Sampling design trade-offs in occupancy studies with imperfect detection: examples and software.

Researchers have used occupancy, or probability of occupancy, as a response or state variable in a variety of studies (e.g., habitat modeling), and occupancy is increasingly favored by numerous state, federal, and international agencies engaged in monitoring programs. Recent advances in estimation methods have emphasized that reliable inferences can be made from these types of studies if detection and occupancy probabilities are simultaneously estimated. The need for temporal replication at sampled sites to estimate detection probability creates a trade-off between spatial replication (number of sample sites distributed within the area of interest/inference) and temporal replication (number of repeated surveys at each site). Here, we discuss a suite of questions commonly encountered during the design phase of occupancy studies, and we describe software (program GENPRES) developed to allow investigators to easily explore design trade-offs focused on particularities of their study system and sampling limitations. We illustrate the utility of program GENPRES using an amphibian example from Greater Yellowstone National Park, U.S.A.     

Mineral licks: motivational factors for visitation and accompanying disease risk at communal use sites of elk and deer

Free-ranging cervids acquire most of their essential minerals through forage consumption, though occasionally seek other sources to account for seasonal mineral deficiencies. Mineral sources occur as natural geological deposits (i.e., licks) or as anthropogenic mineral supplements. In both scenarios, these sources commonly serve as focal sites for visitation. We monitored 11 licks in Rocky Mountain National Park, north-central Colorado, using trail cameras to quantify daily visitation indices (DVI) and soil consumption indices (SCI) for Rocky Mountain elk (Cervus elaphus) and mule deer (Odocoileus hemionus) during summer 2006 and documented elk, mule deer, and moose (Alces alces) visiting licks. Additionally, soil samples were collected, and mineral concentrations were compared to discern levels that explain rates of visitation. Relationships between response variables; DVI and SCI, and explanatory variables; elevation class, moisture class, period of study, and concentrations of minerals were examined. We found that DVI and SCI were greatest at two wet, low-elevation licks exhibiting relatively high concentrations of manganese and sodium. Because cervids are known to seek Na from soils, we suggest our observed association of Mn with DVI and SCI was a likely consequence of deer and elk seeking supplemental dietary Na. Additionally, highly utilized licks such as these provide an area of concentrated cervid occupation and interaction, thus increasing risk for environmental transmission of infectious pathogens such as chronic wasting disease, which has been shown to be shed in the saliva, urine, and feces of infected cervids.     

Normalisation models for accounting for fat content in stable isotope measurements in salmonid muscle tissue

Stable isotope analysis is increasingly used in ecological studies. Because lipid content influences δ¹³C, lipids should be removed from lipid-rich samples before δ¹³C analysis. To account for differences in δ¹³C arising from differences in lipid content, relationships between lipid content, C:N ratio and Δδ¹³C with lipid removal can be used to normalise lipid content to uniform levels. We investigate these relationships for salmonid muscle and evaluate the suitability of previously published normalisation equations for these fish. Salmonids with a wide range of condition (muscle lipid content = 3–35% of dry weight) were considered. There were no consistent relationships between lipid content or C:N ratio and Δδ¹⁵N. There were linear relationships between C:N ratio and lipid content (L = −16.53 + 6.27 × C:N); C:N ratio and Δδ¹³C (Δδ¹³C = −1.87 + 0.65 × C:N); and lipid content and Δδ¹³C (Δδ¹³C = 0.01 + 0.10 × L), which should be used on salmonid stable isotope studies.     

The protection of wildlife from mortality: hypothesis and results for risk assessment

Wildlife deaths associated with cyanide-bearing tailings dams are a significant environmental issue that has affected the gold mining industries for many years and still characterized by little knowledge about how to measure, monitoring, reduce or eliminate those deaths. The purpose of this paper is statistically to determine: the potential for establishing causal relations between exposure to cyanide (in its most common species relevant to tailings) and response (measured by death counts), to develop a protocol of data analysis, the understanding of the significance of data gaps, and the effect of likely risk management interventions to achieve the goals of the International Cyanide Management Code (ICMC); [ICMC The International Cyanide Management Institute. International cyanide management code, the international cyanide management institute 2005, www.cyanidecode.org.]. However, operator's certification under the ICMC is difficult because of the limited data and potentially serious under-estimation of the death counts. This is due to observational skill and monitoring frequency, the small size of the carcasses, large extent of tailings facilities, carcasses loss by; entombment in tailings, sink, or taken by scavenging wildlife. This (1st order or bounding) assessment results focus on bird-deaths, which appear to be most frequent at sites where elevated cyanide concentrations are found. Those results indicate that the empirical causal associations we generate support the hypotheses that: This paper also develops the basis for a complete risk assessment study to be based on additional data gathering activities and detailed statistical analyses. These two activities, combined with a risk management plan also being developed, will provide a tool for compliance with the ICMC.     

Improving occupancy estimation when two types of observational error occur: non-detection and species misidentification

Efforts to draw inferences about species occurrence frequently account for false negatives, the common situation when individuals of a species are not detected even when a site is occupied. However, recent studies suggest the need to also deal with false positives, which occur when species are misidentified so that a species is recorded as detected when a site is unoccupied. Bias in estimators of occupancy, colonization, and extinction can be severe when false positives occur. Accordingly, we propose models that simultaneously account for both types of error. Our approach can be used to improve estimates of occupancy for study designs where a subset of detections is of a type or method for which false positives can be assumed to not occur. We illustrate properties of the estimators with simulations and data for three species of frogs. We show that models that account for possible misidentification have greater support (lower AIC for two species) and can yield substantially different occupancy estimates than those that do not. When the potential for misidentification exists, researchers should consider analytical techniques that can account for this source of error, such as those presented here.     

Use of the superpopulation approach to estimate breeding population size: an example in asynchronously breeding birds

Many populations of animals are fluid in both space and time, making estimation of numbers difficult. Much attention has been devoted to estimation of bias in detection of animals that are present at the time of survey. However, an equally important problem is estimation of population size when all animals are not present on all survey occasions. Here, we showcase use of the superpopulation approach to capture-recapture modeling for estimating populations where group membership is asynchronous, and where considerable overlap in group membership among sampling occasions may occur. We estimate total population size of long-legged wading bird (Great Egret and White Ibis) breeding colonies from aerial observations of individually identifiable nests at various times in the nesting season. Initiation and termination of nests were analogous to entry and departure from a population. Estimates using the superpopulation approach were 47-382% larger than peak aerial counts of the same colonies. Our results indicate that the use of the superpopulation approach to model nesting asynchrony provides a considerably less biased and more efficient estimate of nesting activity than traditional methods. We suggest that this approach may also be used to derive population estimates in a variety of situations where group membership is fluid.     

Factors determining the hatching success of Antarctic krill <Emphasis Type="Italic">Euphausia superba</Emphasis> embryo: lipid and fatty acid composition

The present study addresses the effect of maternal diet on hatching success and condition of embryos and larvae of Antarctic krill Euphausia superba. Lipid and fatty acid content and composition were determined in field and laboratory samples. Developmental stages analyzed in embryos included: multiple-cell, gastrula, and limb-bud stages. Larval stages analyzed included: nauplius I, nauplius II, and metanauplius. Laboratory-reared embryos were spawned by gravid females incubated under three feeding groups: (1) phytoplankton mixture, (2) phytoplankton mixture and minced clam, and (3) phytoplankton mixture, minced clam, and commercial larval food. Hatching success was highest in group 3 (100%), lowest in group 1 (0%), and highly variable in field samples (0–48%). Lipid decreased slightly in embryos during embryonic development, while large decreases in lipid were found during nauplius development. High levels of 18:2(n-6), 20:4(n-6), and 22:6(n-3) observed with group 3 samples coincided with high hatching success in krill embryos. The ratio of 22:6(n-3)/20:5(n-3) also correlated to hatching success of embryos. The fatty acid profile of embryos in group 3 was similar to that of the field-collected embryos, reflecting the contribution of the commercial larval food in the maternal diet. In our study, the maternal diet was found to influence the fatty acid composition of embryos and in turn affects the hatching success of krill. Specific polyunsaturated fatty acids appeared to play important roles in embryogenesis in krill.     

Biochemical composition of Nyctiphanes australis and its possible use as an aquaculture feed source: Lipids,pigments and fluoride content

Nyctiphanes australis contained, on a dry weight basis, an average of 52% crude protein and 5.0 to 9.5% lipid. The fatty acid profile of N. australis was markedly unsaturated, with a mean total 3 fatty acid content of 48.6±2.4% of total fatty acids. N. australis contained high levels of the essential long-chain polyunsaturated fatty acids eicosapentaenoic (EPA, 20:53) and docosahexaencic (DHA, 22:63), ranging from 16.6 to 36.5% and 11.1 to 24.8%, respectively. The concentration of total carotenoids ranged from 137 to 302 g g^–1 dry wt, with no significant differences in concentrations found with season or life stage. The carotenoids were comprised of 79.5% astaxanthin and 20.5% canthaxanthin. The lipid and pigment compositions of N. australis suggest that the species could serve as a suitable feed source for cultured salmonids. Like other euphausiids, N. australis contained high levels of fluoride, with a seasonal range between 277 and 3507 g g^–1 dry wt. The high fluoride levels found in N. australis would not detract from its potential as a feed source for salmonids because ingested fluoride is largely absorbed by the skeleton.     

Grazing of phytoplankton by copepods in eastern Antarctic coastal waters

Chlorophyll a, primary productivity and grazing by copepods on phytoplankton were measured in the upper water column during the summer of 1994/1995 at a coastal site near Davis Station, East Antarctica. Chlorophyll a was at a maximum in mid-December, then dropped markedly as the coastal fast ice melted and broke‐out. Phytoplankton biomass increased again from mid‐ to late‐February. Copepods accounted for at least 65% of zooplankton biomass in the water column before sea ice break‐out, whereas larval polychaetes and ctenophores dominated after ice break‐out. Oncaeacurvata was the numerically dominant species throughout the study. The highest grazing rate (8.7 mg C␣m⁻³␣d⁻¹) was recorded on 21 December when O.␣curvata accounted for 64% of the total. Grazing had decreased markedly by 28 December (0.9 mg C m⁻³ d⁻¹); again O. curvata accounted for over 50% of the total ingested. Copepod grazing increased after ice break-out until the last experiment on 20 February (⋍5 mg C␣m⁻³␣d⁻¹). The main species responsible for grazing during this period were O. curvata, Oithonasimilis, Calanoidesacutus and unidentified copepod nauplii. It was estimated that copepods removed between 1 and 5% of primary productivity. Received: 11 October 1996 / Accepted: 22 October 1996