Academic literature on the topic 'Single-season occupancy models'

The Himalayan red panda is an endangered mammal endemic to Eastern Himalayan and South Western China. Data deficiency often hinders understanding of their spatial distribution and habitat use, which is critical for species conservation planning. We used sign surveys covering the entire potential red panda habitat over 22,453 km2 along the mid-hills and high mountains encompassing six conservation complexes in Nepal. To estimate red panda distribution using an occupancy framework, we walked 1,451 km along 446 sampled grid cells out of 4,631 grid cells in the wet season of 2016. We used single-species, single-season models to make inferences regarding covariates influencing detection and occupancy. We estimated the probability of detection and occupancy based on model-averaging techniques and drew predictive maps showing site-specific occupancy estimates. We observed red panda in 213 grid cells and found covariates such as elevation, distance to water sources, and bamboo cover influencing the occupancy. Red panda detection probability p^(SE) estimated at 0.70 (0.02). We estimated red panda site occupancy (sampled grid cells) and landscape occupancy (across the potential habitat) Ψ^(SE) at 0.48 (0.01) and 0.40 (0.02) respectively. The predictive map shows a site-specific variation in the spatial distribution of this arboreal species along the priority red panda conservation complexes. Data on their spatial distribution may serve as a baseline for future studies and are expected to aid in species conservation planning in priority conservation complexes.

The presence and density of two sympatric, large-sized vipers (the Gaboon viper, Bitis gabonica and the nose-horned viper, Bitis nasicornis) were studied along several transects, during both dry and wet seasons, and at different times of day, in southern Nigeria (West Africa). Three habitat types were found along the various transects (mature rain forest (MF), secondary rain forest (SF), swamp forest (SW)). The detection probabilities for these vipers were modelled with a set of competing models, and the various models were ordered by Akaike Information Criterion procedures. Two classes of models were used: the single-season model, and the multi-species model. The best models (single-season model) suggested that: for the Gaboon viper, habitat types SF and SW were particularly important in detecting this species, especially during the rainy season at 08h00–16h00. For nose-horned vipers, the best models had SW and MF as site-covariates. Application of the multi-species model revealed that there were different detection functions if both species are present at a site, with a ‘negative’ interaction of occupancy between the species. Females and males were similarly detectable in a logistic regression model, but feeding status and pregnancy slightly increased detection probability in a logistic regression model. Viper density was modelled by a DISTANCE sampling procedure. The density of one species tended to be inversely correlated to the density of the other, suggesting that (1) the rain-forest environment does not support abundant populations of both vipers when sympatric, and (2) the two Bitis species subtly partition the habitat resources.

Abstract Land-use change is a global threat to biodiversity, but how land-use change affects species beyond the direct effect of habitat loss remains poorly understood. We developed an approach to isolate and map the direct and indirect effects of agricultural expansion on species of conservation concern, using the threatened giant anteater (Myrmecophaga tridactyla) in the Gran Chaco as an example. We reconstructed anteater occupancy change between 1985 and 2015 by fitting single-season occupancy models with contemporary camera-trap data and backcasting the models to 1985 and 2000 land-cover/use maps. Based on this, we compared the area of forest loss (direct effect of agricultural expansion) with the area where forests remained but occupancy still declined (indirect effect of agricultural expansion). Anteater occupancy decreased substantially since 1985, particularly after 2000 when agriculture expanded rapidly. Between 1985 and 2015, ~ 64,000 km2 of forest disappeared, yet occupancy declined across a larger area (~ 102,000 km2), extending far into seemingly untransformed habitat. This suggests that widespread sink habitat has emerged due to agricultural land-use change, and that species may lose their habitat through direct and indirect effects of agricultural expansion, highlighting the urgent need for broad-scale conservation planning in the Chaco. Appropriate management responses could proactively protect more habitat where populations are stable, and restore habitat or address causes of mortality in areas where declines occur. Our work also highlights how occupancy modelling combined with remote sensing can help to detect the direct and indirect effects of agricultural expansion, providing guidance for spatially targeting conservation strategies to halt extinctions.

AbstractInformation on the distribution and abundance of the forest elephant Loxodonta cyclotis is needed to allocate limited resources appropriately and set conservation goals for the species. However, monitoring at large scales in forest habitats is complicated, expensive and time consuming. We investigated the potential of applying interview-based occupancy analysis as a tool for the rapid assessment of the distribution and relative abundance of forest elephants in eastern Cameroon. Using single-season occupancy models, we explored the covariates that affect forest elephant occupancy and detectability, and identified spatial and temporal patterns in population change and occupancy. Quantitative and qualitative socio-demographic data offer additional depth and understanding, placing the occupancy analysis in context and providing valuable information to guide conservation action. Detectability of forest elephants has decreased since 2008, which is consistent with the decline in perceived abundance in occupied sites. Forest elephants occupy areas outside protected areas and outside the known elephant range defined by IUCN. Critical conservation attention is required to assess forest elephant populations and the threats they face in these poorly understood areas. Interview-based occupancy analysis is a reliable and suitable method for a rapid assessment of forest elephant occupancy on a large scale, as a complement to, or the first stage in, a monitoring process.

Context The global reduction of amphibian biodiversity as a result of the disease chytridiomycosis (caused by the fungus Batrachochytrium dendrobatidis; Bd) has highlighted the need to accurately detect local population declines in association with Bd presence. Although Bd has spread globally, some remote regions such as the Tasmanian Wilderness World Heritage Area (1.40 million ha; TWWHA) in Australia, remain largely, but not entirely, disease free. The Tasmanian tree frog (Litoria burrowsae) resides primarily within TWWHA boundaries, and is believed to be susceptible to chytridiomycosis. Aims In the absence of historical abundance data, we used a single-season multi-state site-occupancy model to investigate the impact of Bd on L. burrowsae populations, on factors affecting species detection and to inform ongoing surveillance and conservation. Methods We recorded frog detection and ranked call intensity (estimation of population size) from repeated independent surveys within a season to estimate the role of covariates, such as presence of Bd and environmental variables, on species occupancy and detection probability. Key results Modelling revealed large frog populations are more likely to be present at naturally formed than human-formed ponds, strong winds negatively affect detection of populations, and time after sunset affects detection of large populations. Large frog populations were more likely to be Bd-negative; however, models including Bd presence were not well supported, in part a result of the small number of Bd-positive sites recorded. Conclusions and Implications The utility of site-occupancy modelling in understanding the impact of disease on populations is little known, but has the potential to improve the accuracy and efficiency of many conservation programs.

In 2013, we conducted a baseline study on the presence, distribution and occupancy of medium- to large-sized mammals in Bolivia along the San Buenaventura-Ixiamas road that runs parallel to the Madidi National Park and Natural Area of Integrated Management boundary and cuts through the Tacana Indigenous Territory and a number of neighboring private properties. Establishing a 3 km buffer on each side of the road, we studied an 865 km2 area divided into 1 km2 cells and sampled a total of 356 of these cells. In each cell, we established one 300 m transect divided into 25 m sections and registered wildlife sign, mainly footprints, from eight wildlife species or species groups. The transects were placed either along streams (75% of cells) or within forest (25% of cells). Using single-season single-species occupancy models we estimated occupancy (ψ) for Tapirus terrestris (ψ = 0.39), Pecari tajacu (ψ = 0.5), Mazama americana (ψ = 0.56), Dasyprocta spp. (ψ = 0.59), Cuniculus paca (ψ = 0.56), Leopardus spp. (ψ = 0.33), and use for Tayassu pecari (ψ = 0.17) and Panthera onca (ψ = 0.11). Occupancy and use results verified community perceived wildlife corridors between Madidi and its area of influence. We identified additional corridors along many streams crossing the San Buenaventura-Ixiamas road. This connectivity is not only important for wildlife, but also from a food security perspective for the indigenous communities that depend on wildlife as an important source of protein. The results will be used to mitigate the impact of road improvements through the identification of priority areas for maintaining connectivity between Madidi and the surrounding landscape.

Abstract Effective habitat conservation is predicated on maintaining high levels or increasing local persistence probability of the species it purports to protect. Thus, methodological approaches that improve the inferential value of local persistence are of utmost value to guide conservation planning as they inform area selection processes. Herein we used the painted bunting Passerina ciris, a species of conservation interest in North Carolina, as an illustrative case that combined single-season, single-species occupancy analyses and a threats and risk decision support tool to rank five areas of conservation interest in terms of local persistence probability. We used survey data from two seasons (2008–2009) grouped into 21 natal dispersal sampling units and land-cover data from 12 habitat classes to establish the relationship between local occupancy probability and habitat. Occupancy increased most strongly with increasing amount of maritime forest. Projections to year 2050, relative to year 2000, indicated that a potential loss of maritime forest of 200–1,300 ha, depending on the area of interest. Projected loss was lowest at Bald Head Island–Wilmington (2%) and highest at Camp Lejune (27%). Bald Head Island–Wilmington ranked highest in projected local persistence probability (0.91; 95% confidence interval [CI] = 0.53–0.99), whereas Top Sail–Hammocks Beach Park ranked lowest (0.28; 95% CI = 0.03–0.82). Estimates of local persistence offer decision-makers another criterion to prioritize areas for conservation and help guide efforts aimed at maintaining or enhancing local persistence. These include in situ habitat management, expanding or connecting existing areas of interest. In the future, we recommend the use of multiseason occupancy models, coupled with measures of uncertainty of land-cover projections, to strengthen inferences about local persistence, particularly useful in nonstationary landscapes driven by human activities.

Abstract ContextTo understand the ecological consequences of predator management, reliable and accurate methods are needed to survey and detect predators and the species with which they interact. Recently, poison baits have been developed specifically for lethal and broad-scale control of feral cats in Australia. However, the potential non-target effects of these baits on other predators, including native apex predators (dingoes), and, in turn, cascading effects on lower trophic levels (large herbivores), are poorly understood. AimsWe examined the effect that variation in camera trapping-survey design has on detecting dingoes, feral cats and macropodids, and how different habitat types affect species occurrences. We then examined how a feral cat poison baiting event influences the occupancy of these sympatric species. MethodsWe deployed 80 remotely triggered camera traps over the 2410-km2 Matuwa Indigenous Protected Area, in the semiarid rangelands of Western Australia, and used single-season site-occupancy models to calculate detection probabilities and occupancy for our target species before and after baiting. Key resultsCameras placed on roads were ~60 times more likely to detect dingoes and feral cats than were off-road cameras, whereas audio lures designed to attract feral cats had only a slight positive effect on detection for all target species. Habitat was a significant factor affecting the occupancy of dingoes and macropodids, but not feral cats, with both species being positively associated with open woodlands. Poison baiting to control feral cats did not significantly reduce their occupancy but did so for dingoes, whereas macropodid occupancy increased following baiting and reduced dingo occupancy. ConclusionsCamera traps on roads greatly increase the detection probabilities for predators, whereas audio lures appear to add little or no value to increasing detection for any of the species we targeted. Poison baiting of an invasive mesopredator appeared to negatively affect a non-target, native apex predator, and, in turn, may have resulted in increased activity of large herbivores. ImplicationsManagement and monitoring of predators must pay careful attention to survey design, and lethal control of invasive mesopredators should be approached cautiously so as to avoid potential unintended negative ecological consequences (apex-predator suppression and herbivore release).

AbstractHabitat loss and fragmentation are affecting populations of forest dwelling mammalian carnivores worldwide. In southern Chile, a biodiversity hotspot, anthropogenic activities have resulted in high loss of native forest cover. The guiña, or kodkod cat, Leopardus guigna is a small forest-dwelling felid with a narrow range in the temperate forest of southern Chile. The few existing studies of the species have suggested that it is almost exclusively restricted to large tracts of native forest. This paper reports a study in the temperate forest within a fragmented Andean piedmont landscape which demonstrates that smaller forest fragments in the farmland matrix are playing a key role in the persistence of the guiña. We estimated occupancy in both continuous native forest and remnant forest fragments and, with single-species/single-season models, evaluated the extent to which forest cover, habitat type and proximity to protected areas have a modulating effect on occupancy. A continuous survey during 2008–2009, in three seasons of 90–100 days each, accumulated 6,200 camera trap days and returned 47 photographs of guiña. Total detection in fragments was higher than in continuous forests, with detection confirmed in almost 70% of studied fragments. We found that probability of a site being occupied significantly increased with forest cover (adult/secondary forest, scrubland) and probability was low (< 0.2) in sites with < 50% of surrounding forest cover. Our study highlights the importance of remnant forest fragments in the mosaic of extensive agriculture for the spatial dynamics of a guiña population and hence for the future conservation of the species.

Context Designing effective long-term monitoring strategies is essential for managing wildlife populations. Implementing a cost-effective, practical monitoring program is especially challenging for widespread but locally rare species. Early successional habitat preferred by the New England cottontail (NEC) has become increasingly rare and fragmented, resulting in substantial declines from their peak distribution in the mid-1900s. The introduction of a possible competitor species, the eastern cottontail (EC), may also have played a role. Uncertainty surrounding how these factors have contributed to NEC declines has complicated management and necessitated development of an appropriate monitoring framework to understand possible drivers of distribution and dynamics. Aims Because estimating species abundance is costly, we designed presence–absence surveys to estimate species distributions, test assumptions about competitive interactions, and improve understanding of demographic processes for eastern cottontails (EC) and New England cottontails (NEC). The survey protocol aimed to balance long-term management objectives with practical considerations associated with monitoring a widespread but uncommon species. Modelling data arising from these observations allow for estimation of covariate relationships between species status and environmental conditions including habitat and competition. The framework also allows inference about species status at unsurveyed locations. Methods We designed a monitoring protocol to collect data across six north-eastern USA states and, using data collected from the first year of monitoring, fit a suite of single-season occupancy models to assess how abiotic and biotic factors influence NEC occurrence, correcting for imperfect detectability. Key results Models did not provide substantial support for competitive interactions between EC and NEC. NEC occurrence patterns appear to be influenced by several remotely sensed habitat covariates (land-cover classes), a habitat-suitability index, and, to a lesser degree, plot-level habitat covariates (understorey density and canopy cover). Conclusions We recommend continuing presence–absence monitoring and the development of dynamic occupancy models to provide further evidence regarding hypotheses of competitive interactions and habitat influences on the underlying dynamics of NEC occupancy. Implications State and federal agencies responsible for conserving this and other threatened species can engage with researchers in thoughtful discussions, based on management objectives, regarding appropriate monitoring design to ensure that the allocation of monitoring efforts provides useful inference on population drivers to inform management intervention.

A destruição de florestas tropicais é intensa e pode levar à extinção de espécies sensíveis à fragmentação. Na Mata Atlântica, mamíferos com importantes funções no equilíbrio do ecossistema, como Panthera onca (onça-pintada), já estão ausentes em grande parte do bioma. Logo, é de extrema urgência compreender os processos que influenciam na permanência dessas espécies em uma área, para evitar futuras extinções locais. Assim, o objetivo geral deste estudo foi analisar as influências das características ambientais sobre a riqueza e ocorrência de mamíferos terrestres de médio e grande porte e as relações espaço-temporais entre o predador de topo, mesopredadores e presas em uma área de Mata Atlântica contíngua ao Parque Estadual da Serra do Mar com recente histórico de perturbação (Parque das Neblinas, Bertioga, SP). A coleta de dados foi realizada por armadilhamento fotográfico, durante 90 dias em 2013 e 2014, em 27 pontos amostrais, distantes 1 km entre si. As características ambientais avaliadas foram altitude, densidade de drenagem, precipitação média, temperatura média, número de palmitos (Euterpe edulis) e presença de trilhas naturais. Para analisar as influências do ambiente sobre a riqueza e ocorrência de espécies (com mais de três registros por ano) foram utilizados Modelos Lineares Generalizados. Para as demais análises, as espécies foram agrupadas em predador, mesopredadores, presas de grande, médio e pequeno porte. O período e sobreposição de atividade destes grupos foram estimados por meio da densidade de Kernel. A abundância foi estimada para mesopredadores e presas, através de modelos N-mixture. Para analisar a probabilidade de ocupação e detecção do predador de topo foram usados modelos de ocupação single-season. Foram amostrados 18 mamíferos terrestres de médio e grande porte, dos quais nove estão ameaçados de extinção ((Cabassous unicinctus (tatu-de-rabo-mole), Cuniculus paca (paca), Leopardus guttulus (gato-do-mato-pequeno), Leopardus pardalis (jaguatirica), Leopardus wiedii (gato-maracajá), Pecari tajacu (cateto), Puma concolor (onça-parda), Puma yagouaroundi (gato-mourisco) e Tapirus terrestris (anta)). A riqueza de espécies foi positivamente influenciada pelo maior volume de chuvas e a ocorrência da maioria das espécies (C. unicinctus, Dasypus novemcinctus (tatu-galinha), P. concolor, Sylvilagus brasiliensis (tapiti) e T. terrestris) foi influenciada pela densidade de drenagem em 2013. Em 2014, a riqueza não foi explicada por nenhuma característica e apenas quatro espécies sofreram influência de alguma característica ambiental. O predador de topo registrado foi catemeral, os mesopredadores e presas de grande porte mostraram-se mais noturnos e presas de médio e pequeno porte foram mais diurnas. Presas menores apresentaram a maior sobreposição total com o predador (Δ1=0,72). A influência sobre a probabilidade de ocupação da área pelo predador variou entre os anos, tendo sido pela abundância de presas de grande e pequeno porte, em 2013, e pela abundância de presas de médio porte, em 2014. A detecção foi influenciada apenas em 2014, de forma negativa pelas ocasiões. A partir destes resultados foi possível identificar as características ambientais que devem ser mantidas na área, como a disponibilidade de recursos hídricos e abundância de presas, a fim de conservar das espécies resilientes.
The destruction of tropical forests is alarming and may lead to the extinction of species susceptible to fragmentation. In the Atlantic Forest, mammals with important functions in the ecosystem balance, such as Panthera onca (jaguar), are already absent in part of the biome. Therefore, it is urgent to understand the processes that influence the permanence of these species in an area, in order to prevent future local extinctions. Thus, this study aimed to analyze the influence of environmental characteristics on the richness and occurrence of terrestrial mammals of medium and large size; as well as the spatio-temporal relationship between the top predator, mesopredator and preys, in the Atlantic foreste area continuos continuous with Serra do Mar State Park, with recent degradation history (Neblinas Park, Bertioga, State of São Paulo). Sample data was collected by camera trapping for 90 days in 2013 and 2014, 27 sampling points 1km distant from each other. The environmental characteristics were altitude, drainage density, average rainfall, average temperature, number of palm hearts (Euterpe edulis) and the presence of nature trails. Generalized Linear Models were used to analyze the environmental influences on the richness and occurrence of species (with more than 3 records per year). For the other analyses, species were grouped into predator, mesopredators, preys of large, medium and small size. The period and overlap activity of these groups were estimated by the Kernel density. Abundance was estimated for mesopredators and prey through N-mixture models. Single-season occupancy models were used to analyze the probability of occupancy and detection of top predators. A total of 18 terrestrial mammals of medium and large size were sampled, with nine of them being threatened with extinction: Cabassous unicinctus (naked-tailed armadillo), Cuniculus paca (paca), Leopardus guttulus (oncilla), Leopardus pardalis (ocelot), Leopardus wiedii (margay), Pecari tajacu (collared peccary), Puma concolor (cougar), Puma yagouaroundi (jaguarundi) and Tapirus terrestris (tapir). In the 2013, the species richness was positively influenced by the largest volume of precipitation and the species occurrence (C. unicinctus, Dasypus novemcinctus (tatu-galinha), P. concolor, Sylvilagus brasiliensis (tapiti) e T. terrestris) was interfered by the drainage density. In 2014, richness was not explained by any of the environmental characteristics mentioned and only four species have suffered influence of them. The top predator recorded was catemeral, the mesopredator and large prey were mainly nocturnal and prey of medium and small size were mainly daylight. Smaller prey had the highest total overlap with the predator (Δ1=0.72). The influence on the probability of occupancy of the area by the predator varied between the years: in 2013 it was the abundance of large and small preys, and in 2014, the influence was the abundance of medium preys. The detection was negatively influenced by the occasion only in 2014. Our findings showed the environmental characteristics that should be maintained in the area, such as water resources and abundance of prey, for conservation of Atlantic Forest and its fauna community.

A parametric estimation algorithm is described for system design criteria selection in Ground Source Heat Pump (GSHP) Heating, Ventilation and Air Conditioning (HVAC) applications requiring dissipation of annual cycle excess thermal energy to the air, i.e., a hybrid mode. The model applies a combination of order-of-magnitude scaling (OMS) and classical non-dimensional flow and heat transfer methods. The objective is to develop a simplified parametric range display for selection of design values. Application requirements and constraints map into the solution space for specific design value selections. The annual thermal budget cycle is configured to time-phase the earth-stored excess energy from the cooling season for dissipation in the heating season using water to ambient forced-air (fan-coil) cooling. Estimators for an application are developed for the quantity, spacing and depth of well bores and the loop flow rate range based on Reynolds number and Nusselt number correlations for water and earth thermal properties. A case study application in two parts is described. The GSHP system uses a common working fluid (water) in a closed loop serving all 70 zones to furnish heating, cooling, domestic water heating, and exterior walkway deicing for an 80,000 sq. ft. area, 54 apartment, senior, center in Dallas Texas, USA. In 1999, the initial Phase I facility of 55,000 sq. ft. area was occupied using the full capacity flow system design without the dissipation coolers. In 2004 the coolers were included with the expansion to full occupancy. Design parameter values, operating experience, energy use, and the rationale for the demonstrated compatibility of the single solution for essentially two applications are described.