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.     

Scale-dependent response diversity of seabirds to prey in the North Sea

Functional response diversity is defined as the diversity of responses to environmental change among species that contribute to the same ecosystem function. Because different ecological processes dominate on different spatial and temporal scales, response diversity is likely to be scale dependent. Using three extensive data sets on seabirds, pelagic fish, and zooplankton, we investigate the strength and diversity in the response of seabirds to prey in the North Sea over three scales of ecological organization. Two-stage analyses were used to partition the variance in the abundance of predators and prey among the different scales of investigation: variation from year to year, variation among habitats, and variation on the local patch scale. On the year-to-year scale, we found a strong and synchronous response of seabirds to the abundance of prey, resulting in low response diversity. Conversely, as different seabird species were found in habitats dominated by different prey species, we found a high diversity in the response of seabirds to prey on the habitat scale. Finally, on the local patch scale, seabirds were organized in multispecies patches. These patches were weakly associated with patches of prey, resulting in a weak response strength and a low response diversity. We suggest that ecological similarities among seabird species resulted in low response diversity on the year-to-year scale. On the habitat scale, we suggest that high response diversity was due to interspecific competition and niche segregation among seabird species. On the local patch scale, we suggest that facilitation with respect to the detection and accessibility of prey patches resulted in overlapping distribution of seabirds but weak associations with prey. The observed scale dependencies in response strength and diversity have implications for how the seabird community will respond to different environmental disturbances.     

Quantifying the importance of regional and local filters for community trait structure in tropical and temperate zones

The influence of regional and local processes on community structure is a major focus of ecology. Classically, ecologists have used local-regional richness regressions to evaluate the role of local and regional processes in determining community structure, an approach that has numerous flaws. Here, we implemented a novel trait-based approach that treats local and regional influences as a continuum, rather than a dichotomy. Using hylid frogs (Hylidae), we compared trait dispersion among members of local species assemblages to the trait dispersion in the regional assemblage from which they were drawn. Similarly, we compared trait dispersion in the regional assemblages to dispersion in the continental species pool. We estimated the contributions of local and regional filters, and we compared their strength in temperate and tropical zones. We found that regional and local filters explained 80% of the total variation among local assemblages in community body size dispersion. Overall, regional filters reduced trait dispersion, and local filters increased it, a pattern driven by particularly strong antagonistic effects in temperate zones that reduced the realized total variation by more than 40%. In contrast, local and regional filters acted in concert in tropical regions. Patterns within the tropics did not differ from the random expectation based on a null model, but within the temperate zone, local community filtering was stronger than expected by chance. Furthermore, in temperate regions, antagonistic regional and local filtering masked from 76% to 90% of the total variation in trait dispersion. Together, these results suggest that there are fundamental differences in the scale and identity of the processes determining community structure in temperate and tropical regions.     

Lake to land subsidies: experimental addition of aquatic insects increases terrestrial arthropod densities

Aquatic insects are a common and important subsidy to terrestrial systems, yet little is known about how these inputs affect terrestrial food webs, especially around lakes. Myvatn, a lake in northern Iceland, has extraordinary midge (Chironomidae) emergences that result in large inputs of biomass and nutrients to terrestrial arthropod communities. We simulated this lake-to-land resource pulse by collecting midges from Myvatn and spreading their dried carcasses on 1-m2 plots at a nearby site that receives very little midge deposition. We hypothesized a positive bottom-up response of detritivores that would be transmitted to their predators and would persist into the following year. We sampled the arthropod community once per month for two consecutive summers. Midge addition resulted in significantly different arthropod communities and increased densities of some taxa in both years. Detritivores, specifically Diptera larvae, Collembola, and Acari increased in midge-addition plots, and so did some predators and parasitoids. Arthropod densities were still elevated a year after midge addition, and two years of midge addition further increased the density of higher-order consumers (e.g., Coleoptera and Hymenoptera). Midge addition increased arthropod biomass by 68% after one year and 108% after two years. By manipulating the nutrient pulse delivered by midges we were able to elucidate food web consequences of midge deposition and spatial and temporal dynamics that are difficult to determine based on comparative approaches alone. Resources cross ecosystem boundaries and are assimilated over time because of life-history strategies that connect aquatic and terrestrial food webs and these systems cannot be fully understood in isolation from each other.     

Habitat modification affects recruitment of abalone in central New Zealand

The habitat experienced during early life-history stages can determine the number and quality of individuals that recruit to adult populations. In a field experiment, biogenic habitat complexity was manipulated (presence or absence of foliose macroalgae) at two depths (2–3 m and 5–6 m) and the habitat-dependent effects on recruitment of the black foot abalone (Haliotis iris) were examined at three field sites along the south coast of Wellington, New Zealand (41°20′S, 174°47′E), between July and November 2005. Recruit density (<5 weeks post-settlement) was measured on cobbles covered with crustose coralline algae. Habitats of low complexity (barrens treatments) had consistently greater densities of recruits than habitats of high complexity (algae treatments). However, recruits in algae habitats were larger, and for deep habitats, there was greater survival in algae habitats compared with barrens habitats. While depth had no significant effect on early recruit (<2 weeks post-settlement) density, late recruit (<5 weeks post-settlement) density was greater in shallow habitats, and so it seems recruit survival was greater in shallow habitats. In this experiment, algal habitat complexity had strong effects on early recruit abundance, but habitat-dependent variations in recruit growth and survival may modify initial patterns of abundance and determine recruitment to adult abalone populations.     

Predicting intertidal organism temperatures with modified land surface models

Animals and plants in the marine intertidal zone live at the interface between terrestrial and marine environments. This zone is likely to be a sensitive indicator of the effects of climate change in coastal ecosystems, because of several key characteristics including steep environmental gradients, rapid temperature changes during tide transitions, fierce competition for limited space, and a community of mostly sessile organisms. Here we describe a modular modeling approach using modifications to a meteorological land surface model to determine body temperatures of the ecologically dominant rocky intertidal mussel Mytilus californianus, as a tool that can be used as a proxy for ecological performance. We validate model results against in situ measurements made with biomimetic body temperature sensors. Model predictions lie within the range of variability of biomimetic measurements, based on observations over a 4-year period at sites along 1700 km of the US west coast from southern California (34.5°N) to northern Washington (48.4°N). Our modular approach can be easily applied to many situations in the intertidal zone, including bare rock, mussel, barnacle, and algal beds, salt-marsh grasses, and sand- and mud-flats, by modifying the “vegetation layer” in a standard meteorological land surface model. Biophysical models such as these, which link ecological processes to changing climates through predictions of body temperature, are essential for understanding biogeographic patterns of physiological stress and mortality risk.     

Hydrologic and Phosphorus Export Behavior of Small Streams in Commercial Poultry‐Pasture Watersheds1

Romeis, J. Joshua, C. Rhett Jackson, L. Mark Risse, Andrew N. Sharpley, and David E. Radcliffe, 2011. Hydrologic and Phosphorus Export Behavior of Small Streams in Commercial Poultry‐Pasture Watersheds. Journal of the American Water Resources Association (JAWRA) 1‐19. DOI: 10.1111/j.1752‐1688.2011.00521.x Abstract: Few watershed‐scale studies have evaluated phosphorus export in streamflow from commercial poultry‐pasture operations. Continuous streamflow and mixed‐frequency water quality datasets were collected from nine commercial poultry‐pasture (AG) and three forested (FORS) headwater streams (2.4‐44 ha) in the upper Etowah River basin of Georgia to estimate total P (TP) loads and examine variability of hydrologic response and water quality of storm and nonstorm‐flow regimes. Data collection duration ranged from 18 to 22 months, and approximately 1,600 water quality samples were collected. Significant (p < 0.1) inverse relationships were detected between peak flow response variables and both drainage area and fraction of forest cover. Order‐of‐magnitude differences in TP and dissolved reactive P (DRP) concentration were observed between AG and FORS sites and among AG sites. TP yields of FORS sites ranged from 0.01 to 0.1 kg P/ha. Yields of AG sites ranged from 0.031 to 3.17 kg P/ha (median = 0.354 kg P/ha). With 95% confidence intervals, AG yields ranged from 0.025 to 13.1 kg P/ha. These small‐watershed‐scale yields were similar to field‐scale yields measured in other studies in other regions. TP yields were significantly related to area‐weighted Mehlich‐1 soil test P concentrations (p = 0.0073) and base‐flow water sample P concentrations (p ≤ 0.0005). Water quality sampling during base‐flow conditions may be a useful screening tool for P risk‐based management programs.     

A Multi‐Agency Nutrient Dataset Used to Estimate Loads,Improve Monitoring Design,and Calibrate Regional Nutrient SPARROW Models1

Saad, David A., Gregory E. Schwarz, Dale M. Robertson, and Nathaniel L. Booth, 2011. A Multi‐Agency Nutrient Dataset Used to Estimate Loads, Improve Monitoring Design, and Calibrate Regional Nutrient SPARROW Models. Journal of the American Water Resources Association (JAWRA) 47(5):933‐949. DOI: 10.1111/j.1752‐1688. 2011.00575.x Abstract: Stream‐loading information was compiled from federal, state, and local agencies, and selected universities as part of an effort to develop regional SPAtially Referenced Regressions On Watershed attributes (SPARROW) models to help describe the distribution, sources, and transport of nutrients in streams throughout much of the United States. After screening, 2,739 sites, sampled by 73 agencies, were identified as having suitable data for calculating long‐term mean annual nutrient loads required for SPARROW model calibration. These sites had a wide range in nutrient concentrations, loads, and yields, and environmental characteristics in their basins. An analysis of the accuracy in load estimates relative to site attributes indicated that accuracy in loads improve with increases in the number of observations, the proportion of uncensored data, and the variability in flow on observation days, whereas accuracy declines with increases in the root mean square error of the water‐quality model, the flow‐bias ratio, the number of days between samples, the variability in daily streamflow for the prediction period, and if the load estimate has been detrended. Based on compiled data, all areas of the country had recent declines in the number of sites with sufficient water‐quality data to compute accurate annual loads and support regional modeling analyses. These declines were caused by decreases in the number of sites being sampled and data not being entered in readily accessible databases.     

Movements and wintering areas of breeding age Thick-billed Murre <Emphasis Type="Italic">Uria lomvia</Emphasis> from two colonies in Nunavut,Canada

The non-breeding movements of marine birds were poorly known until recently, but this information is essential to understanding the risk to different geographical populations from events on the wintering grounds. We tracked the migration routes and wintering areas of Thick-billed Murre Uria lomvia from two breeding colonies in eastern Canada: Coats Island in northern Hudson Bay and The Minarets, Baffin Island, during the period August 2007–May 2008 using geolocation loggers. Birds from The Minarets moved south rapidly post-breeding and wintered principally off Newfoundland and southern Labrador, or between Newfoundland and southern Greenland, remaining south of 55°N until at least the spring equinox. Those from Coats Island remained in Hudson Bay until at least mid-November, after which they moved rapidly through Hudson Strait to winter in southern Davis Strait and the northern Labrador Sea, mostly north of 55°N. Many individuals stayed throughout the winter in areas of heavy ice cover. Adults from the two colonies appear to be completely segregated in winter and those from Coats Island probably did not enter the area of the winter hunt in Newfoundland. Unexpectedly, some birds from The Minarets wintered in waters beyond the continental slope and outside the distribution of pack ice, demonstrating that particular individuals can be wholly pelagic throughout the winter. Coats Island birds returned through Hudson Strait as soon as open water areas became available in spring. Their sojourn in Hudson Bay coincided very closely with the occurrence of areas with <90% ice cover. In spite of the relatively large error in positions obtained from geolocation loggers, our results demonstrated the value of these devices by uncovering a number of previously unknown aspects of Thick-billed Murre non-breeding ecology in the Northwest Atlantic. Comparison of the non-breeding ecology based on SST experienced in winter show that the winter niche is broader than hitherto assumed, demonstrating that separate populations may experience different selection in the face of climate change.     

Prey selection in <Emphasis Type="Italic">Octopus rubescens</Emphasis>: possible roles of energy budgeting and prey nutritional composition

This study explores the relationship between energy budgeting and prey choice of Octopus rubescens. Seventeen male Octopus rubescens were collected between June 2006 and August 2007 from Admiralty Bay, Washington. Prey choices made by individuals in the laboratory deviated widely from those expected from a simple optimal foraging model. O. rubescens chose the crab Hemigrapsus nudus over the clam Nuttallia obscurata as prey by a ratio of 3:1, even though prey energy content and handling times suggested that this octopus could obtain 10 times more energy intake per unit time when choosing the latter compared to the former prey species. Octopus energy budgets were similar when consuming either of the prey species except for lipid extraction efficiency that was significantly higher in octopuses consuming H. nudus. This suggests that lipid digestibility may play an important role in the prey choice of O. rubescens.