Estimated Occupancy Rates Research Articles

Observers are a key source of detection heterogeneity and biased occupancy estimates in species monitoring

Reliable assessments of population status and trends underpin conservation management efforts but are complicated by the fact that imperfect detection is ubiquitous in monitoring data. We explore the most commonly considered variables believed to influence detection probabilities, quantifying how they influence detectability and assessing how occupancy rates are impacted when a variable is ignored. To do so, we used data from two multi-species amphibian monitoring programmes, collected by volunteers and professional surveyors.Our results suggest that although detection rates varied substantially in relation to commonly considered factors such as seasonal and annual effects, ignoring these factors in the analysis of monitoring data had negligible effect on estimated occupancy rates. Variation among surveyors in detection probabilities turned out to be most important. It was high and failing to account for it led to occupancy being underestimated. Importantly, we identified that heterogeneity among observers was as high for professional surveyors as for volunteers, highlighting that this issue is not restricted to citizen-science monitoring.Occupancy modelling has greatly improved the reliability of inference from species monitoring data, yet capturing the relevant sources of variation remains a challenge. Our results highlight that variation among surveyors is a key source of heterogeneity, and that this issue is just as pertinent to data collected by experts as by volunteers. Detection heterogeneity should be accounted for when analysing monitoring data. Furthermore, efforts to increase training of field crews and collecting data to quantify differences between observer abilities are important to avoid biased inference resulting from unmodelled observer differences.

Bayesian time-varying occupancy model for West Nile virus in Ontario, Canada

Occupancy models determine the true presence or absence of a species by adjusting for imperfect detection in surveys. They often assume that species presences can be detected only if sites are occupied during a sampling season. We extended these models to estimate occupancy rates that vary throughout a sampling season as well as account for spatial dependence among sites. For these methods, we constructed a fast Gibbs sampler with the Pólya-Gamma augmentation strategy to conduct inference on covariate effects. We applied these methods to evaluate how environmental conditions and surveillance practices are associated with the presence of West Nile virus in mosquito traps across Ontario, Canada from 2002 to 2017. We found that urban land cover and warm temperatures drove viral occupancy, whereas viral testing on pools with higher proportions of Culex mosquitoes was more likely to result in a positive test for West Nile virus. Models with time-varying occupancy effects achieved much lower Watanabe-Akaike information criteria than models without such effects. Our final model had strong predictive performance on test data that included some of the most extreme seasons, demonstrating the promise of these methods in the study of pathogens spread by mosquito vectors.

Monitoring Occupancy of Bats with Acoustic Data: Power and Sample Size Recommendations

Bats are difficult to study due to their nocturnal, cryptic, and highly vagile nature. Ongoing advances in acoustic recording hardware and call classification software have made species detection and activity monitoring more feasible. Our objectives were to determine the effort necessary to monitor bat assemblages using an occupancy framework and acoustic data and to provide guidelines for researchers interested in developing similar monitoring programs. We collected data at 2 study areas in South Texas from June through September in 2015, 2016, and 2017. We used Pettersson D500X Mk II real-time full-spectrum detectors and classified sound files using SonoBat bat call analysis software. We attempted to collect data during 2 visits to individual sites, with up to 5 consecutive nights per visit each year. We estimated occupancy rates for each species in each study area using occupancy models in Program MARK and included terms to define trends in detection probability through the season. Over the 3 years of our study, we sampled 106 sites with 803 sampling nights and classified a total of 2880 sound files to 7 species. Data sets for 6 of the species supported models indicating that detection probability varied throughout our sampling period. Our results generally indicate that sample sizes between 10 and 20 sites would be required to detect declines in occupancy of 50% over 25 years using 10 nights per site with a starting occupancy rate of 0.70. Detecting declines of 30% in 10 years may require >75 sampling sites. Finally, our analysis shows that recognizing seasonal variation in detection probability, and then timing surveys accordingly, can greatly reduce sample size requirements.

Potential effect of habitat disturbance on reproduction of the critically endangered harlequin frog Atelopus varius in Las Tablas, Costa Rica

We studied a population of Atelopus varius in Las Tablas Protected Zone in southwest Costa Rica, where we estimated occupancy rates of tadpoles along the Cotón River. In addition, we report the first tadpoles observed in the wild in 20 years. Tadpole rate of occupancy was greater in habitat containing native forest than in disturbed areas bordering cattle pasture. This same pattern was also reflected in adult hotspots, where encounter rates were higher for adults in habitat surrounded by forest versus pasture. We present evidence for the potential effect of habitat modification on the presence and reproduction of A. varius and suspect that over time this modification impacts the species’ demography. However, further study is necessary before we can confirm that habitat change alone was the key factor involved in patterns of decline for the species.

The farmland refuge of the last Andalusian Buttonquail population

The last populations of threatened taxa usually survive in low-impacted areas, whose protection and management is critical for its conservation. However, they can also be located in humanized and highly dynamic areas, whose management can be extremely challenging. The Andalusian buttonquail (Turnix sylvaticus sylvaticus) is the critically endangered nominal subspecies of the common buttonquail, a largely unknown species due to its secretive habits. Here, we show how the last Andalusian buttonquail population is restricted to a small, intensively used agricultural area (4,675 ha) in the Atlantic coast of Morocco, where the birds adapt their life cycle to a fast crop rotation. Buttonquails occupy crops in the flowering and fruiting stages, thus changing the preferred crop types along the year, although Alfalfa fields were occupied in all seasons. We used estimated occupancy rates in different crops to obtain seasonal (2017) and year-to-year population estimates (2011, 2014 and 2017). Numbers showed wide seasonal fluctuations between the lowest in winter and the maximum in summer (112–719 individuals). Year-to-year summer estimates also showed wide variations and large uncertainties, ranging between a maximum 1,890 estimated in 2011 and a minimum in 2014 with 492 individuals. The last population estimate available was 596 in 2017. The area is suffering a rapid shift from traditional irrigation farming towards practices more akin to commercial industrial agriculture. The conservation of this critically endangered taxon is highly dependent on the maintenance of traditional farming practices and a rational on-site agricultural modernization.

Determining feeder space allowance across feed forms and water availability in the feeder for growing-finishing pigs

Objectives: To evaluate a method of determining the optimal feeder space allowance for pigs. Materials and methods: Trial 1 used eight pens of 12 pigs to determine total eating time in pigs to estimate occupancy rates of a single-space feeder. Feed was provided in four combinations of feed form (mash versus pelleted) and water availability in the feeder (dry versus wet-dry). Eating behavior of pigs was video-recorded during both growing and finishing phases. Trial 2 used 560 pigs for the growing phase and 454 pigs for the finishing phase. Effects of feeder occupancy rate (< 80%, 95%, 110%, and 125% for the growing phase; 80%, 103%, and 125% for the finishing phase) on total eating time and growth performance were determined. Results: Both feed form (P < .01) and water availability in the feeder (P < .001) affected total eating time and, consequently, feeder occupancy rate. Pigs spent more time eating a dry mash diet than any other diet by water combination during both growing (P < .001) and finishing (P < .01) phases. As feeder occupancy rate increased to above 80%, either eating time (P < .05) or growth performance (P < .05) decreased. Implications: When testing levels of feeder space allowance and identifying the optimum, the designated number of pigs per feeder space should be determined according to feeder occupancy rates under different production settings. Optimal feeder space allowance should maintain both productivity and eating time of pigs.

Evidence for Range Contraction of Snowshoe Hare in Pennsylvania

Abstract In Pennsylvania, Lepus americanus (Snowshoe Hare) is near the southern limits of its range and at risk of range contraction because of loss of early-successional forest and impacts of climate change. We used hunter-harvest data to investigate changes in the distribution of Snowshoe Hare in Pennsylvania (1983–2011), forest inventory and land-use data to assess changes in amount and distribution of early-successional forest (1988–2011), and occupancy modeling (2004) to identify habitat and climate variables that explain the current distribution of Snowshoe Hare. We determined presence of Snowshoe Hare based on visual sightings, observations of tracks, and DNA analysis of fecal pellets, and used repeated visits to sampling sites and occupancy models to estimate occupancy rates (Ψ). Hunter-harvest data indicated the range of Snowshoe Hare in Pennsylvania contracted towards northwestern and northeastern portions of the state. Based on occupancy modeling, Snowshoe Hare were most likely to occupy early-...

A comparison of line-transect distance sampling methods for estimating gopher tortoise population densities

Line-transect distance sampling (LTDS) is increasingly used to estimate gopher tortoise (Gopherus polyphemus) densities. The process requires detecting tortoise burrows, and then determining occupancy. We compared 3 LTDS approaches that differ in how burrow detection and occupancy data are integrated, and 2 search strategies. Surveys were conducted at Avon Park Air Force Range in South-central Florida, USA, from April through October 2009. These include 1) LTDS using data from occupied burrows only; 2) LTDS with burrows treated as “clusters” of size 1 or 0 depending on occupancy; 3) LTDS to estimate burrow densities, with occupancy modeling to estimate occupancy rates; and 4) 2 search strategies: standard versus expanded searches. The LTDS method produced reliable burrow density estimates, and tortoise densities were estimated most precisely and with least effort using data from occupied burrows only. However, any method could be biased if burrow occupancy is uncertain. Indeed, in the Florida scrub and pine flatwoods habitats, video-camera scoping was hindered by groundwater or obstructions, resulting in undetermined occupancy for 45% of burrows. Improving scope technologies and surveying during the dry season has improved subsequent results for xeric habitats; however, research is needed to improve detectability of tortoises in mesic habitats with flooded burrows. If occupancy is uncertain, we recommend collecting data on all burrows, irrespective of occupancy, so that burrow densities can be estimated even if occupancy cannot. We do not recommend expanding the search area with sigmoid search paths adjacent to transects owing to potential violations of assumptions, nor use of occupancy modeling, because model requirements may lead to unacceptable exclusion of data. © 2015 The Wildlife Society.

Estimating occupancy and abundance of caracal in a semi-arid habitat, Western India

We estimated the occupancy and abundance of caracal (Felis caracal) using camera traps in the core area of Ranthambhore Tiger Reserve (RTR), a semi-arid habitat, in Western India, from 2006 to 2009. Caracals were detected in 17 of 28 grids, yielding a naive occupancy estimate of 0.61. After accounting for imperfect detection (P = 0.17 ± 0.04 [SE]), the proportion of sites occupied (occupancy) was 87 %. Caracal abundance was ∼28.17 ± 3.02 individuals in the study area. Based on the total area available for caracals (588 km2), the average expected density was as 4.8 caracals per 100 km2. Information on caracal occupancy and abundance in the Indian sub-continent has not been documented or published, and this is the first attempt to estimate occupancy rates and the approximate population size of the caracal in RTR. Hence, our data should be used as baseline information for making future management and conservation strategies for the species in this and similar landscapes.

Taking the lead on climate change: modelling and monitoring the fate of an Amazonian frog

AbstractClimate change is expected to have important impacts on biodiversity. However, cases showing explicit links between species decline and climate are scarce, mostly because of a lack of baseline data. Tropical ectotherms with narrow altitudinal ranges are particularly sensitive to climate change; for example the frogPristimantis espedeusmay be at risk, with only nine populations known to date in French Guiana, all on isolated massifs. Ecological niche modelling indicated that these populations could disappear by 2070. To facilitate testing of this prediction we conducted a study to design an efficient, cost-effective monitoring protocol, combining occupancy rate estimations using passive acoustic recorders, and abundance estimations using acoustic repeated counts and capture–mark–recapture. We found the passive recorders to be effective, with a detection probability of 0.8. Two recording sessions were sufficient to estimate occupancy rates reliably. A minimum of 57 surveyed sites were required to detect a decline of 15% in occupancy between two consecutive monitoring events. Acoustic repeated counts and capture–mark–recapture yielded similar density estimates (1.6 and 1.8 calling males per 100 m2, respectively). Based on these results we present a protocol based on passive acoustic recording and abundance monitoring to monitorP. espedeuspopulations.

Occupancy and Abundance Modeling of the Endangered Yellowcheek Darter in Arkansas

The Yellowcheek Darter (Etheostoma moorei) is a rare fish endemic to the Little Red River watershed in the Boston Mountains of northern Arkansas. Remaining populations of this species are geographically isolated and declining, and the species was listed in 2011 as federally endangered. Populations have declined, in part, due to intense seasonal stream drying and inundation of lower reaches by a reservoir. We used a kick seine sampling approach to examine distribution and abundance of Yellowcheek Darter populations in the Middle Fork and South Fork Little Red River. We used presence data to estimate occupancy rates and detection probability and examined relationships between Yellowcheek Darter density and environmental variables. The species was found at five Middle Fork and South Fork sites where it had previously been present in 2003–2004. Occupancy rates were >0.6 but with wide 95% CI, and where the darters occurred, densities were typical of other Ozark darters but highly variable. Detection probability and density were positively related to current velocity. Given that stream drying has become more extreme over the past 30 years and anthropogenic threats have increased, regular monitoring and active management may be required to reduce extinction risk of Yellowcheek Darter populations.

Estimating Occupancy of Rare Fishes using Visual Surveys, with a Comparison to Backpack Electrofishing

There is an ongoing need to monitor the status of imperiled fishes in the southeastern United States using effective methods. Visual surveys minimize harm to target species, but few studies have specifically examined their effectiveness compared to other methods or accounted for imperfect species detection. We used snorkel surveys to estimate detection probability and site occupancy for rare fishes in the Toccoa River system of north Georgia. We also carried out backpack electrofishing at a subset of sites to compare detection probabilities for both methods. The probability of detecting Percina aurantiaca (Tangerine Darter) and Etheostoma vulneratum (Wounded Darter) while snorkeling was relatively high, averaging 30% and 22%, respectively, and naïve and estimated occupancy rates (i.e., corrected for incomplete species detection) were almost identical for both species. The probability of detecting Erimystax insignis (Blotched Chub) while snorkeling was relatively low (9%), and their estimated occupancy rate (86%) was much higher than we detected in our survey. Detection was negatively related to depth and substrate size for Blotched Chub and positively related to depth for Tangerine Darter. Compared to snorkeling, the probability of detecting a species while backpack electrofishing was higher for Wounded Darter (40%) and comparable for Blotched Chub (11%). Tangerine Darter, however, were never captured while electrofishing even though they occurred at all four sites where both methods were used. Our study demonstrates the successful use of snorkel sampling to estimate occupancy rates of rare fishes in a large, clear southeastern river and illustrates the importance of accounting for imperfect species detection.

Estimating site occupancy rates for aquatic plants using spatial sub-sampling designs when detection probabilities are less than one

Estimation of site occupancy rates when detection probabilities are <1 is well established in wildlife science. Data from multiple visits to a sample of sites are used to estimate detection probabilities and the proportion of sites occupied by focal species. In this article we describe how site occupancy methods can be applied to estimate occupancy rates of plants and other sessile organisms. We illustrate this approach and the pitfalls of ignoring incomplete detection using spatial data for 2 aquatic vascular plants collected under the Upper Mississippi River's Long Term Resource Monitoring Program (LTRMP). Site occupancy models considered include: a naïve model that ignores incomplete detection, a simple site occupancy model assuming a constant occupancy rate and a constant probability of detection across sites, several models that allow site occupancy rates and probabilities of detection to vary with habitat characteristics, and mixture models that allow for unexplained variation in detection probabilities. We used information theoretic methods to rank competing models and bootstrapping to evaluate the goodness-of-fit of the final models. Results of our analysis confirm that ignoring incomplete detection can result in biased estimates of occupancy rates. Estimates of site occupancy rates for 2 aquatic plant species were 19–36% higher compared to naive estimates that ignored probabilities of detection <1. Simulations indicate that final models have little bias when 50 or more sites are sampled, and little gains in precision could be expected for sample sizes >300. We recommend applying site occupancy methods for monitoring presence of aquatic species.

Status and Distribution of Breeding Secretive Marshbirds in the Delta of Arkansas

We surveyed the Lower Mississippi Alluvial Valley of Arkansas (“the Delta”) during the breeding seasons of 2005 and 2006 using the national marshbird monitoring protocol for secretive marshbirds. We detected and documented breeding by Podilymbus podiceps (Pied-billed Grebe), Ixobrychus exilis (Least Bittern), Rallus elegans (King Rail), and Gallinula chloropus (Common Moorhen). We detected but did not document breeding by Botaurus lentiginosus (American Bittern), Porphyrula martinica (Purple Gallinule), and Fulica americana (American Coot), all of which have been documented to breed in the Delta. Our estimated occupancy rates for breeding marshbirds in the study area ranged from a low of 6% for the King Rail in 2006 to a high of 27% for the Least Bittern in 2005. The range of these occupancy rates are low and reflect the rarity of secretive marshbirds in the Delta. Secretive marshbird occupancy rates were higher in the southern third of the Delta, probably because wetlands were more abundant or of higher quality there.

Habitat Occupancy by Rusty Blackbirds Wintering in the Lower Mississippi Alluvial Valley

The Rusty Blackbird (Euphagus carolinus) has declined by 90% since the 1960s, possibly from conversions of forested wetlands in the southeastern U.S. to agriculture. Because its habitat use during the nonbreeding season had not been quantified, we estimated occupancy rates of Rusty Blackbirds wintering in the lower Mississippi Alluvial Valley in relation to habitat type (four types of bottomland forest and adjacent agricultural fields), tree density, canopy cover, and water cover. In January and February, we surveyed 89 sites eight times during 2006, 117 and 109 sites 10 times during 2007 and 2008, respectively. Occupancy of individual birds, estimated from their presence or absence at a site, was generally high and greater in 2006 (0.71) than during either 2007 (0.43) or 2008 (0.37). Occupancy of flocks, estimated from presence or absence of ≥20 individuals, was highest in 2006 (0.46), lowest in 2007 (0.17), and intermediate in 2008 (0.30), possibly because of water levels fluctuating from year to year. Rusty Blackbirds were not as specialized in habitat use as expected; habitat characteristics did not consistently predict occupancy of either individuals or flocks. Occupancy of individuals increased with canopy cover during 2007, and occupancy of flocks decreased with tree density during 2006. In 2008, occupancy of individuals increased with tree density and was higher in wet bottomland forest (0.51) than in other habitats (0.31–0.35). Further research is needed to determine whether this lack of habitat specificity is widespread and possibly the result of diverse food requirements during the nonbreeding season.

Assessing Detection Probabilities of Larval Amphibians and Macroinvertebrates in Isolated Ponds

Isolated ponds provide vital habitat for an array of vertebrates and invertebrates. Given the potential decline in protection of isolated ponds and the increase in urbanization in northeastern North America, knowledge of the condition of this aquatic resource is essential for developing revisions to existing regulations, conservation efforts, and restoration initiatives. We were interested in the ability of rapid assessment methods, which require only one site visit, to estimate the condition of isolated ponds. During 2008, we conducted dip-net surveys at 10-day intervals from mid-May to late July 2008 at each of 36 isolated ponds in Rhode Island. We calculated detection probabilities for larval amphibian species and predatory macroinvertebrate families and assessed factors influencing detection probabilities. Most taxa displayed distinct seasonal phenologies in detection probabilities. Pond depth and vegetative characteristics also influenced detection probabilities of many taxa. Based on seasonal variation in detection probabilities, rapid assessment methods would not be effective to monitor overall biodiversity of isolated ponds in southern New England. Rather, multiple visits would be required to estimate occupancy rates of pond-breeding amphibians or aquatic macroinvertebrates if they were used as ecological indicators of pond condition.