Spatial patch occupancy patterns of the Lower Keys marsh rabbit

Reliable estimates of presence or absence of a species can provide substantial information on management questions related to distribution and habitat use but should incorporate the probability of detection to reduce bias. We surveyed for the endangered Lower Keys marsh rabbit (Sylvilagus palustris hefneri) in habitat patches on 5 Florida Key islands, USA, to estimate occupancy and detection probabilities. We derived detection probabilities using spatial replication of plots and evaluated hypotheses that patch location (coastal or interior) and patch size influence occupancy and detection. Results demonstrate that detection probability, given rabbits were present, was <0.5 and suggest that naïve estimates (i.e., estimates without consideration of imperfect detection) of patch occupancy are negatively biased. We found that patch size and location influenced probability of occupancy but not detection. Our findings will be used by Refuge managers to evaluate population trends of Lower Keys marsh rabbits from historical data and to guide management decisions for species recovery. The sampling and analytical methods we used may be useful for researchers and managers of other endangered lagomorphs and cryptic or fossorial animals occupying diverse habitats. © 2011 The Wildlife Society.     

Occupancy in dynamic systems: accounting for multiple scales and false positives using environmental DNA to inform monitoring

Occupancy is an important metric to understand current and future trends in populations that have declined globally. In addition, occupancy can be an efficient tool for conducting landscape-scale and long-term monitoring. A challenge for occupancy monitoring programs is to determine the appropriate spatial scale of analysis and to obtain precise occupancy estimates for elusive species. We used a multi-scale occupancy model to assess occupancy of Columbia spotted frogs in the Great Basin, USA, based on environmental DNA (eDNA) detections. We collected three replicate eDNA samples at 220 sites across the Great Basin. We estimated and modeled ecological factors that described watershed and site occupancy at multiple spatial scales simultaneously while accounting for imperfect detection. Additionally, we conducted visual and dipnet surveys at all sites and used our paired detections to estimate the probability of a false positive detection for our eDNA sampling. We applied the estimated false positive rate to our multi-scale occupancy dataset and assessed changes in model selection. We had higher naïve occupancy estimates for eDNA (0.37) than for traditional survey methods (0.20). We estimated our false positive detection rate per qPCR replicate at 0.023 (95% CI: 0.016–0.033). When the false positive rate was applied to the multi-scale dataset, we did not observe substantial changes in model selection or parameter estimates. Conservation and resource managers have an increasing need to understand species occupancy in highly variable landscapes where the spatial distribution of habitat changes significantly over time due to climate change and human impact. A multi-scale occupancy approach can be used to obtain regional occupancy estimates that can account for spatially dynamic differences in availability over time, especially when assessing potential declines. Additionally, this study demonstrates how eDNA can be used as an effective tool for improved occupancy estimates across broad geographic scales for long-term monitoring.     

Quantifying the impacts of bushfire on populations of wild koalas (Phascolarctos cinereus): Insights from the 2019/20 fire season

The impact of bushfire events on wild Koala (Phascolarctos cinereus) populations is poorly understood. Following the 2019/2020 bushfire season in eastern Australia, we resurveyed 123 field sites for which contemporaneous (current koala generation) pre‐fire survey data were available. Field sites were distributed across six fire grounds between Foster and Ballina on the north coast of New South Wales. At these sites, pre‐fire naïve occupancy levels by koalas ranged from 25% to 71% of the sampled habitat, while post‐fire naïve occupancy levels ranged from 0% to 47%. The median reduction in the naïve occupancy rate by koalas when considered across all six fire grounds was 71% when standardized against pre‐fire occupancy levels. Field data provided strong corroboration between site‐based, post‐fire foliage canopy cover estimates and modelled Google Earth Engine Burnt Area Map (GEEBAM) fire‐severity categories. In terms of GEEBAM fire‐severity categories, koala survival was five times more likely in areas where forest canopies were modelled as Unburnt or Partially burnt, compared to areas where forest canopies were Fully burnt. The capacity of bushfire‐affected koala populations to recover from the 2019/20 fire season will be conditional upon size of the original population in each fire‐affected area, the enactment and implementation of supportive, recovery‐themed management regimes, future inter‐fire intervals and associated intensities. Management actions necessary to assist recovery actions are discussed.     

Changes in Kit Fox Defecation Patterns During the Reproductive Season: Implications for Noninvasive Surveys

Abstract: Noninvasive survey methods based on analyzing DNA extracted from feces can be useful for carnivores that are difficult to study by other methods. Changes in fecal deposition patterns associated with reproduction in kit foxes (Vulpes macrotis) might affect results of such surveys. We used a trained dog to collect fresh scats on 2-km transects in the home ranges of 11 radiocollared female kit foxes in January, February, and March 2008 and determined sex of the individual that deposited the scats by amplifying the zinc finger protein gene. Female foxes give birth in mid-February to mid-March. We found a similar number of scats each month. In January, the sex ratio of the scats was not different from the expected 1:1. However, in February there were almost 2 male scats for every female scat and in March there were >8 male scats for every female scat. Comparing March to January, there were more male scats on all 11 transects and fewer female scats on 10 of 11 transects. Around the time pups are born, both sexes appear to show changes in fecal deposition patterns that make it easier to find male scats and harder to find female scats. Effects of these changes on survey results will vary depending on the purpose and design of the survey. Surveys to determine distribution and relative abundance would probably not be negatively affected by these changes. However, if surveys to estimate abundance are conducted during the reproductive season, they could result in an underestimate of population size unless the increased heterogeneity in scat detectability is taken into account.     

Evaluating monitoring methods to guide adaptive management of a threatened amphibian (Litoria aurea)

Prompt detection of declines in abundance or distribution of populations is critical when managing threatened species that have high population turnover. Population monitoring programs provide the tools necessary to identify and detect decreases in abundance that will threaten the persistence of key populations and should occur in an adaptive management framework which designs monitoring to maximize detection and minimize effort. We monitored a population of Litoria aurea at Sydney Olympic Park over 5 years using mark–recapture, capture encounter, noncapture encounter, auditory, tadpole trapping, and dip‐net surveys. The methods differed in the cost, time, and ability to detect changes in the population. Only capture encounter surveys were able to simultaneously detect a decline in the occupancy, relative abundance, and recruitment of frogs during the surveys. The relative abundance of L. aurea during encounter surveys correlated with the population size obtained from mark–recapture surveys, and the methods were therefore useful for detecting a change in the population. Tadpole trapping and auditory surveys did not predict overall abundance and were therefore not useful in detecting declines. Monitoring regimes should determine optimal survey times to identify periods where populations have the highest detectability. Once this has been achieved, capture encounter surveys provide a cost‐effective method of effectively monitoring trends in occupancy, changes in relative abundance, and detecting recruitment in populations.     

Detection distance and environmental factors in conservation detection dog surveys

Surveys using conservation detection dogs have grown increasingly popular as an efficient means to gather monitoring data, particularly for elusive and low-density species such as carnivores. Working with dogs can greatly increase the area surveyed for wildlife and the detection rate of survey targets. Due to the confounding effects of scent dispersion and dog movement, however, it can be difficult to estimate the area searched in a survey. Additionally, although detection dogs have been used in studies under a wide range of air temperature, humidity, and wind conditions, little research has examined how environmental factors affect detection dogs' effectiveness for wildlife surveys. Between 2003 and 2005, we trained 2 dogs to assist us with surveys for mammalian carnivore scats in northern California. We conducted controlled search trials to assess how the dogs' scat detection rates were affected by the distance of scats from the transect search line, as well as variation in six environmental factors. Both dogs detected >75% of scats located within 10 m, and the dogs' detection rates decreased with increasing distance of scats from the transect line. Among environmental factors, precipitation was the most important variable explaining variation in scat detection rates for both dogs. Precipitation likely degrades or removes scats from the landscape over time, and detection rates increase as scat begins to accumulate following the last substantial (>5 mm) rain event of the year. If scat accumulation is not controlled for in ecosystems with a strong seasonal pattern of rainfall, it could lead to considerable bias in study results. We recommend that researchers report the conditions under which conservation detection dog surveys took place and analyze how detection rates vary as a function of distance, temperature, precipitation, humidity, wind, and other locally important environmental factors. © 2010 The Wildlife Society.     

The use of infrared‐triggered cameras for surveying phasianids in Sichuan Province,China

We report on the use of infrared‐triggered cameras as an effective tool to survey phasianid populations in Wanglang and Wolong Nature Reserves, China. Surveys at 183 camera‐trapping sites recorded 30 bird species, including nine phasianids (one grouse and eight pheasant species). Blood Pheasant Ithaginis cruentus and Temminck’s Tragopan Tragopan temminckii were the phasianids most often detected at both reserves and were found within the mid‐elevation range (2400–3600 m asl). The occupancy rate and detection probability of both species were examined using an occupancy model relative to eight sampling covariates and three detection covariates. The model estimates of occupancy for Blood Pheasant (0.30) and Temminck’s Tragopan (0.14) are close to the naïve estimates based on camera detections (0.27 and 0.13, respectively). The estimated detection probability during a 5‐day period was 0.36 for Blood Pheasant and 0.30 for Temminck’s Tragopan. The daily activity patterns for these two species were assessed from the time/date stamps on the photographs and sex ratios calculated for Blood Pheasant (152M : 72F) and Temminck’s Tragopan (48M : 21F). Infrared cameras are valuable for surveying these reclusive species and our protocol is applicable to research or monitoring of phasianids.     

Towards more efficient large-scale DNA-based detection of terrestrial mammal predators from scats

The DNA detection of wildlife from environmental samples has the potential to contribute significantly to wildlife management and ecological research. In terrestrial ecosystems, much work has focused on the identification of mammal predators from faecal (scat) samples. However, the relatively high time and financial costs of collecting and analysing scat DNA remain barriers to more widespread implementation of such DNA detection methods, especially for high-throughput surveys. Here, we evaluate methods used for DNA extraction from scats, as applied to detection of the Australian red fox, an introduced predator. We compare the relative costs of two approaches: the method previously used to screen thousands of scat samples in surveys over several years, and a modified version which involves swabbing scats at the time of collection and using a mechanised liquid handling platform to extract DNA from the swabs. We demonstrate that mechanised DNA extraction from swabs is more efficient than manual DNA extraction from whole scats, in terms of both time and resources. This provides a means for rapid, high-throughput screening of scats for the presence of mammal predators, enabling time-effective management responses to non-invasive surveys.     

Comparing contemporary models to traditional indices to estimate abundance of desert bighorn sheep

Aerial surveys for large ungulates produce count data that often underrepresent the number of animals. Errors in count data can lead to erroneous estimates of abundance if they are not addressed. Our objective was to address imperfect detection probability by developing a framework that produces realistic and defensible estimates of bighorn sheep (Ovis canadensis) abundance. We applied our framework to a population of desert bighorn sheep (O. c. nelsoni) in the Great Basin, Nevada, USA. We captured and marked 24 desert bighorn sheep with global positioning system (GPS)-collars and then conducted helicopter surveys naïve to the locations of collared animals. We developed a Bayesian integrated data model to leverage information from telemetry data, helicopter survey counts, and habitat characteristics to estimate abundance while accounting for availability and perception probability (i.e., detection given availability). Distance to ridgeline, terrain ruggedness, tree cover, and slope influenced perception probability of sheep given they were viewable from the helicopter. There was also annual variation in perception probability (2018: median = 0.64, credible interval [CrI] = 0.37–0.87; 2019: median = 0.81, CrI = 0.49–0.97). The abundance estimates from the integrated data model decreased from 2018 (594; 95% CrI = 537–656) to 2019 (487; 95% CrI = 436–551). In addition, accounting for availability and imperfect perception resulted in greater estimates of abundance compared to traditional directed search methods, which were 340 for 2018 and 320 for 2019. Our modeling framework can be used to generate more defensible population estimates of bighorn sheep and other large mammals that have been surveyed in a similar manner.     

Monitoring site occupancy for American mink in its native range

American mink (Neovison vison) are secretive, semi-aquatic carnivores that often require noninvasive methods based on field signs such as tracks and scat for determining their spatial distribution. Most previous assessments of survey methods for American mink have been conducted in the United Kingdom where mink are an invasive species. We evaluated survey techniques for American mink in riparian habitat in its native range in the midwestern United States. We used occupancy modeling to compare detection rates between walking surveys and mink raft surveys, and we evaluated the potential for environmental covariates and observer bias to influence detectability from walking surveys. Per-survey detection probabilities were greater for walking surveys (0.72) than for mink rafts (0.39). Walking surveys also were cheaper and easier to conduct in small streams prone to flooding when compared to mink raft surveys. However, detection probabilities from walking surveys were affected by observer bias, recent rainfall, substrate, and date. We recommend walking surveys for determining the distribution of American mink in riparian habitat in the Midwest if occupancy modeling is applied to adjust for environmental and observer effects on detectability. We used such an approach to demonstrate occupancy dynamics of mink were related to variable water depths, which has implications for how this carnivore might be influenced by climate change. Mink rafts standardize the substrate for recording mink tracks and reduce the likelihood of observer effects. For studies using many volunteers, we recommend mink rafts for determining site occupancy by American mink. © 2011 The Wildlife Society.     

Using bioacoustics to enhance the efficiency of spotted owl surveys and facilitate forest restoration

The California spotted owl (Strix occidentalis occidentalis) is an older-forest associated species that resides at the center of forest management planning in the Sierra Nevada and Southern California, USA, which are experiencing increasingly large and severe wildfires and drought-related tree mortality. We leveraged advances in passive acoustic survey technologies to develop an acoustically assisted survey design that could increase the efficiency and effectiveness of project-level surveys for spotted owls, allowing surveys to be completed in a single year instead of in multiple years. We deployed an array of autonomous recording units (ARUs) across a landscape and identified spotted owl vocalizations in the resulting audio using BirdNET. We then evaluated spatio-temporal patterns in spotted owl vocalizations near occupied territories and the ability of a crew naïve to the location of occupied territories to locate spotted owls based on patterns of acoustic detections. After only 3 weeks of acoustic surveys, ≥1 ARU within 750 m of all 17 occupied territories obtained spotted owl detections across ≥2 nights. When active surveys using broadcast calling were conducted near ARUs with spotted owl detections by surveyors naïve to territory occupancy status and locations, surveyors located owls in 93% to 100% of occupied territories with ≤3 surveys. To further improve the efficiency of spotted owl surveys, we developed a statistical model to identify and prioritize areas across the Sierra Nevada for different survey methods (active only, acoustically assisted, no surveys) based on the expected probability of occupancy predicted from remotely sensed measurements of tree height and historical occupancy. Depending on managers' tolerance for false negatives, this model could help identify large areas that might not benefit from surveys based on low expected occupancy probabilities and areas where acoustically assisted surveys might enhance survey effectiveness and efficiency. Collectively, these findings can help managers streamline the survey process and thus increase the pace of forest restoration while minimizing potential near-term adverse effects on California spotted owls.     

The importance of incorporating imperfect detection in biodiversity assessments: a case study of small mammals in an Australian region

Aim Assessments of biodiversity are an essential requirement of conservation management planning. Species distributional modelling is a popular approach to quantifying biodiversity whereby occurrence data are related to environmental covariates. An important confounding factor that is often overlooked in the development of such models is uncertainty due to imperfect detection. Here, I demonstrate how an analytical approach that accounts for the bias due to imperfect detection can be applied retrospectively to an existing biodiversity survey data set to produce more realistic estimates of species distributions and unbiased covariate relationships. Location Pilbara biogeographic region, Australia. Methods As a component of the Pilbara survey, presence/absence (i.e. undetected) data on small ground‐dwelling mammals were collected. I applied a multiseason occupancy modelling approach to six of the most common species encountered during this survey. Detection and occupancy rates, as well as extinction and colonization probabilities, were determined, and the influence of covariates on these parameters was examined using the multi‐model inference approach. Results Detection probabilities for all six species were considerably lower than 1.0 and varied across time and species. Naïve estimates of occupancy underestimated occupancy rates corrected for species detectability by up to 45%. Seasonal variation in occupancy status was attributed to changes in detection for two of the focal species, while reproductive events explained variation in occupancy in three others. Covariates describing the substrate strongly influenced site occupancy for most of the species modelled. A comparison of the occupancy model with a generalized linear model, assuming perfect detection, showed that the effects of the covariates were underestimated in the latter model. Main conclusions The application of the multiseason occupancy modelling approach to the Pilbara mammal data set demonstrated a powerful framework for examining changes in site occupancy, as well as local colonization and extinction rates of species which are not confounded by variable species detection rates.     

A simple landscape-scale test of a spatially explicit population model: patch occupancy in fragmented south-eastern Australian forests

The results of a landscape‐scale test of ALEX, a widely used metapopulation model for Population Viability Analysis (PVA), are described. ALEX was used to predict patch occupancy by the laughing kookkaburra and the sacred kingfisher in patches of eucalypt forest in south‐eastern Australia. These predictions were compared to field surveys to determine the accuracy of the model. Predictions also were compared to a “naïve” null model assuming no fragmentation effects.
The naïve null model significantly over‐predicted the number of eucalypt patches occupied by the sacred kingfisher, but the observed patch occupancy was not significantly different from that predicted using ALEX. ALEX produced a better fit to the field data than the naïve null model for the number of patches occupied by the laughing kookaburra. Nevertheless, ALEX still significantly over‐predicted the number of occupied patches, particularly remnants dominated by certain forest types – ribbon gum and narrow‐leaved peppermint. The predictions remained significantly different from observations, even when the habitat quality of these patches was reduced to zero. Changing the rate of dispersal improved overall predicted patch occupancy, but occupancy rates for the different forest types remained significantly different from the field observations. The lack of congruence between field data and model predictions could have arisen because the laughing kookaburra may move between an array of patches to access spatially separated food and nesting resources in response to fragmentation. Alternatively, inter‐specific competition may be heightened in a fragmented habitat. These types of responses to fragmentation are not incorporated as part of traditionally applied metapopulation models. Assessments of predictions from PVA models are rare but important because they can reveal the types of species for which forecasts are accurate and those for which they are not. This can assist the collection of additional empirical data to identify important factors affecting population dynamics.     

Comparison of occupancy modeling and radiotelemetry to estimate ungulate population dynamics

Radiotelemetry and unmarked occupancy modeling have been used to estimate animal population growth, but have not been compared for ungulates. We compared white-tailed deer (Odocoileus virginianus) population growth estimates from radiomarked individuals and occupancy modeling of unmarked individuals and evaluated advantages and disadvantages of each method. Estimates of population growth were obtained using remote camera (N = 54/year) detection/non-detection occupancy surveys of unmarked deer and from survival and recruitment data of radiomarked adult females (N = 87) and neonate fawns (N = 127) in a predominantly forested region of the Upper Peninsula of Michigan, USA, 2009–2011. We hypothesized that occupancy models and radiotelemetry data would have similar population growth trends because both methods sampled the same temporally closed population. Percent changes in camera trap data generally reflected finite population growth (λ) of radiomarked deer which increased (λ = 1.10 ± 0.01) from 2009 to 2010, but decreased (λ = 0.87 ± 0.02) from 2010 to 2011. Also, unmarked adult female abundance and fawn:adult female ratios generally reflected trends in radiomarked deer survival and recruitment. Royle–Nichols occupancy model abundance estimates had wide confidence intervals, which may preclude using this method from accurately estimating deer population growth. Radiotelemetry provided more precise population growth estimates, while allowing collection of vital rates and location data. However, the Royle–Nichols occupancy model may be preferred to radiotelemetry because it reflected yearly variation in population growth with reduced labor and no invasive marking. Researchers should consider the objectives and logistics of their study when choosing a specific method.     

Multi-species monitoring of rare wetland fishes should account for imperfect detection of sampling devices

Accuracy in estimating occupancy of a threatened species is important for conservation but false absences bias many monitoring programs. Imperfect detection is especially relevant to surveys of rare wetland fishes which are often small-bodied and cryptic. Many factors influence probability of detection, including fish size and abundance, habitat characteristics and sampling devices. Imperfect detection can be addressed by accounting for probability of detection when estimating occupancy by modelling detection/non-detection data collected in replicate surveys. Three ecological specialists were once common in habitats associated with Lake Alexandrina at the terminus of the Murray–Darling Basin, Australia. The threatened Murray Hardyhead (Craterocephalus fluviatilis), Southern Pygmy Perch (Nannoperca australis) and Yarra Pygmy Perch (N. obscura) are now rare in the region following population collapses during a prolonged drought, and ongoing monitoring aims to assess their statuses for management purposes. This study compares probability of detection of the rare wetland fishes and cohabiting species during 2 years of multi-species monitoring using contrasting sampling devices (fyke and seine). The findings suggest large variations in estimated probability of detection can occur between devices for Murray Hardyhead and Southern Pygmy Perch. Yarra Pygmy Perch was undetected during the study. Overall, the findings show multi-species monitoring programs using a single sampling device may wrongly estimate the occupancy of a target fish. By accounting for imperfect detection, multi-species monitoring programs will improve inferences regarding population status, recovery and habitat quality of fishes to more accurately inform wetland management.     

Effects of point‐count duration on estimated detection probabilities and occupancy of breeding birds

Increasingly, point‐count data are used to estimate occupancy, the probability that a species is present at a given location; occupancy accounts for imperfect detection, the probability that a species is detected given that it is present. To our knowledge, effects of sampling duration on inferences from models of bird occupancy have not been evaluated. Our objective was to determine whether changing count duration from 5 to 8 min affected inferences about the occupancy of birds sampled in the Chesapeake Bay Lowlands (eastern United States) and the central and western Great Basin (western United States) in 2012 and 2013. We examined the proportion of species (two doves, one cuckoo, two swifts, five hummingbirds, 11 woodpeckers, and 122 passerines) for which estimates of detection probability were ≥ 0.3. For species with single‐season detection probabilities ≥ 0.3, we compared occupancy estimates derived from 5‐ and 8‐min counts. We also compared estimates for three species sampled annually for 5 yr in the central Great Basin. Detection probabilities based on both the 5‐ and 8‐min counts were ≥ 0.3 for 40% ± 3% of the species in an ecosystem. Extending the count duration from 5 to 8 min increased the detection probability to ≥ 0.3 for 5% ± 0.5% of the species. We found no difference in occupancy estimates that were based on 5‐ versus 8‐min counts for species sampled over two or five consecutive years. However, for 97% of species sampled over 2 yr, precision of occupancy estimates that were based on 8‐min counts averaged 12% ± 2% higher than those based on 5‐min counts. We suggest that it may be worthwhile to conduct a pilot season to determine the number of locations and surveys needed to achieve detection probabilities that are sufficiently high to estimate occupancy for species of interest.     

Comparing direct and indirect methods to estimate detection rates and site use of a cryptic semi-aquatic carnivore

Monitoring animal populations can be challenging, particularly when working with species that are cryptic, rare, or occur at low densities. The northern river otter (Lontra canadensis) is a cryptic, semi-aquatic carnivore that has been intensively studied in recent decades, yet much of what is known about its ecology is a result of studies that have employed indirect methods of detection and monitoring. These indirect methods, such as latrine or other sign surveys, have been the primary approach used for studying distribution, abundance, and habitat use of otters, with minimal representation of direct methods. In this study, we compared direct (camera traps) and indirect (scat count surveys) methods of evaluating detection probabilities and site use patterns of otters at latrines. We found that the direct method produced a significantly greater monthly detection probability than the indirect method and that camera surveys resulted in fewer occurrences of false negatives than scat surveys. However, the number of scats deposited at a site was positively correlated with number of visits by otters at a site (Tau-b = 0.675). Thus, while cameras outperformed scat counts in terms of detection, the two methods were comparable in determining intensity of site use. We conclude that, depending on the parameter of interest, scat counts may be an acceptable surrogate for more direct methods of monitoring otters and other cryptic species. We caution, however, that in the absence of comparative methodological data, direct methods such as camera trapping should be preferred when making inferences about animal distribution, abundance, or habitat use.     

Long-term demographic surveys reveal a consistent relationship between average occupancy and abundance within local populations of a butterfly metapopulation

Species distribution models are the tool of choice for large-scale population monitoring, environmental association studies and predictions of range shifts under future environmental conditions. Available data and familiarity of the tools rather than the underlying population dynamics often dictate the choice of specific method – especially for the case of presence–absence data. Yet, for predictive purposes, the relationship between occupancy and abundance embodied in the models should reflect the actual population dynamics of the modelled species. To understand the relationship of occupancy and abundance in a heterogeneous landscape at the scale of local populations, we built a spatio-temporal regression model of populations of the Glanville fritillary butterfly Melitaea cinxia in a Baltic Sea archipelago. Our data comprised nineteen years of habitat surveys and snapshot data of land use in the region. We used variance partitioning to quantify relative contributions of land use, habitat quality and metapopulation covariates. The model revealed a consistent and positive, but noisy relationship between average occupancy and mean abundance in local populations. Patterns of abundance were highly variable across years, with large uncorrelated random variation and strong local population stochasticity. In contrast, the spatio-temporal random effect, habitat quality, population connectivity and patch size explained variation in occupancy, vindicating metapopulation theory as the basis for modelling occupancy patterns in fragmented landscapes. Previous abundance was an important predictor in the occupancy model, which points to a spillover of abundance into occupancy dynamics. While occupancy models can successfully model large-scale population structure and average occupancy, extinction probability estimates for local populations derived from occupancy-only models are overconfident, as extinction risk is dependent on actual, not average, abundance.     

Transgenerational soil‐mediated differences between plants experienced or naïve to a grass invasion

Invasive species may undergo rapid change as they invade. Native species persisting in invaded areas may also experience rapid change over this short timescale relative to native populations in uninvaded areas. We investigated the response of the native Achillea millefolium to soil from Holcus lanatus‐invaded and uninvaded areas, and we sought to determine whether differential responses between A. millefolium from invaded (invader experienced) and uninvaded (invader naïve) areas were mediated by soil community changes. Plants grown from seed from experienced and naïve areas responded differently to invaded and uninvaded soil with respect to germination time, biomass, and height. Overall, experienced plants grew faster and taller than their naïve counterparts. Naïve native plants showed negative feedbacks with their home soil and positive feedbacks with invaded soil; experienced plants were less responsive to soil differences. Our results suggest that native plants naïve to invasion may be more sensitive to soil communities than experienced plants, consistent with recent studies. While differences between naïve and experienced plants are transgenerational, our design cannot differentiate between differences that are genetically based, plastic, or both. Regardless, our results highlight the importance of seed source and population history in restoration, emphasizing the restoration potential of experienced seed sources.     

Occupancy Models for Monitoring Marine Fish: A Bayesian Hierarchical Approach to Model Imperfect Detection with a Novel Gear Combination

Occupancy models using incidence data collected repeatedly at sites across the range of a population are increasingly employed to infer patterns and processes influencing population distribution and dynamics. While such work is common in terrestrial systems, fewer examples exist in marine applications. This disparity likely exists because the replicate samples required by these models to account for imperfect detection are often impractical to obtain when surveying aquatic organisms, particularly fishes. We employ simultaneous sampling using fish traps and novel underwater camera observations to generate the requisite replicate samples for occupancy models of red snapper, a reef fish species. Since the replicate samples are collected simultaneously by multiple sampling devices, many typical problems encountered when obtaining replicate observations are avoided. Our results suggest that augmenting traditional fish trap sampling with camera observations not only doubled the probability of detecting red snapper in reef habitats off the Southeast coast of the United States, but supplied the necessary observations to infer factors influencing population distribution and abundance while accounting for imperfect detection. We found that detection probabilities tended to be higher for camera traps than traditional fish traps. Furthermore, camera trap detections were influenced by the current direction and turbidity of the water, indicating that collecting data on these variables is important for future monitoring. These models indicate that the distribution and abundance of this species is more heavily influenced by latitude and depth than by micro-scale reef characteristics lending credence to previous characterizations of red snapper as a reef habitat generalist. This study demonstrates the utility of simultaneous sampling devices, including camera traps, in aquatic environments to inform occupancy models and account for imperfect detection when describing factors influencing fish population distribution and dynamics.