fish Culture Station (Grand Isle, VT, USA) and after stocking into Vermont waters. The Owhi strain is used in recreational fisheries because it has good post-stocking survival, but these fish are sensitive to furunculosis. Our data indicated that the Rome strain had a food conversion rate of 1.3 that was slightly less than the 1.1 conversion rate of the Owhi brook trout. The growth rate measured as Monthly Temperature Units per inch (MTU/in.) among Rome brook trout (24.9 MTU/in.) was better than the Owhi brook trout (29.5 MTU/in.). Both the average length (23.6 cm) and weight (159.7 g) of individual Rome brook trout were superior to those of the Owhi strain (20.4 cm and 78.2 g, respectively). Just prior to stocking, survival within the hatchery was 84% among the Rome trout, but only 51% among the Owhi brook trout and mortality was attributed to a persistent epizootic of furunculosis. Microbiological assays indicated that the prevalence of A. salmonicida in dermal mucus attained equivalent levels within both strains of fish at different phases of the production cycle. The level of systemic infection, however, was regulated to a much greater extent by the Rome strain of brook trout throughout production. Our results indicated that the Rome brook trout strain satisfies management objectives for establishing an effective recreational brook trout fishery. Use of this strain also reduces management issues that complicate production when A. salmonicida is enzootic.

Vermont

Modeling individual animal histories with multistate capture–recapture models

Many fields of science begin with a phase of exploration and description, followed by investigations of the processes that account for observed patterns. The science of ecology is no exception, and recent decades have seen a focus on understanding key processes underlying the dynamics of ecological systems. In population ecology, emphasis has shifted from the state variable of population size to the demographic processes responsible for changes in this state variable: birth, death, immigration, and emigration. In evolutionary ecology, some of these same demographic processes, rates of birth and death, are also the determinants of fitness. In animal population ecology, the estimation of state variables and their associated vital rates is especially problematic because of the difficulties in sampling such populations and detecting individual animals. Indeed, early capture–recapture models were developed for the purpose of estimating population size, given the reality that all animals are not caught or detected at any sampling occasion. More recently, capture–recapture models for open populations were developed to draw inferences about survival in the face of these same sampling problems. The focus of this paper is on multi‐state mark–recapture models (MSMR), which first appeared in the 1970s but have undergone substantial development in the last 15 years. These models were developed to deal explicitly with biological variation, in that animals in different “states” (classes defined by location, physiology, behavior, reproductive status, etc.) may have different probabilities of survival and detection. Animal transitions between states are also stochastic and themselves of interest. These general models have proven to be extremely useful and provide a way of thinking about a remarkably wide range of important ecological processes. These methods are now at a stage of refinement and sophistication where they can readily be used by biologists to tackle a wide range of important issues in ecology. In this paper, we draw together information on the state of the art in multistate mark–recapture methods, explaining the models and illustrating their use. We provide a modeling philosophy and a series of general principles on how to conduct analyses. We cover key issues and features, and we anticipate the ways in which we expect the models to develop in the years ahead.

Advances in Ecological Research

Information technology challenges of biodiversity and ecosystems informatics

Computer scientists, biologists, and natural resource managers recently met to examine the prospects for advancing computer science and information technology research by focusing on the complex and often-unique challenges found in the biodiversity and ecosystem domain. The workshop and its final report reveal that the biodiversity and ecosystem sciences are fundamentally information sciences and often address problems having distinctive attributes of scale and socio-technical complexity. The paper provides an overview of the emerging field of biodiversity and ecosystem informatics and demonstrates how the demands of biodiversity and ecosystem research can advance our understanding and use of information technologies.

Information Systems

Responses to in vitro and in vivo immunisations with Aeromonas salmonicida O antigen bacterins in rainbow trout (Oncorhynchus mykiss)

Immunological assays were developed to test for the effects of immunisation with Aeromonas salmonicida O antigen bacterin in rainbow trout ( Oncorhynchus mykiss ) in vitro and in vivo . Trout spleen sections were immunised in vitro by incubation in media containing 100, 10, and 1 μ g ml −1 of the A. salmonicida O antigen. After 10 days at 15°C, the individual sections were minced and cell suspensions assayed for the effects of the bacterin on non-specific and specific immune responses. Assays of the cell suspensions showed that the neutrophil oxidative activity, phagocytic capabilities, numbers of plaque-forming cells (PFC) and circulating antibody titres all increased in proportion to the bacterin dosage. Trout immunised in vivo with 100 μ g by injection and by 100 μ g ml −1 bath with the O antigen, showed similar responses to spleen sections immunised in vitro . The appearance of non-specific PFC against unlabelled sheep red blood cells was highest in spleens immunised in vitro and in the fish immunised by injection; non-specific PFC rarely occurred in O antigen bathed fish and in control fish. The development of these assays may enable biologists to follow the effects on the non-specific defence mechanisms and the specific immune response in cultivated fish populations after, immunisation with A. salmonicida bacterins and thus aid in the development of protective vaccination against furunculosis.

Fish and Shellfish Immunology

Analysis options for estimating status and trends in long-term monitoring

This chapter describes methods for estimating long-term trends in ecological parameters. Other chapters in this volume discuss more advanced methods for analyzing monitoring data, but these methods may be relatively inaccessible to some readers. Therefore, this chapter provides an introduction to trend analysis for managers and biologists while also discussing general issues relevant to trend assessment in any long-term monitoring program. For simplicity, we focus on temporal trends in population size across years. We refer to the survey results for each year as the “annual means” (e.g. mean per transect, per plot, per time period). The methods apply with little or no modification, however, to formal estimates of population size, other temporal units (e.g. a month), to spatial or other dimensions such as elevation or a north–south gradient, and to other quantities such as chemical or geological parameters. The chapter primarily discusses methods for estimating population-wide parameters rather than studying variation in trend within the population, which can be examined using methods presented in other chapters (e.g. Chapters 7, 12, 20). We begin by reviewing key concepts related to trend analysis. We then describe how to evaluate potential bias in trend estimates. An overview of the statistical models used to quantify trends is then presented. We conclude by showing ways to estimate trends using simple methods that can be implemented with spreadsheets.

Book chapter