The combined effects of habitat quality, breeder experience and sociobiology on population demography are poorly understood. Natural fire regimes, which influence habitat quality and sociobiology, have been replaced by controlled fire management in most ecosystems. Managing fire mosaics (vegetation at different ages since fire) can be important to sustain species in fire-maintained habitats, but requirements are usually poorly defined. Source-sink theory provides a foundation to quantify such habitat heterogeneity, but source-sink applications are largely focused on modeling. We quantified how habitat quality, breeder experience and non-breeding adult helpers affected Florida scrub-jay (Aphelocoma coerulescens) recruitment to describe source-sink heterogeneity within local populations. We used 22 years of census data of uniquely marked Florida scrub-jays to measure recruitment at 36 sites and combined that data with habitat-specific survival to characterize habitat-specific demography. To define habitat quality at the territory scale, we used static habitat features (soils, scrub oak cover) and dynamic habitat states (shrub heights and open sandy patches) that resulted from fire mosaics. Habitat quality most affected recruitment followed by the presence of helpers; fire mosaics, described by habitat states, determined whether territories functioned as strong sources, weak sources or sinks. Subdividing landscapes into habitat states allowed quantification of the fire mosaic at the territory scale and population scale, as the proportions of habitat states can predict local population growth rates. Our approach provides an example of how characterizing habitat quality at the territory scale, relative to source-sink categories, can explain habitat heterogeneity within local populations and inform fire management. bs_bs_banner Animal Conservation. Print

Quantifying habitat occupancy of the southeastern beach mouse Peromyscus polionotus niveiventris is important for managing this threatened species throughout its limited range. Tracking tubes were used to detect the southeastern beach mouse in coastal areas on the federal lands of the Kennedy Space Center, Cape Canaveral Air Force Station, and Canaveral National Seashore. Because this method relied on observations of footprints, detections of beach mice were confounded by the co-occurrence of cotton mice Peromyscus gossypinus, which have wider but slightly overlapping footprint widths. Mice of both species were captured and footprinted using tracking tubes to collect a database of footprints of known identity. These data were used to develop a Bayesian hierarchical model of the cutoff width at which a print could be assigned as a beach mouse with a known probability of error. Specifically, within the model, observed footprint widths were used to estimate a mean and variance of footprint width for each species, while accounting for variation between individual mice. Then, a distribution of new footprint widths was generated for each species by drawing from their modeled distributions. Finally, the new footprints were compared with a range of potential cutoff widths to evaluate the proportion of times the correct decision to exclude or accept the footprint was made. We graphically evaluated the performance of the cutoff widths and chose one that traded off between reducing false positives and retaining more correct detections for use in occupancy models. We explored the use of the cutoff width using occupancy models that allow for false-positive detections, and found that the use of the cutoff performed as expected. Over 40% of primary dune habitat on the Kennedy Space Center was occupied by beach mice during the period sampled. The proportion of vegetated habitat at a site had a negative influence on detection probability. No ecological covariates had a measurable influence on beach mouse occupancy, probably due to the limited range of environmental variation in the sampled region. The use of a cutoff for footprint width resulted in a reliable method to deal with false-positive detections in tracking tubes with small mammals and allowed the use of occupancy models that rely on certain detection.

Adult nonbreeders are important for the stability and conservation of many species despite that their functional roles are often undervalued. Nonbreeders can buffer breeding population sizes and help their kin raise new generations of offspring, but in high numbers can compete and have negative effects. Long‐term studies are useful for elucidating relationships among nonbreeder population parameters, such as density, survival, and transitions to breeding status. Florida scrub‐jays are cooperative breeders where young delay breeding often for many years and are at risk of extinction across most of their range. Our objectives were to estimate how population covariates (pair density and mean family size) influenced Florida scrub‐jay adult nonbreeder survival and breeding transitions using long‐term data of uniquely marked birds and multistate capture–recapture models. The evolution and maintenance of Florida scrub‐jay delayed breeding has been attributed to living in crowded and sharply delineated habitat at Archbold Biological Station, the site of longest long‐term study. Contrastingly, most habitat we studied had a dynamic mixture of habitat quality with mean family sizes and pair densities much lower than the stable, optimal habitat at Archbold Biological Station. Despite having densities below carrying capacity, Florida scrub‐jays still delayed breeding. We found that greater mean family size was associated with greater breeder survival, possibly because nonbreeders contributed to predator detection and territory defense. Nonbreeder‐to‐breeder transitions increased with increased annual breeder mortality rates but were influenced little by population densities. Most Florida scrub‐jays became breeders by replacing dead breeders within occupied territories, and many male and female nonbreeders inherited their territories upon the death of their parents. Nonbreeders buffered changes in the breeding population supporting greater recognition of nonbreeder population roles within field and modeling studies.

Fecundity, the number of young produced by a breeding pair during a breeding season, is a primary component in evolutionary and ecological theory and applications.Fecundity can be influenced by many environmental factors and requires long-term study due to the range of variation in ecosystem dynamics. Fecundity data often include a large proportion of zeros when many pairs fail to produce any young during a breeding season due to nest failure or when all young die independently after fledging. We conducted color banding and monthly censuses of Florida scrub-jays (Aphelocoma coerulescens) across 31 years, 15 populations, and 761 territories along central Florida's Atlantic coast. We quantified how fecundity (juveniles/pair-year) was influenced by habitat quality, presence/absence of nonbreeders, population density, breeder experience, and rainfall, with a zero-inflated Bayesian hierarchical model including both a Bernoulli (e.g., brood success) and a Poisson (counts of young) submodel, and random effects for year, population, and territory. The results identified the importance of increasing "strong" quality habitat, which was a mid-successional state related to fire frequency and extent, because strong territories, and the proportion of strong territories in the overall population, influenced fecundity of breeding pairs. Populations subject to supplementary feeding also had greater fecundity.Territory size, population density, breeder experience, and rainfall surprisingly had no or small effects. Different mechanisms appeared to cause annual variation in fecundity, as estimates of random effects were not correlated between the success and count submodels. The increased fecundity for pairs with nonbreeders, compared to pairs without, identified empirical research needed to understand how the proportion of low-quality habitats influences population recovery and sustainability, because dispersal into low-quality habitats can drain nonbreeders from strong territories and decrease overall fecundity. We also describe how long-term study resulted in reversals in our understanding because of complications involving habitat quality, sociobiology, and population density.

Track tubes are a noninvasive, efficient method to monitor populations of small mammals that can be implemented on a large landscape scale and are a cost-effective approach for certain sampling situations. As with all field sampling tools, modifications are made depending on research objectives, habitat being sampled, and target species. We conducted two experiments with the objective to increase efficiency and decrease labor while retaining high detection probabilities as part of an Annual Multi-Agency Regional Southeastern Beach Mouse Peromyscus polionotus niveiventris Habitat Occupancy Survey. We conducted studies along a contiguous 72-km coastline of the Cape Canaveral Barrier Island Complex in east-central Florida, USA, that includes the Kennedy Space Center, Cape Canaveral Air Force Station, and Canaveral National Seashore. We conducted the experiments to address several issues that had regularly compromised our survey data. One experiment assessed the ideal length of deployment times for track tubes in various habitat types with multiple species where southeastern beach mice were previously detected. Another experiment, determined how to restrict certain meso-mammal species (raccoons Procyon lotor, and eastern spotted skunks Spilogale putorius) from knocking over the tubes or reaching into the tubes, thus reducing disturbance that results in missing data; or from entering the tubes (cotton rats Sigmodon hispidus), thereby obscuring any potential or actual footprints of the southeastern beach mouse or other targeted species. We observed an increase in the detection rate of southeastern beach mice in track tubes with increased nights of deployment (likelihood ratio test v 2 ¼ 18.71, df ¼ 3, P , 0.001) with the greatest increase between 3 nights and 6 nights and apparent leveling off between nights 9 and 12 and a large decrease in the detection rate of southeastern beach mice in track tubes with 0.5-in. (1.3-cm) excluders compared with the other-size excluders (likelihood ratio test v 2 ¼ 167.89, df ¼ 5, P , 0.001). We also found that 1-in. (2.5-cm) excluders prevented access by meso-mammals or entry by cotton rats and did not adversely affect the detection of either beach mice or cotton mice Peromyscus gossypinus, but did reduce disturbance and resulted in fewer missing data. These statistically significant process improvements have application for others involved with small mammal monitoring and species management. Citation: Oddy DM, Stolen ED, Gann SL, Legare SA, Weiss SK, Holloway-Adkins KG. 2018. Increasing detection by reducing disturbance and excluding nontarget small mammal species: an occupancy study approach.

Habitat occupancy models, designed to deal with non‐detection of a target species in occupied sites, have been expanded to allow for false‐positive detections when species are mistakenly detected in unoccupied sites. When a subset of the data are unambiguous detections, such occupancy models can produce reliable results. However, if not properly accounted for, heterogeneity in the rate of false‐positive detection between sites may bias estimates of habitat occupancy. We studied habitat occupancy of the southeastern beach mouse (Peromyscus polionotus niveiventris), a species along Florida's Atlantic coast that is threatened due to the reduction of its core range by over 79% since 1950. Southeastern beach mice were detected based on their footprints in track tubes, but because of co‐occurrence of the cotton mouse (Peromyscus gossypinus) with overlapping footprint size, we had to allow for possible false‐positive detections. Differences in the relative abundance of these two species between habitats may have resulted in heterogeneity in the false‐positive rate. By combining uncertain (track tube) and certain (live capture) detection methods, we were able to use covariates to account for heterogeneity in false‐positive detection rates between habitats. Southeastern beach mouse habitat occupancy was higher in coastal dune and strand habitat than in coastal scrub or interior scrub habitats. The rate of false‐positive detections was much higher in coastal scrub habitat than in coastal dune and strand habitat or interior scrub habitat, reinforcing the need for methods that accommodate heterogeneity in the rate of false positives to reduce bias in estimates of habitat occupancy. Using simulations, we show that heterogeneity in the false‐positive detection rate leads to bias in habitat occupancy estimates unless properly accounted for. We also discuss how differences in relative abundance between the target species and a confusing species can directly impact the heterogeneity of false‐positive detections.

Juvenile survival in birds is difficult to estimate but this vital rate can be an important consideration for management decisions. We estimated juvenile survival of cooperatively breeding Florida Scrub-Jays (Aphelocoma coerulescens) in a landscape degraded by fire suppression and fragmentation using data from marked (n = 325) and unmarked juveniles (n = 1,306) with an integrated hierarchical Bayesian model. To assess the combined analyses, we also analyzed these datasets separately, with a Cormack-Jolly-Seber (CJS) model (marked) and young model (unmarked). Our data consisted of monthly censuses of territorial family groups from Florida Scrub-Jay populations in East Central Florida collected over a 22-yr period. Juvenile survival was estimated from July when young Florida Scrub-Jays begin developing independence to March when they become first year individuals and grouped according to the habitat quality class of their natal territory that were based on shrub height (with intermediate shrub heights being optimal and short and tall shrub heights being suboptimal) and the presence of sandy openings (the preferred open having many sandy openings; closed not having enough). Parameter estimates in the combined analysis were intermediate to the separate analyses. Notable differences among the separate analyses were that suboptimal habitat survival was lower in the unmarked analysis, the unmarked analysis showed a linear effect of time not seen in the marked analysis, and there was an effect of male breeder death in the marked but not unmarked analysis. The combined data analysis provided more inference than did either data set analyzed separately including juveniles in optimal-closed territories unexpectedly had higher survival than those in optimal-open, survival increased through time, and male breeder death had a negative effect on survival. This study suggests that optimal-closed habitat may play an important role in juvenile Florida Scrub-Jay survival perhaps by providing better cover from predators and warrants further investigation for management implications.