Small sample bias in dynamic occupancy models

Occupancy models may be used to estimate the probability that a randomly selected site in an area of interest is occupied by a species (ψ), given imperfect detection (p). This method can be extended, given multiple survey periods, to permit the estimation of seasonal probabilities of ψ, colonization (γ), persistence (φ), and extinction (1 − φ) in season t. We evaluated the sampling properties of estimators of these parameters using simulated data across a range of the parameters, differing levels of sites and visits, with a published dynamic occupancy model (Royle and Kery 2007). Bias depended largely on p and the number of visits, but also on the number of sites, ψ_t, γ, and 1 − φ. To decrease bias in all parameters to near zero, our results suggest that the number of required visits will depend on p, such that the probability of detection at an occupied site is near 0.9, and the required number of sites will be near 60 for ψ_t estimation and 120 or greater for γ and 1 − φ estimation. Published 2012. This article is a U.S. Government work and is in the public domain in the USA.     

Relationship between wildfire,salvage logging,and occupancy of nesting territories by northern spotted owls

The northern spotted owl (Strix occidentalis caurina) is one of the most intensively studied raptors in the world; however, little is known about the impacts of wildfire on the subspecies and how they use recently burned areas. Three large-scale wildfires in southwest Oregon provided an opportunity to investigate the short-term impacts of wildfire and salvage logging on site occupancy of spotted owls. We used Program MARK to develop single-species, multiple-season models of site occupancy using data collected during demographic surveys of spotted owl territories. In our first analysis, we compared occupancy dynamics of spotted owl nesting territories before (1992–2002) and after the Timbered Rock burn (2003–2006) to a reference area in the south Cascade Mountains that was not affected recently by wildfire. We found that the South Cascades had greater colonization probabilities than Timbered Rock before and after wildfire ( , 95% CI = 0.60–2.03), and colonization probabilities declined over time at both areas ( , 95% CI = −0.12 to 0.00). Extinction probabilities were greater at South Cascades than at Timbered Rock prior to the burn ( , 95% CI = 0.23–2.62); however, Timbered Rock had greater extinction probabilities following wildfire ( , 95% CI = 0.29–2.62). The Timbered Rock and South Cascades study areas had similar patterns in site occupancy prior to the Timbered Rock burn (1992–2001). Furthermore, Timbered Rock had a 64% reduction in site occupancy following wildfire (2003–2006) in contrast to a 25% reduction in site occupancy at South Cascades during the same time period. This suggested that the combined effects of habitat disturbances due to wildfire and subsequent salvage logging on private lands negatively affected site occupancy by spotted owls. In our second analysis, we investigated the relationship between wildfire, salvage logging, and occupancy of spotted owl territories at the Biscuit, Quartz, and Timbered Rock burns from 2003 to 2006. Extinction probabilities increased as the combined area of early seral forests, high severity burn, and salvage logging increased within the core nesting areas ( , 95% CI = 0.10–3.66). We were unable to identify any relationships between initial occupancy or colonization probabilities and the habitat covariates that we considered in our analysis where the β coefficient did not overlap zero. We concluded that site occupancy of spotted owl nesting territories declined in the short-term following wildfire, and habitat modification and loss due to past timber harvest, high severity fire, and salvage logging jointly contributed to declines in site occupancy. © 2013 The Wildlife Society.     

When and where to move: Dynamic occupancy models explain the range dynamics of a food nomadic bird under climate and land cover change

Globally, long‐term research is critical to monitor the responses of tropical species to climate and land cover change at the range scale. Citizen science surveys can reveal the long‐term persistence of poorly known nomadic tropical birds occupying fragmented forest patches. We applied dynamic occupancy models to 13 years (2002–2014) of citizen science‐driven presence/absence data on Cape parrot (Poicephalus robustus), a food nomadic bird endemic to South Africa. We modeled its underlying range dynamics as a function of resource distribution, and change in climate and land cover through the estimation of colonization and extinction patterns. The range occupancy of Cape parrot changed little over time (ψ = 0.75–0.83) because extinction was balanced by recolonization. Yet, there was considerable regional variability in occupancy and detection probability increased over the years. Colonizations increased with warmer temperature and area of orchards, thus explaining their range shifts southeastwards in recent years. Although colonizations were higher in the presence of nests and yellowwood trees (Afrocarpus and Podocarpus spp.), the extinctions in small forest patches (≤227 ha) and during low precipitation (≤41 mm) are attributed to resource constraints and unsuitable climatic conditions. Loss of indigenous forest cover and artificial lake/water bodies increased extinction probabilities of Cape parrot. The land use matrix (fruit farms, gardens, and cultivations) surrounding forest patches provides alternative food sources, thereby facilitating spatiotemporal colonization and extinction in the human‐modified matrix. Our models show that Cape parrots are vulnerable to extreme climatic conditions such as drought which is predicted to increase under climate change. Therefore, management of optimum sized high‐quality forest patches is essential for long‐term survival of Cape parrot populations. Our novel application of dynamic occupancy models to long‐term citizen science monitoring data unfolds the complex relationships between the environmental dynamics and range fluctuations of this food nomadic species.     

Rare but not lost: Endemic mountain lizard occupancy following megafire and grazing disturbances

Wildfire and grazing by invasive herbivores can influence habitat suitability for ground-dwelling fauna, such as reptiles. Australia has a large and diverse reptile fauna, with the Australian Alps bioregion in the southeast of the continent supporting a disproportionately high number of threatened species. In this bioregion, many species are threatened by fire, habitat loss or modification, and invasive species. The range of one such threatened endemic lizard, Cyclodomorphus praealtus (family Scincidae), was impacted by the 2019–20 megafires and is also subject to widespread grazing by invasive species. We investigated the relationship between C. praealtus site occupancy and fire and grazing. We completed 2045 surveys across 120 sites over 4 years, detecting the species at 43% of sites and increasing the species' known geographic range. Using single season detection occupancy models, we found C. praealtus occupancy was not associated with elevation, vegetation height or whether the site was burnt, but was positively associated with grazing activity. Our results indicate that C. praealtus has the capacity to persist following a single fire in some cases, and that habitats with high occupancy probabilities are subject to high grazing pressure. However, our results do not rule out more nuanced impacts associated with these disturbances, which affect a large proportion of C. praealtus' habitat. Our cumulative detection probability calculations revealed that considerable survey effort is often required to determine C. praealtus site occupancy. We therefore recommend that impact assessments assume species presence within areas of suitable habitat within the species' range. Our study improves our understanding of disturbance impacts on C. praealtus' occupancy, while demonstrating the need for sufficiently resourced impact assessments for cryptic and threatened species.     

Monitoring occurrence,extinction, and colonization probabilities for gibbon populations

All gibbon species (Family: Hylobatidae) are considered threatened with extinction and recognized on the International Union for Conservation of Nature Red List of Threatened Species. Because gibbons are one of the most threatened families of primates, monitoring their status is now critically important. Long-term monitoring programs applying occupancy approaches, in addition to assessing occurrence probability, improves understanding of other population parameters such as site extinction or colonization probabilities, which elucidate temporal and spatial changes and are therefore important for guiding conservation efforts. In this study, we used multiple season occupancy models to monitor occurrence, extinction, and colonization probabilities for northern yellow-cheeked crested gibbon Nomascus annamensis in three adjacent protected areas in the Central Annamites mountain range, Vietnam. We collected data at 30 listening posts in 2012, 2014, and 2016 using the auditory point count method. Occurrence probabilities were highest in 2012 (0.74, confidence interval [CI]: 0.56–0.87) but slightly lower in 2014 (0.66, CI: 0.51–0.79) and 2016 (0.67, CI: 0.49–0.81). Extinction probabilities during the 2012–2014 and 2014–2016 intervals were 0.26 (0.14–0.44) and 0.25 (0.12–0.44), respectively. Colonization probabilities during 2012–2014 were 0.44 (0.19–0.73) and between 2014 and 2016 was 0.51 (0.26–0.75). Although local site extinctions have occurred, high recolonization probability helped to replenish the unoccupied sites and kept the occurrence probability stable. Long-term monitoring programs which use occurrence probability alone might not fully reveal the true dynamics of gibbon populations. We strongly recommend including multiple season occupancy models to monitor occurrence, extinction, and colonization probabilities in long-term gibbon monitoring programs.     

Land use drivers of species re‐expansion: inferring colonization dynamics in Eurasian otters

Aim Land use intensity has been recognized as one of the major determinants of native species declines. The re‐expansion of species previously constrained by habitat degradation has been rarely investigated. Here, we use site occupancy models incorporating imperfect detection to identify the land use drivers of the re‐expansion of the Eurasian otter (Lutra lutra). Location Czech Republic. Methods We applied multi‐season occupancy models to otter presence–non‐detection data collected in three national surveys (1992, 2000, 2006) at 552 sites (11.2 × 12 km grid cells). Model parameters included site occupancy, colonization and extinction probabilities, and detection probability at a sub‐site level. We modelled changes in occupancy over time as a function of agricultural, urban and industrial land use and change in the extent of agricultural land use. Results Under the best fitting model, occupancy was estimated to be 34.6% in 1992, 51.3% in 2000 and 83.7% in 2006. Detection probability was neither perfect nor constant. Occupancy probability in 1992 was negatively related to land use gradients. Colonization was more likely to occur where a reduction in agricultural land was larger. Variation in extinction and colonization rates along land use gradients resulted in increased occupancy in industrial and especially urban landscapes. Conversely, occupancy remained almost unchanged along agricultural gradients. Main conclusions Dynamics of otter expansion were strongly associated with the two main patterns of the rapid environmental transition that has taken place in the Czech Republic since the early 1990s. Results show that a reduction in intensive agricultural land use led to an increase in otter distribution, providing evidence of the impact of agricultural land use on stream ecosystems. Moreover, otters recolonized urban and industrial landscapes, probably as a result of extensive reduction in water pollution from point sources. Our results suggest that active conservation of otter populations should focus on restoration of freshwater habitat at large scales, especially in agricultural landscapes.     

Metapopulation dynamics of a beetle species confined to burned forest sites in a managed forest region

Despite increasing awareness of the theoretical importance of habitat dynamics on metapopulations, only a few empirical studies have been conducted. We aimed to increase our understanding of how patch size, dynamics and connectivity affect colonization–extinction dynamics and the occurrence patterns of a beetle (Stephanopachys linearis), which breeds only in burned trees, existing as dynamic habitat patches that have become rare in managed forest landscapes. We assessed species’ presence/absence twice in all known habitat patches (i.e. > 1 ha sites where forest fires had occurred during the previous 2–15 yr) in a 200 × 150 km region of central Sweden, dominated by managed boreal forest. Evaluated over six years, the colonization rate was 47% and the local extinction risk was 65%. Probability of colonization increased with patch size (number of suitable trees in a site) and connectivity to occupied patches within 30 km, and decreased with increasing time since fire. Local extinction risk decreased with habitat patch size but increased, unexpectedly, with connectivity. Occurrence increased with patch size and decreased with increasing time since fire. At a regional scale, S. linearis tracks the fire dynamics by colonising sites with burned trees and by becoming extinct at rates which make the species rare at sites where burnt trees are more than eight years old. In managed boreal forest landscapes, a large proportion of sites may be created by prescribed burning (in our study area: 82%), and consequently human decisions strongly affect the future amount of habitat for fire‐dependent species and its spatial distribution. Stephanopachys linearis uses burned sites more often if more trees are retained and, to some extent, if sites are concentrated in those parts of a region that already support high population densities of the species.     

Ecological Disturbance Through Patch-Burn Grazing Influences Lesser Prairie-Chicken Space Use

Across portions of the western Great Plains in North America, natural fire has been removed from grassland ecosystems, decreasing vegetation heterogeneity and allowing woody encroachment. The loss of fire has implications for grassland species requiring diverse vegetation patches and structure or patches that have limited occurrence in the absence of fire. The lesser prairie-chicken (Tympanuchus pallidicinctus) is a declining species of prairie-grouse that requires heterogeneous grasslands throughout its life history and fire has been removed from much of its occupied range. Patch-burn grazing is a management strategy that re-establishes the fire-grazing interaction to a grassland system, increasing heterogeneity in vegetation structure and composition. We evaluated the effects of patch-burn grazing on lesser prairie-chicken space use, habitat features, and vegetation selection during a 4-year field study from 2014–2017. Female lesser prairie-chickens selected 1- and 2-year post-fire patches during the lekking season, ≥4-year post-fire patches during the nesting season, and year-of-fire and 1-year post-fire patches during post-nesting and nonbreeding seasons. Vegetation selection during the lekking season was not similar to available vegetation in selected patches, suggesting that lesser prairie-chickens cue in on other factors during the lekking season. During the nesting season, females selected nest sites with greater visual obstruction, which was available in ≥4-year post-fire patches; during the post-nesting season, females selected sites with 15–25% bare ground, which was available in the year-of-fire, 1-year post-fire, and 2-year post-fire patches; and during the nonbreeding season they selected sites with lower visual obstruction, available in the year-of-fire and 1-year post-fire patches. Because lesser prairie-chickens selected all available time-since-fire patches during their life history, patch-burn grazing may be a viable management tool to restore and maintain lesser prairie-chicken habitat on the landscape. © 2021 The Wildlife Society.     

Using Grazing to Manage Herbaceous Structure for a Heterogeneity-Dependent Bird

Grazing management recommendations often sacrifice the intrinsic heterogeneity of grasslands by prescribing uniform grazing distributions through smaller pastures, increased stocking densities, and reduced grazing periods. The lack of patch-burn grazing in semi-arid landscapes of the western Great Plains in North America requires alternative grazing management strategies to create and maintain heterogeneity of habitat structure (e.g., animal unit distribution, pasture configuration), but knowledge of their effects on grassland fauna is limited. The lesser prairie-chicken (Tympanuchus pallidicinctus), an imperiled, grassland-obligate, native to the southern Great Plains, is an excellent candidate for investigating effects of heterogeneity-based grazing management strategies because it requires diverse microhabitats among life-history stages in a semi-arid landscape. We evaluated influences of heterogeneity-based grazing management strategies on vegetation structure, habitat selection, and nest and adult survival of lesser prairie-chickens in western Kansas, USA. We captured and monitored 116 female lesser prairie-chickens marked with very high frequency (VHF) or global positioning system (GPS) transmitters and collected landscape-scale vegetation and grazing data during 2013–2015. Vegetation structure heterogeneity increased at stocking densities ≤0.26 animal units/ha, where use by nonbreeding female lesser prairie-chickens also increased. Probability of use for nonbreeding lesser prairie-chickens peaked at values of cattle forage use values near 37% and steadily decreased with use ≥40%. Probability of use was positively affected by increasing pasture area. A quadratic relationship existed between growing season deferment and probability of use. We found that 70% of nests were located in grazing units in which grazing pressure was <0.8 animal unit months/ha. Daily nest survival was negatively correlated with grazing pressure. We found no relationship between adult survival and grazing management strategies. Conservation in grasslands expressing flora community composition appropriate for lesser prairie-chickens can maintain appropriate habitat structure heterogeneity through the use of low to moderate stocking densities (<0.26 animal units/ha), greater pasture areas, and site-appropriate deferment periods. Alternative grazing management strategies (e.g., rest-rotation, season-long rest) may be appropriate in grasslands requiring greater heterogeneity or during intensive drought. Grazing management favoring habitat heterogeneity instead of uniform grazing distributions will likely be more conducive for preserving lesser prairie-chicken populations and grassland biodiversity. © 2021 The Wildlife Society.     

Evaluating the effects of landscape configuration on site occupancy and movement dynamics of odonates in Iowa

Odonates contribute highly to global biodiversity and are considered good indicators of environmental quality, but they are under-studied and quantitative information on their habitat associations is lacking. Our objective was to examine the effects of landscape configuration on site occupancy and movement dynamics of four odonate species in Iowa: Tramea onusta, Epitheca princeps, Pantala flavescens, and Calopteryx maculata. We conducted standardized visual encounter surveys for odonates at 233 public properties in Iowa from 2007 to 2011 and computed landscape variables within a 200, 600 m, and 1 km radius of each surveyed site. Using a robust design occupancy model in Program MARK, we estimated detection probability and site occupancy, site extinction, and site colonization probabilities for each species. We found few significant effects of landscape variables on site occupancy, extinction, or colonization, although landscape variables at 600 m were included in the best model for all species. Detection probability (SE) ranged from 0.30 (0.04) for Pantala flavescens to 0.49 (0.04) for Calopteryx maculata. Our study provides information to aid habitat restoration and management efforts on sites having suitable characteristics in the surrounding landscape and ultimately help conserve odonates.     

Estimating occupancy dynamics in an anuran assemblage from Louisiana,USA

Effective monitoring programs are designed to track changes in the distribution, occurrence, and abundance of species. We developed an extension of Royle and Kéry's (2007) single species model to estimate simultaneously temporal changes in probabilities of detection, occupancy, colonization, extinction, and species turnover using data on calling anuran amphibians, collected from 2002 to 2006 in the Lower Mississippi Alluvial Valley of Louisiana, USA. During our 5-year study, estimates of occurrence probabilities declined for all 12 species detected. These declines occurred primarily in conjunction with variation in estimates of local extinction probabilities (cajun chorus frog [Pseudacris fouquettei], spring peeper [P. crucifer], northern cricket frog [Acris crepitans], Cope's gray treefrog [Hyla chrysoscelis], green treefrog [H. cinerea], squirrel treefrog [H. squirella], southern leopard frog [Lithobates sphenocephalus], bronze frog [L. clamitans], American bullfrog [L. catesbeianus], and Fowler's toad [Anaxyrus fowleri]). For 2 species (eastern narrow-mouthed toad [Gastrophryne carolinensis] and Gulf Coast toad [Incilius nebulifer]), declines in occupancy appeared to be a consequence of both increased local extinction and decreased colonization events. The eastern narrow-mouthed toad experienced a 2.5-fold increase in estimates of occupancy in 2004, possibly because of the high amount of rainfall received during that year, along with a decrease in extinction and increase in colonization of new sites between 2003 and 2004. Our model can be incorporated into monitoring programs to estimate simultaneously the occupancy dynamics for multiple species that show similar responses to ecological conditions. It will likely be an important asset for those monitoring programs that employ the same methods to sample assemblages of ecologically similar species, including those that are rare. By combining information from multiple species to decrease the variance on estimates of individual species, our results are advantageous compared to single-species models. This feature enables managers and researchers to use an entire community, rather than just one species, as an ecological indicator in monitoring programs. © 2011 The Wildlife Society.     

Site Occupancy Dynamics of Northern Spotted Owls in the Eastern Cascades,Washington, USA, 1990–2003

Abstract: Northern spotted owls (Strix occidentalis caurina) have received intense research and management interest since their listing as a threatened species by the United States Fish and Wildlife Service in 1990. Several spotted owl (Strix occidentalis) response variables have been examined in various investigations, but recent advances in statistical modeling permit evaluations of temporal and spatial variability in site occupancy, local-extinction, and colonization probabilities while incorporating imperfect detection probabilities. Following recent work by other researchers on site occupancy dynamics of spotted owls in Oregon, USA, we evaluated temporal variability of detection, occupancy, local-extinction, and colonization probabilities for spotted owls, as well as potential influences of barred owl (Strix varia) presence on these parameters. We used spotted owl survey data collected from 1990 to 2003 on a study area in the eastern Cascades Mountains, Washington, USA, to compare competing occupancy models from Program PRESENCE using Akaike's Information Criterion. Detection probabilities for individual spotted owls ranged from 0.54 to 0.80 if barred owls were not detected during the survey season and from 0.19 to 0.71 if barred owls were detected during the survey season. Pair detection probabilities ranged from 0.27 to 0.67 if barred owls were not detected during an individual survey and from 0.09 to 0.36 if barred owls were detected during an individual survey. During the study, site occupancy probabilities for spotted owl pairs declined by approximately 50%. For all spotted owls, both singles and pairs, site occupancy probabilities declined moderately during the study. Barred owl presence was negatively associated with spotted owl detection probabilities, and it had a positive association with local-extinction probabilities for all spotted owls, both singles and pairs. Given that our study area has supported higher densities of barred owls for longer periods than other study areas, our results may provide insight into how barred owls have influenced spotted owl site occupancy dynamics in adjacent British Columbia, Canada, or will influence spotted owl site occupancy dynamics in Oregon and California, USA, in the future.     

高原鼠兔在不同植被覆盖的立地占据、局部灭绝和建群率研究

青藏高原的草地生态系统被野生动物和家畜广泛地利用。大型有蹄类动物的放牧和小型哺乳类动物的挖掘行为,会改变其栖息地的植物群落。基于拉萨市墨竹工卡县日多镇年村牦牛(Bos grunniens)放牧的实践,我们发现高原鼠兔(Ochotona curzoniae)立地占域率、建群和区域灭绝率与栖息地变量之间存在一定的格局关系。为了了解高原鼠兔立地占域率、建群和区域灭绝率与栖息地之间的关系,我们采用多季节性立地占据模型,利用Presence软件对相关数据进行分析。结果表明,高原鼠兔局部灭绝率与植被覆盖度之间存在正相关性,而与建群率之间则呈负相关性。     

Effects of controlled livestock grazing and annual prescribed fire on epigeal termite mounds in a savannah woodland in Burkina Faso

The diversity and abundance of epigeal termite mounds were investigated in response to controlled livestock grazing and annual prescribed fire in a Sudanian savannah-woodland in Tiogo State Forest. Sampling of termite mounds was carried out in 4×4 subplots of 0.25 ha in a split-plot experimental design during the rainy season in 2002. There were two main plots of which one was fenced to exclude livestock grazing and the second exposed to grazing. Each of the main plots included 4 subplots with annual prescribed fire since 1992 and 4 subplots without fire. Data were collected on the number and characteristics of termite mounds. A mean density of 698 mounds ha⁻¹ was recorded. Mounds built by Trinervitermes spp. were the most abundant followed by Cubitermes spp., Macrotermes subhyalinus and M. bellicosus. The large mound-builders Macrotermes spp. dominated the community interms of basal area (96% of the total) and above-ground volume (99%). The diversity of mound types was notaffected by livestock grazing and annual early prescribed fire (P>0.05). There was no statistical effect of livestock grazing on mound density, whereas a strong depressive effect of annual fire was observed for Trinervitermes spp. mound density (P=0.012). In this ecosystem, annual prescribed fire appeared to be the major determinant for termite mound abundance. Received 2 February 2007; revised 23 October 2007 and 21 January 2008; accepted 22 Feburary 2008.     

Colonization of Pinus halepensis in Mediterranean habitats: consequences of afforestation, grazing and fire

The expansion of P. halepensis from plantations into natural sites of high conservation value is becoming a frequent occurrence across the Mediterranean zone of Israel. We studied how colonization of Pinus halepensis in natural Mediterranean habitats is related to afforestation, cattle grazing and fire. The study was conducted in a Mediterranean garrigue (Shrubland) located in Ramat Hanadiv Nature Park, southern Mt. Carmel region, Israel. The study area (ca. 350 ha) was divided into cells (100 × 100 m) each of which was categorized with respect to distance from planted pines, grazing (grazed since 1990/ungrazed), fire (burned in 1980/unburned), and vegetation structure (garrigue, dense garrigue, dense woodland). The location of colonizing pines, typically three m or more in height, was determined using an aerial photograph. Density of colonizing pines decreased linearly with the distance from planted pines within 300 m from planted pines with a long tail that extended out to ca 1,000 m. Over 90% of the colonizing pines that were found were located within a distance of 300 m (56% of the park area) from planted pines. Colonization was about two times greater under grazing than without grazing. The effects of fire and of the interaction fire × grazing were found insignificant. A separate analysis reveled that colonization was about 2 times larger in patches of sparse woody cover than in those of dense cover. In conclusion, pine colonization was mainly determined by the proximity to seed sources. Additionally, pine colonization was enhanced by cattle grazing probably through reduction of the natural vegetation cover.     

Impacts of a mineral lick‐centred land use system on woody vegetation cover in an East African Savannah

Evaluation of woody vegetation changes with distance from a salt crater was conducted in the semi‐arid rangelands of southern Ethiopia. Data on live woody plants were collected over three seasons at 0, 1, 4, 6, 9 and 12 km from the salt crater. The density and diversity of woody plants differed significantly (p < .01) along the distance gradient. Six woody plant families were identified of which Fabaceae and Burseraceae were the dominant families. Acacia drepanolobium, Acacia nilotica, Commiphora africana and Acacia mellifera were among the severely encroaching woody species. There were high proportions of seedlings and saplings recorded closer to the salt crater showing a vigorous recruitment by woody plants. Woody plant encroachment along the 12‐km transect ranged from a low to severe encroachment, which could be translated into poor rangeland condition. Changes in soil characteristics increased grazing pressure and sedentary settlement around the salt crater, and the breakdown of traditional institutions seems to be major contributing factors to these vegetation changes. We suggest that severely encroached areas could be improved through a combination of methods such as bush clearing, prescribed fire, browsing animals and proper grazing management.     

The relative contribution of local habitat and landscape context to metapopulation processes: a dynamic occupancy modeling approach

Changes in site occupancy across habitat patches have often been attributed to landscape features in fragmented systems, particularly when considering metapopulations. However, failure to include habitat quality of individual patches can mask the relative importance of local scale features in determining distributional changes. We employed dynamic occupancy modeling to compare the strength of local habitat variables and metrics of landscape patterns as drivers of metapopulation dynamics for a vulnerable, high‐elevation species in a naturally fragmented landscape. Repeat surveys of Bicknell's thrush Catharus bicknelli presence/non‐detection were conducted at 88 sites across Vermont, USA in 2006 and 2007. We used an organism‐based approach, such that at each site we measured important local‐scale habitat characteristics and quantified landscape‐scale features using a predictive habitat model for this species. We performed a principal component analysis on both the local and landscape features to reduce dimensionality. We estimated site occupancy, colonization, and extinction probabilities while accounting for imperfect detection. Univariate, additive, and interaction models of local habitat and landscape context were ranked using AICc scores. Both local and landscape scales were important in determining changes in occupancy patterns. An interaction between scales was detected for occupancy dynamics indicating that the relationship of the parameters to local‐scale habitat conditions can change depending on the landscape context and vice versa. An increase in both landscape‐ and local‐scale habitat quality increased occupancy and colonization probability while decreasing extinction risk. Colonization and extinction were both more strongly influenced by local habitat quality relative to landscape patterns. We also identified clear, qualitative thresholds for landscape‐scale features. Conservation of large habitat patches in high‐cover landscapes will help ensure persistence of Bicknell's thrushes, but only if local scale habitat quality is maintained. Our results highlight the importance of incorporating information beyond landscape characteristics when investigating patch occupancy patterns in metapopulations.     

Human disturbance and stage‐specific habitat requirements influence snowy plover site occupancy during the breeding season

Habitat use has important consequences for avian reproductive success and survival. In coastal areas with recreational activity, human disturbance may limit use of otherwise suitable habitat. Snowy plovers Charadrius nivosus have a patchy breeding distribution along the coastal areas on the Florida Panhandle, USA. Our goal was to determine the relative effects of seasonal human disturbance and habitat requirements on snowy plover habitat use. We surveyed 303 sites for snowy plovers, human disturbance, and habitat features between January and July 2009 and 2010. We made multiple visits during three different sampling periods that corresponded to snowy plover breeding: pre‐breeding, incubation, and brood‐rearing and used multi‐season occupancy models to examine whether human disturbance, habitat features, or both influenced site occupancy, colonization (probability of transition from an unoccupied site to an occupied site), and extinction (probability of transition from an occupied site to an unoccupied site). Snowy plover site occupancy and colonization was negatively associated with human disturbance and site extinction was positively associated with human disturbance. Interdune vegetation had a negative effect on occupancy and colonization, indicating that plovers were less likely to use areas with uniform, dense vegetation among dunes. Also, dune shape, beach debris, and access to low‐energy foraging areas influenced site occupancy, colonization, and extinction. Plovers used habitat based on beach characteristics that provided stage‐specific resource needs; however, human disturbance was the strongest predictor of site occupancy. In addition, vegetation plantings used to enhance dune rehabilitation may negatively impact plover site occupancy. Management actions that decrease human disturbance, such as symbolic fencing and signage, may increase the amount of breeding habitat available to snowy plovers on the Florida Panhandle and in other areas with high human activity. The specific areas that require this protection may vary across snowy plover life history stages.     

Spatial dynamics of an invasive bird species assessed using robust design occupancy analysis: the case of the Eurasian collared dove (Streptopelia decaocto) in France

Aim The study of the spatial dynamics of invasive species is a key issue in invasion ecology. While mathematical models are useful for predicting the extent of population expansions, they are not suitable for measuring and characterizing spatial patterns of invasion unless the probability of detection is homogeneous across the distribution range. Here, we apply recently developed statistical approaches incorporating detection uncertainty to characterize the spatial dynamics of an invasive bird species, the Eurasian collared dove (Streptopelia decaocto). Location France. Methods Data on presence/absence of doves were recorded from 1996 to 2004 over 1045 grid cells (28 × 20 km) covering the entire country. Each grid cell included five point counts spaced along a route, which was visited twice a year, allowing for an estimation of detection probability. Each route was assigned to one of six geographical regions. We used robust design occupancy analysis to assess spatial and temporal variation in parameters related to the spatial dynamics of the species. These parameters included occupancy rate, colonization and local extinction probabilities. Our inference approach was based on the selection of the most parsimonious model among competitive models parametrized with conditional probabilities. Results The probability of detecting the presence of doves on a given route was high. However, we found evidence to incorporate detection uncertainty in inference processes about spatial dynamics, since detection probability was neither perfect (i.e. it was < 1), nor constant over space and time. Results showed a clear positive trend in occupancy rate over the study period, increasing from 55% in 1996 to 76% in 2004. In addition, occupancy rate differed among regions (range: 37–79%) and further analysis showed that colonization probability by region was positively related to occupancy rate. Finally, local extinction probability was lower than colonization probability and showed a tendency to decrease over the study period. Main conclusions Our results emphasize the importance of estimating detection probabilities in order to draw proper inferences about the spatial and temporal dynamics of the invasion pattern of the collared dove. In contrast to the perceived spatial dynamics from national atlas surveys, we provide evidence that the range of this species is currently increasing in France. Other results, such as regional specificity in colonization probabilities and time variation in local extinction are consistent with expectations from invasion and metapopulation theory.