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Effective management of the threatened Antillean manatee (Trichechus manatus manatus) in Puerto Rico requires reliable estimates of population size. Estimates are needed to assess population responses to management actions, and whether recovery objectives have been met. Aerial surveys have been conducted since 1976, but none adjusted for imperfect detection. We summarize surveys since 1976, report on current distribution, and provide population estimates after accounting for apparent detection probability for surveys between June 2010 and March 2014. Estimates in areas of high concentration (hotspots) averaged 317 ± 101, three times higher than unadjusted counts (104 ± 0.56). Adjusted estimates in three areas outside hotspots also differed markedly from counts (75 ± 9.89 versus 19.5 ± 3.5). Average minimum island-wide estimate was 386 ± 89, similar to the maximum estimate of 360 suggested in 2005, but fewer than the 700 recently suggested by the Puerto Rico Manatee Conservation Center. Manatees were more widespread than previously understood. Improving estimates, locally or island-wide, will require stratifying the island differently and greater knowledge about factors affecting detection probability. Sharing our protocol with partners in nearby islands (e.g., Cuba, Jamaica, Hispaniola), whose populations share genetic make-up, would contribute to enhanced regional conservation through better population estimates and tracking range expansion.El manejo efectivo del manatí antillano amenazado en Puerto Rico requiere estimados de tamaños de poblaciónes confiables. Dichas estimaciones poblacionales son necesarias para evaluar las respuestas a las acciones de manejo, y para determinar si los objetivos de recuperación han sido alcanzados. Se han realizado censos aéreos desde 1976, pero ninguno de ellos han sido ajustados para detecciones imperfectas. Aquí resumimos los censos desde 1976, actualizamos la distribución, y reportamos los primeros estimados poblacionales ajustados para la probabilidad de detección aparente en los censos de Junio 2010 a Marzo 2014. Las estimaciones poblacionales en áreas de mayor concentración del manatí promedió 317 ± 103, tres veces más abundante que los conteos sin ajuste (104 ± 0.56). Las estimaciones poblacionales en tres áreas fuera de las áreas de mayor concentración del manatí también fueron marcadamente diferentes (75 ± 9.89 vs 19.5 ± 3.5). El estimado mínimo poblacional en la isla entera fue de 386 ± 89, similar al estimado máximo de 360 sugerido en el año 2005, pero menor a los 700 sugeridos recientemente por el Centro de Conservación de Manatíes de Puerto Rico. Documentamos que el manatí tiene una distribución más amplia de lo que se sabía con anterioridad. El mejoramiento de los estimados poblacionales locales o a nivel de isla requerirá que se estratifique a la isla en forma diferente y que se investiguen los factores que influencian a la probabilidad de detección. Compartir protocolos como este con colaboradores de islas vecinas (por. ej., Cuba, Jamaica, Española), cuyas poblaciones de manatíes comparten material genético, contribuiría a la conservación regional mediante mejores estimaciones poblacionales y monitoreo de la expansión de su ámbito doméstico.

Distance sampling and capture-recapture methods have been widely used to estimate density and abundance of wildlife populations. We propose a population estimator for a mark-resighting study where in the resighting stage perpendicular distance data is recorded. In this situation, one can analyze the collected data as a capture-recapture study, as a line transect study or develop a combined model that allows us to estimate the probability of seeing an animal (or an object) on the transect line (i.e., g(0)) and to test whether or not that probability is one (g(0) = 1). A simulation study is carried out to evaluate the performance of the proposed estimator, and compare its efficiency relative to that of the Lincoln-Petersen, the Chapman and the traditional line transect estimators. An example based on some stake data is presented to illustrate the estimation procedure.

Shorebird populations face increasing challenges as rising sea levels and growing human populations constrain their breeding habitats. On recreational beaches, the nesting season often coincides with a season of high visitor use, increasing the potential for conflict, which may negatively influence beach-nesting shorebird species. We designed a field experiment to study the responses of nesting American Oystercatchers (Haematopus palliatus) to off-road passenger vehicles (ORVs) at Cape Hatteras and Cape Lookout National Seashores in North Carolina, USA. We used continuous video and heart rate recordings to assess changes in the behavior and physiology of incubating oystercatchers. We conducted driving experiments affecting 7 nesting pairs in 2014 and 19 nesting pairs in 2015, between April and July of each year. Experimental treatments were repeated throughout the incubation period for each nest. Although responses were highly variable within and among pairs, paired randomized permutation tests i...

Population structure must be considered when developing mark-recapture (MR) study designs as the sampling of individuals from multiple populations (or subpopulations) may increase heterogeneity in individual capture probability. Conversely, the use of an appropriate MR study design which accommodates heterogeneity associated with capture occasion varying covariates due to animals moving between 'states' (i.e. geographic sites) can provide insight into how animals are distributed in a particular environment and the status and connectivity of subpopulations. The multistate closed robust design (MSCRD) was chosen to investigate: (i) the demographic parameters of Indo-Pacific bottlenose dolphin (Tursiops aduncus) subpopulations in coastal and estuarine waters of Perth, Western Australia; and (ii) how they are related to each other in a metapopulation. Using 4 years of year-round photo-identification surveys across three geographic sites, we accounted for heterogeneity of capture probability based on how individuals distributed themselves across geographic sites and characterized the status of subpopulations based on their abundance, survival and interconnection. MSCRD models highlighted high heterogeneity in capture probabilities and demographic parameters between sites. High capture probabilities, high survival and constant abundances described a subpopulation with high fidelity in an estuary. In contrast, low captures, permanent and temporary emigration and fluctuating abundances suggested transient use and low fidelity in an open coastline site. Estimates of transition probabilities also varied between sites, with estuarine dolphins visiting sheltered coastal embayments more regularly than coastal dolphins visited the estuary, highlighting some dynamics within the metapopulation. Synthesis and applications. To date, bottlenose dolphin studies using mark-recapture approach have focussed on investigating single subpopulations. Here, in a heterogeneous coastal-estuarine environment, we demonstrated that spatially structured bottlenose dolphin subpopulations contained distinct suites of individuals and differed in size, demographics and connectivity. Such insights into the dynamics of a metapopulation can assist in local-scale species conservation. The MSCRD approach is applicable to species/populations consisting of recognizable individuals and is particularly useful for characterizing wildlife subpopulations that vary in their vulnerability to human activities, climate change or invasive species.

In populations of long-lived species, adult survival typically has a relatively high influence on population growth. From a management perspective, however, adult survival can be difficult to increase in some instances, so other component rates must be considered to reverse population declines. In North Carolina, USA, management to conserve the American Oystercatcher (Haematopus palliatus) targets component vital rates related to fecundity, specifically nest and chick survival. The effectiveness of such a management approach in North Carolina was assessed by creating a three-stage female-based deterministic matrix model. Isoclines were produced from the matrix model to evaluate minimum nest and chick survival rates necessary to reverse population decline, assuming all other vital rates remained stable at mean values. Assuming accurate vital rates, breeding populations within North Carolina appear to be declining. To reverse this decline, combined nest and chick survival would need to increase from 0.14 to ≤ 0.27, a rate that appears to be attainable based on historical estimates. Results are heavily dependent on assumptions of other vital rates, most notably adult survival, revealing the need for accurate estimates of all vital rates to inform management actions. This approach provides valuable insights for evaluating conservation goals for species of concern.

Canis latrans (Coyote) recently expanded into the southeastern United States, creating ecologically novel interactions with other species. However, relatively few studies have examined vital rates of southeastern Coyotes or estimated vital rates where individuals are protected from hunting and trapping. In 2011, we captured and attached GPS radiocollars to 31 Coyotes at Fort Bragg Military Installation, NC, where Coyote harvest was restricted. We used a 12-month period (February 2011–January 2012) and known-fate modeling in Program MARK to estimate annual survival. Model-selection results indicated the time-varying model (S[t]) was the most parsimonious model, and. annual survival was 0.80 (95% CI = 0.60–0.91). We documented 7 mortalities, including 2 from vehicles, 2 from offsite trapping, and 3 from unknown causes. Estimated Coyote survival rates at Fort Bragg were similar to most other estimates from the southeastern US. Anthropogenic causes of mortality were important even though hunting and ...

With increasing human pressures on wildlife comes a responsibility to monitor them effectively, particularly in an environment of declining research funds. Scarce funding resources compromise the level and efficacy of monitoring possible to detect trends in abundance, highlighting the priority for developing cost-effective programs. A systematic and rigorous sampling regime was developed to estimate abundance of a small, genetically isolated spinner dolphin ( Stenella longirostris ) population exposed to high levels of human activities. Five monitoring scenarios to detect trends in abundance were evaluated by varying sampling effort, precision, power, and sampling interval. Scenario 1 consisted of monthly surveys, each of 12 days, used to obtain the initial two consecutive annual abundance estimates. Scenarios 2, 3, and 4 consisted of a reduced effort, while Scenario 5 doubled the effort of Scenario 1. Scenarios with the greatest effort (1 and 5) produced the most precise abundance estimates (CV = 0.09). Using a CV = 0.09 and power of 80%, it would take 9 years to detect a 5% annual change in abundance compared with 12 years at a power of 95%. Under this best-case monitoring scenario, if the trend was a decline, the population would have decreased by 37% and 46%, respectively, prior to detection of a significant decline. With the potential of a large decline in a small population prior to detection, the lower power level should be used to trigger a management intervention. The approach presented here is applicable across taxa for which individuals can be identified, including terrestrial and aquatic mammals, birds, and reptiles.

Fisheries managers are increasingly required to develop regulatory frameworks to more effectively manage recreational catches in the marine environment. Although the limitations of conventional controls such as size and bag limits and restricted seasons are recognized, harvest tags that are commonly used to regulate hunting, are rarely applied in marine recreational fisheries. Following overfishing of snapper ( Chrysophrys auratus ) in Shark Bay, Western Australia, a broad range of management reforms were progressively introduced from 1998 onwards to limit recreational catches and assist stock recovery. Since 2003, these included a harvest tag system in Freycinet Estuary whereby a limited number of harvest tags were made available each year via a ballot. The effectiveness of harvest tags in terms of stock rebuilding and acceptance by recreational fishers was evaluated using: annual phone surveys of all harvest tag recipients between 2011 and 2013; analysis of compliance statistics collected between 2004 and 2015; and interviews with experienced compliance officers. The overall costs of administration and compliance were also assessed. The capacity of harvest tags to successfully constrain the total annual recreational catch contributed to the recovery of the snapper stock in Freycinet Estuary to management target levels within a 10–12 year timeframe. The majority of harvest tag recipients interviewed considered harvest tags were effective in the management of snapper; cost per tag was reasonable; and compliance in the fishery was high. High levels of compliance are essential if harvest tags are to provide a robust management tool to limit total catch and a useful reference frame for angler surveys. Harvest tags have considerable potential with other marine recreational fisheries where catch limits are required to rebuild and sustain valuable but vulnerable fish stocks.

Mycophagous bioturbators provide ecosystem services that can be important for the resilience and restoration of ecosystems. Among the Australian mammals, mycophagy is most prevalent within the Potoroidae (bettongs and potoroos). However, proportionally more species of Potoroidae are either recently extinct or currently threatened than any other mammalian family in Australia, and they are among the least studied. The critically endangered woylie, or brush-tailed bettong (Bettongia penicillata), is a mycophagous, ground dwelling 'ecosystem engineer' that was one of Australia's most abundant and widely distributed potoroids prior to European settlement. After substantial range contraction, however, the remaining indigenous populations are now restricted to eucalypt forests in south-western Australia. Using an experimental approach, we investigated the population responses of the woylie to timber harvesting in these forests. Nine treatments, including varying logging intensities and unharvested controls, were applied at 22 sites. The abundance of the woylie in the harvested areas, in unharvested stands between logged areas, and in extensive unharvested stands outside the harvest management area were compared using a replicated before-after-control-impact (BACI) repeated measures design and capture-mark-recapture modelling. A total of 5860 captures of 815 individuals were recorded during 35 trapping sessions over 16 years (one year preceding, two years during, and 13 years after disturbance). Capture rate was a good index of abundance for this species and woylie abundance, survivorship and recruitment were not adversely affected by silvicultural practices in the jarrah (Eucalyptus marginata) forest. On the contrary, the harvested areas may have afforded some localised protection when an unrelated, species-wide decline began three years after harvesting disturbance ended; woylie numbers declined by up to 77% and 95% in harvested and unharvested areas, respectively. Thus the nature and spatial extent of the timber harvesting regimes investigated in this study were not a major threatening process for this species. However, ongoing monitoring and evaluation are necessary to ensure that timber harvesting activities remain benign in the face of a changing climate, possible increased mortality from introduced predators, disease, and further declines in the abundance of this critically endangered marsupial.

Unbiased estimators of abundance and density are fundamental to the study of animal ecology and critical for making sound management decisions. Capture–recapture models are generally considered the most robust approach for estimating these parameters but rely on a number of assumptions that are often violated but rarely validated. Mark-resight models, a form of capture–recapture, are well suited for use with noninvasive sampling methods and allow for a number of assumptions to be relaxed. We used ancillary data from continuous video and radio telemetry to evaluate the assumptions of mark-resight models for abundance estimation on a barrier island raccoon (Procyon lotor) population using camera traps. Our island study site was geographically closed, allowing us to estimate real survival and in situ recruitment in addition to population size. We found several sources of bias due to heterogeneity of capture probabilities in our study, including camera placement, animal movement, island physiography, and animal behavior. Almost all sources of heterogeneity could be accounted for using the sophisticated mark-resight models developed by McClintock et al. (2009b) and this model generated estimates similar to a spatially explicit mark-resight model previously developed for this population during our study. Spatially explicit capture–recapture models have become an important tool in ecology and confer a number of advantages; however, non-spatial models that account for inherent individual heterogeneity may perform nearly as well, especially where immigration and emigration are limited. Non-spatial models are computationally less demanding, do not make implicit assumptions related to the isotropy of home ranges, and can provide insights with respect to the biological traits of the local population. © 2015 The Wildlife Society.

The extensive breeding range of many shorebird species can make integration of survey data problematic at regional spatial scales. We evaluated the effectiveness of standardized repeated count surveys coordinated across 8 agencies to estimate the abundance of American Oystercatcher (Haematopus palliatus) breeding pairs in the southeastern United States. Breeding season surveys were conducted across coastal North Carolina (90 plots) and the Eastern Shore of Virginia (3 plots). Plots were visited on 1–5 occasions during April–June 2013. N-mixture models were used to estimate abundance and detection probability in relation to survey date, tide stage, plot size, and plot location (coastal bay vs. barrier island). The estimated abundance of oystercatchers in the surveyed area was 1,048 individuals (95% credible interval: 851–1,408) and 470 pairs (384–637), substantially higher than estimates that did not account for detection probability (maximum counts of 674 individuals and 316 pairs). Detection pro...

So far in this book, we have focused on scenarios where the occupancy status of only a single species is of interest. As outlined in Chapter 2 , there are a number of ecological applications where inference is desired about the presence or absence of multiple species across a set of sampling units. In this chapter we turn our attention to investigations of co-occurrence for two or more species, from detection/nondetection data. Specifically, we demonstrate how imperfect detection can lead to misleading conclusions about the nature of any co-occurrence interaction between two species, and describe modeling approaches that have been developed to examine patterns, and the underlying dynamic processes, of species co-occurrence. These modeling approaches enable detection probabilities to be incorporated directly into our inferential framework, and are very flexible: allowing detection probabilities to depend on the number of species present at a unit, and for a potential lack of independence of species detections in the same survey occasions. Our presentation of the modeling approaches draws heavily from the methods described in previous chapters. Examples are provided of their application, investigating co-occurrence patterns for two salamander species in Great Smoky Mountains National Park, USA, and dynamics of northern spotted owl and barred owl interactions in western Oregon, USA.

Unmodeled variation, or heterogeneity, in detection probabilities will result in biased estimates of occupancy probabilities. In this chapter we consider occupancy models that allow for heterogeneous detection probability among units, including models with discrete support (finite mixtures) or continuous mixtures such as the beta or logit-normal models, and we also consider the Royle and Nichols (2003) model that arises by considering that heterogeneity in detection probability is derived from variation in abundance. We also note how covariates that are thought to influence detection probability can also be incorporated. Examples are given of fitting and interpreting these models to avian detection/nondetection data, and anuran calling survey data.

The topics covered in this book get more complicated as the reader progresses through the chapters. In this short chapter we offer some of our final thoughts on the general topic of occupancy modeling. We believe there is still plenty of scope for extensions and novel applications of the current set of methods, but that further investigation of study design, model limitations, and assessing model, fit should be research priorities over the next decade.

Another type of multi-species studies, are those focused on community-level metrics such as species richness. In this chapter we detail how some of the single-species occupancy models described in earlier chapters have been applied, or extended, for use in such studies, while accounting for imperfect detection. We highlight how Bayesian methods using MCMC are particularly useful in such settings to easily calculate relevant community-level summaries based on presence/absence data. These modeling approaches can be used to assess richness at a single point in time, or to investigate changes in the species pool over time.

The occupancy status of sampling units will often change over meaningful timescales, which is of interest in many areas of ecology, including metapopulation studies, studies of distributional change, and monitoring programs. In this chapter we turn our attention to the problem of estimating changes in occupancy from data collected over multiple seasons, where occupancy is defined in terms of two possible states, species presence or absence. We consider two general approaches for modeling changes in occupancy over time: (1) a model where underlying dynamics are implied but not explicitly accounted for (effectively combining several single-season models); and (2) explicitly modeling potential changes in the occupancy state of a unit over time with colonization and local extinction probabilities. Both types of model can be used to obtain time-specific estimates of occupancy and estimates of rate of change, or ‘trend’, in occupancy, which is the focus of many species monitoring programs. However, the explicit dynamics modeling approach can yield greater understanding about the underlying vital rates, colonization and local extinction, that govern occupancy dynamics (i.e., why is there a trend), which may be useful when investigators seek to influence the rate of change in occupancy. Predictor variables or covariates can be incorporated into the models to investigate effects of environmental variables and management actions on these rate parameters. We believe that this chapter may be the most important in the book, as studies that extend over multiple seasons provide the strongest inferences about processes that influence occupancy dynamics and determine observed occupancy patterns.

Frameworks for modeling the underlying dynamics of species occurrence using a two-state, or multi-state, occupancy variable, were introduced in Chapters 8 and 9. In this chapter, extensions, potential uses, and practical insights for these models are outlined. Topics covered include false positive detections, autocorrelated within-season detections, spatial correlation in occupancy dynamics, investigating occupancy dynamics, sensitivity of occupancy to changes in dynamics and heterogeneous detection probabilities. These topics will enable practitioners to gain a better understanding of why species occurrence has changed, which should lead to improved knowledge of how the species functions within a landscape, and may result in more targeted management actions in a management or conservation context.

Species presence/absence or occurrence metrics are widely used in many areas of ecology, such as species range or distribution, habitat relationships, metapopulation dynamics, and monitoring. In this chapter we review many of the ecological, and some non-ecological, settings where such measures have been used, noting that in many cases imperfect detection, or false absences, have the potential to result in misleading inferences. We give examples of how occupancy modeling that accounts for imperfect detection could be, or has been, applied in these situations.

Designing a good study is often as much an art as a science. It is a combination of taking the study objectives, knowledge about the intended statistical methods and species biology (the ‘science’), with practical considerations because of the logistical limitations to obtain a design for collecting the required data (the ‘art’). In this chapter, we discuss the importance of defining key occupancy components (e.g., unit, season, survey, etc.). We describe optimal designs that provide the most precise estimates of occupancy for a given set of resource constraints, and provide some general recommendations. The ideas in this chapter should not be regarded as an instruction book for how to design your study, but a play book of options that may be appropriate in some situations, but not in others. Studies should be designed on a case-by-case basis, as the details of each design (goals, species, environment, etc.) will often be different. Once a satisfactory design has been developed, we recommend that simulation and pilot studies are invaluable tools for assessing whether the design will provide the type and quality of information required to meet the studies' objectives. We remind readers of the ‘Garbage In, Garbage Out’ principle.

Building on design recommendations from the previous chapter, we highlight additional issues that must be considered when designing a multiple-season occupancy study. Specifically, we discuss the time intervals between seasons, rotating panel designs, and trade-offs between the number of units and the number of seasons. We emphasize the importance of a probabilistic sampling scheme for selecting units to survey (i.e., the probability of a unit being selected from the population of units can be defined). Targeting units that are suspected to be occupied (e.g., based on recent presence records) may lead to apparent trends in occupancy, that could be misleading in some circumstances. In general, we recommend longitudinal studies (i.e., survey the same units over multiple seasons) where the interval between sampling seasons matches the temporal resolution of the motivating biological questions. As with single season studies, pilot studies and computer simulations are particularly valuable to assess alternative field methods, and to gain realistic expectations about the limits on what inferences could be drawn from the resulting data. Refining methods and understanding potential limitation before embarking on the full data collection phase, will enable resources to be used more efficiently, and may avoid future disappointments.

Species often exhibit preferences for certain habitat features such that species occurrence is a function of a unit's habitat. However habitat on the landscape will often be dynamic, changing through time via processes such as vegetation succession, human activities, and environmental variation. When habitat is dynamic, it will frequently be useful to partition species occurrence dynamics into components associated with habitat versus other factors. Solely focusing on species occurrence is likely to yield an inadequate descriptor of the system's state, as similar patterns may have very different meanings with respect to system well-being. In this chapter, we discuss methods that model system dynamics using two interrelated components, species occurrence dynamics that depend on habitat and habitat dynamics that (may) depend on species occurrence. Utilizing the multi-state, multi-season occupancy model framework described in Chapter 9 , we highlight the flexible nature of this model to identify important factors for the separate but interrelated processes of habitat and occupancy dynamics. This enables a number of biologically interesting questions about these interrelationships, including species response to ecological succession, natural disturbance frequencies, climate change, and habitat loss and fragmentation associated with human activities. This modeling approach also provides a framework enabling predictions to be made about the future distribution of a species in the face of such dynamics.

The dynamics of species occurrence can also be of interest in situations where ‘occupancy’ is defined in terms of multiple (i.e., > two) states. Imperfect detection means the true occupancy state of surveyed units will not always be observed, and therefore creates ambiguity about true changes in occupancy state. This needs to be accounted for to enable reliable inferences about the underlying dynamic process, and factors that may affect those processes, to be made. Here, the concepts of Chapters 5 and 8 are combined to enable investigation of occupancy dynamics for situations with more than two occupancy states over multiple seasons, while incorporating imperfect detection. We refer to this as a multi-season multi-state occupancy model. The general framework presented in this chapter is very useful and provides the structure for a number of interesting extensions. We believe that multi-state occupancy models dramatically increase our ability to address interesting questions about ecological processes associated with concepts such as source–sink dynamics, disease spread, and changes in the (relative) abundance distribution of species.

Species occurrence at locations of interest is often defined in terms of a dichotomous variable, e.g., species presence/absence, but a greater number of categories or states could be used. Single-season multi-state occupancy models have been developed to investigate and model patterns of species occurrence for two or more occupied states. As in the simpler case, the true occupancy state may not always be observed with certainty due to imperfect detection. In this chapter we detail the development of the single-season multi-state occupancy model, and provide examples of its application. This is a key chapter of this book as many of the more complex extensions presented later utilize this multi-state modeling framework.

This chapter provides important background information about many of the fundamental statistical principles and methods used throughout this book. It is intended for those who may have had little formal training in statistics, however should be a valuable reference for any practitioner. Topics covered include random variables, likelihood functions, expected value and variance calculation, maximum likelihood and Bayesian methods of estimation, incorporating and interpreting predictor variables, hypothesis testing and model selection.

The incidental capture of wildlife in fishing gear presents a global conservation challenge. As a baseline to inform assessments of the impact of bycatch on bottlenose dolphins (Tursiops truncatus) interacting with an Australian trawl fishery, we conducted an aerial survey to estimate dolphin abundance across the fishery. Concurrently, we carried out boat-based dolphin photo-identification to assess short-term fidelity to foraging around trawlers, and used photographic and genetic data to infer longer-term fidelity to the fishery. We estimated abundance at ≈ 2,300 dolphins (95% CI = 1,247–4,214) over the ≈ 25,880-km2 fishery. Mark-recapture estimates yielded 226 (SE = 38.5) dolphins associating with one trawler and some individuals photographed up to seven times over 12 capture periods. Moreover, photographic and genetic re-sampling over three years confirmed that some individuals show long-term fidelity to trawler-associated foraging. Our study presents the first abundance estimate for any Australian pelagic dolphin community and documents individuals associating with trawlers over days, months and years. Without trend data or correction factors for dolphin availability, the impact of bycatch on this dolphin population’s conservation status remains unknown. These results should be taken into account by management agencies assessing the impact of fisheries-related mortality on this protected species.

Monitoring variation in populations of coastal dolphins presents a range of challenges. Many species occur at low local population levels, are cryptic and appear to range over larger areas than presumed. Here we present the results of a three and half year intensive monitoring study undertaken in Darwin Harbor and two neighboring sites (1086 km2). The study comprised multi-site robust design capture-recapture models that yielded estimates of abundance, apparent survival and temporary emigration on three species of coastal dolphins: Australian humpback (Sousa sahulensis), bottlenose (Tursiops sp.) and Australian snubfin (Orcaella heinsohni). Combining all three sites, abundance estimates varied between species. The Australian humpback was the most abundant with a mean of 90, bottlenose were stable at mean of 27 and the Australian snubfin varied widely from 19 to 70 with a mean of 41. Overtime, Australian humpback abundance estimates showed a steady decline in Darwin Harbor but a population increase in the two neighboring sites was recorded, suggesting there were movements out of Darwin Harbor. However, the estimates of movement rates were not sufficiently sensitive to demonstrate this, due to the relatively small size of the local population and consequent low rates of observed movement. The multi-state robust design model offers the potential for assessing abundance estimates and population trends. It is able to distinguish between movements to and from a site from demographic changes on the site that otherwise might be attributed to other factors (i.e., decrease in survival). The study highlights the substantial effort and time required to detect population trends for coastal dolphins by needing to account for movement among sites. However, the reality of assessing the conservation status for coastal dolphins is challenging. Moreover, to enact conservation measures a reassessment at both global and nationals levels of the IUCN Red List categories (A and C) is required.

In this article, we first extend the superpopulation capture-recapture model to multiple states (locations or populations) for two age groups., Wen et al., (2011; 2013) developed a new approach combining capture-recapture data with population assignment information to estimate the relative contributions of in situ births and immigrants to the growth of a single study population. Here, we first generalize Wen et al., (2011; 2013) approach to a system composed of multiple study populations (multi-state) with two age groups, where an imputation approach is employed to account for the uncertainty inherent in the population assignment information. Then we develop a different, individual-level mixture model approach to integrate the individual-level population assignment information with the capture-recapture data. Our simulation and real data analyses show that the fusion of population assignment information with capture-recapture data allows us to estimate the origination-specific recruitment of new animals to the system and the dispersal process between populations within the system. Compared to a standard capture-recapture model, our new models improve the estimation of demographic parameters, including survival probability, origination-specific entry probability, and especially the probability of movement between populations, yielding higher accuracy and precision.

The reef manta ray Manta alfredi aggregates at several sites along the east coast of Australia. Photographic identification and mark–recapture methods were used to report on the site affinity, size and structure of this population of M. alfredi. A total of 716 individuals were identified in 1982–2012, including 636 at Lady Elliot Island (LEI), southern Great Barrier Reef. Over 60 % of individuals identified were resighted at least once during the study period. Multiple resightings within and among years imply a high degree of site affinity by individuals to aggregation sites. One individual was sighted 11 times at LEI over a 30-yr period. The sex ratio of this population was significantly biased towards females (1.2:1 female-to-male ratio), and females were more commonly resighted than males. Robust design population models were used to estimate the population size of the winter aggregation at LEI over a 4-yr period. The models estimated up to 456 (95 % CI 399–535) M. alfredi individuals in the population within one winter season and a high annual apparent survival. This study demonstrated that waters around LEI form a key aggregation site for a large portion of the M. alfredi population in east Australian waters.

The relative contribution of in situ reproduction versus immigration to the recruitment process is important to ecologists. Here we consider a robust design superpopulation capture-recapture model for a population with two age classes augmented with population assignment data. We first use age information to estimate the entry probabilities of new animals originating via in situ reproduction and immigration separately for all except the first period. Then we combine age and population assignment information with the capture-recapture model, which enables us to estimate the entry probability of in situ births and the entry probability of immigrants separately for all sampling periods. Further, this augmentation of age specific capture-recapture data with population assignment data greatly improves the estimators’ precision. We apply our new model to a capture-recapture data set with genetic information for banner-tailed kangaroo rats in Southern Arizona. We find that many more individuals are born in situ than are immigrants for all time periods. Young animals have lower survival probabilities than adults born in situ. Adult animals born in situ have higher survival probabilities than adults that were immigrants.

Abundance and population density are fundamental pieces of information for population ecology and species conservation, but they are difficult to estimate for rare and elusive species. Mark--resight models are popular for estimating population abundance because they are less invasive and expensive than traditional mark-recapture. However, density estimation using mark-resight is difficult because the area sampled must be explicitly defined, historically using ad hoc approaches. We developed a spatial mark--resight model for estimating population density that combines spatial resighting data and telemetry data. Incorporating telemetry data allows us to inform model parameters related to movement and individual location. Our model also allows

Collar-worn deterrents reduce predation by cats while collar-mounted ID enhances return of lost animals. A perception that collars are hazardous limits their use. We defined cases as ‘collar incidents’ (cat snagged its collar or caught a paw), ‘collar injuries’ (veterinary treatment needed for a collar incident), and ‘collar deaths’ (cat died), before integrating data from veterinarians, owners from the general public and owners from a welfare society. Despite biases associated with each of these groups, taken together, the results from these indicated that collar injuries or deaths are rare. Interviews with one hundred and seven veterinarians indicated an average rate of one collar injury observed per 2.3 years of veterinary practice. At one practice, over three years, only 0.33% of 4,460 cat cases were collar injuries, while 180 cat cases at four clinics during August and November 2011 included none. The 63 owners from the general public reported only one collar injury and no deaths in a lifetime of ownership, although 27% experienced collar incidents. In contrast, 22% reported cats needing treatment following road accidents, 53% reported cats needing treatment for fighting injuries and 62% had owned cats killed on the road. Most (62%) of the 55 respondents from a cat welfare society had experienced a collar incident, but only two cats needed treatment. One died. In contrast, 31 and 58% reported cats needing treatment for road accidents and fighting, respectively, and 41% had owned cats killed on the road. Fighting and road accidents are greater hazards to roaming cats than collars, which offer the compensatory benefits of mounting predation deterrents and ID tags.

We estimated natural mortality rates (M) of age-1 Spot Leiostomus xanthurus by using a sonic telemetry approach. Sonic transmitters were surgically implanted into a total of 123 age-1 Spot in two North Carolina estuarine creeks during spring 2009 and 2010, and the fish were monitored by using a stationary acoustic receiver array and manual tracking. Fates of telemetered Spot were inferred based on telemetry information from estimated locations and swimming speeds. Potential competitors of age-1 Spot were assessed through simultaneous otter trawl sampling, while potential predators of Spot were collected using gill nets and trammel nets. The number of inferred natural mortalities was zero in 2009 (based on 29 telemetered Spot at risk) and four in 2010 (based on 52 fish at risk), with fish being at risk for up to about 70 d each year. Catches of potential competitors or predators did not differ between years, and age-1 Spot were not found in analyzed stomach contents of potential predators. Our est...

Fisheries Science, Wildlife Management and Conservation Biology are crucial to the Australian economy and society. Australian doctoral education in these fields assumes that students commence with well-developed relevant skills, or acquire them autodidactically or from their supervisors. We believe that such reliance on autodidactic approaches and supervisor direction are no longer adequate, and argue for compulsory coursework within doctoral programs. Currently, most specialised education in quantitative methods, advanced genetic techniques (including population genetics) or human dimensions is provided in short courses or workshops, if at all. Short courses provide advanced technical knowledge (e.g., an advanced stock assessment workshop for fisheries scientists or population viability analysis workshops for conservation biologists), but they are voluntary. Multiple university and multiple discipline consortia could provide the compulsory postgraduate coursework needed for structured development of quantitative skills in Australian PhDs. Online education should be part of the solution, but it is not a panacea because some material should be taught in person for effective learning. Solutions can build on modified approaches used overseas and in other disciplines in Australia.

Population parameters of poorly marked gregarious species are difficult to estimate. This is the case for common dolphins (Delphinus sp.), a genus known for its lack of distinctive marks resulting in a low mark ratio. Furthermore, the widespread nature of common dolphins results in low recaptures. We developed reliable photo-identification protocols to ensure accurate identification of individuals in the Hauraki Gulf, New Zealand. These protocols combined the use of nicks and notches and pigmentation patterns for identification and included the development of a distinctiveness threshold. The data were further stratified by the level of distinctiveness of each individual (as distinctive or highly-distinctive). Photo-identification surveys were conducted from January 2010 to December 2013. Mark-recapture techniques were implemented through a POPAN super-population approach to estimate seasonal apparent survival, capture probability and abundance of dolphins. A total of 2,083 unique adult common dolphins were identified, 51.3% were classified as D1 (highly distinctive; n = 1,069) and 48.7% as D2 (distinctive; n = 1,014). Of all individuals identified, 34.3% (n = 704) were re-sighted over subsequent years. The proportion of marked dolphins (when compared to unmarked dolphins) was 26.3% for D1 and 46.4% for D1 & D2, respectively. Apparent survival was estimated at 0.767 (CI = 0.694–0.827) for D1 animals, and 0.796 (CI = 0.729–0.850) for D1 & D2 combined. For D1 only, seasonal abundance varied from 732 (CI = 460–1,177) in autumn 2010 to 5,304 (CI = 4,745–5,930) in spring 2013. While the inclusion of D2 individuals may offer a more precise estimate of total abundance, the inability to determine additional sources of bias (for example, arising from under or overestimated mark ratios) meant that estimates for D1 individuals were deemed the least biased for this population. The photo-identification protocol, stratification of the data and steps taken to eliminate potential model violations provided a useful and novel approach to estimate population parameters for common dolphins. These approaches could be implemented for other large gregarious populations (≥500 individuals) of animals with poor natural markings.

We present a Hierarchical Bayesian version of Pollock's Closed Robust Design for studying the survival, temporary migration, and abundance of marked animals. Through simulations and analyses of a bottlenose dolphin photo-identification dataset, we compare several estimation frameworks, including Maximum Likelihood estimation (ML), model-averaging by AICc, as well as Bayesian and Hierarchical Bayesian (HB) procedures. Our results demonstrate a number of advantages of the Bayesian framework over other popular methods. First, for simple fixed-effect models, we show the near-equivalence of Bayesian and ML point-estimates and confidence/credibility intervals. Second, we demonstrate how there is an inherent correlation among temporary migration and survival parameter estimates in the PCRD, and while this can lead to serious convergence issues and singularities among MLEs, we show that the Bayesian estimates were more reliable. Third, we demonstrate that a Hierarchical Bayesian model with carefully thought-out hyperpriors, can lead to similar parameter estimates and conclusions as multi-model inference by AICc model-averaging. This latter point is especially interesting for mark-recapture practitioners, for whom model-uncertainty and multi-model inference have become a major preoccupation. Lastly, we extend the Hierarchical Bayesian PCRD to include full-capture histories (i.e., by modeling a recruitment process) and individual-level heterogeneity in detection probabilities, which can have important consequences for the range of phenomena studied by the PCRD, as well as lead to large differences in abundance estimates. For example, we estimate 8–24% more bottlenose dolphins in the western gulf of Shark Bay than previously estimated by ML and AICc-based model-averaging. Other important extensions are discussed. Our Bayesian PCRD models are written in the BUGS-like JAGS language for easy dissemination and customization by the community of capture-mark-recapture (CMR) practitioners.

Inherent difficulties in determining the sex of free-ranging, sexually monomorphic species often prevents a sex-specific focus on estimating abundance, movement patterns and survival rates. This study provides insights into sex-specific population parameters of Indo-Pacific bottlenose dolphins (Tursiops aduncus). Systematic, boat-based photo-identification surveys (n = 417) were conducted year-round from 2007 to 2013 in coastal and estuarine waters off Bunbury, Western Australia. Pollock's Robust Design was used to quantify population parameters for three datasets: (i) adults and juveniles combined, (ii) adult females and, (iii) adult males. For all datasets, abundance estimates varied seasonally, with general highs during summer and/or autumn, and lows during winter. Dolphins had seasonally structured temporary emigration rates with similar trends between sexes. The derived return rate (1-γ') of temporary emigrants into the study area was highest from winter to spring, indicating that dolphins had a high probability of return into the study area during spring. We suggest that the return of dolphins into the study area and increase in abundance is influenced by the breeding season (summer/autumn). Prey availability is likely a main driver responsible for the movement of dolphins out of the study area during winter. Seasonal apparent survival rates were constant and high (0.98–0.99) for all datasets. High apparent survival rates suggest there is no permanent emigration from the study area. Our sex-specific modeling approach offers a comprehensive interpretation of the population dynamics of a top predator in a coastal and estuarine environment and acts as a model for future sex-based population studies on sexually monomorphic species.

Information on shore-based recreational fishing is essential for the sustainable management of nearshore fish stocks. However, obtaining estimates of catch and effort from such fishing activity can be complex and expensive due to the large spatial scales over which surveys are typically conducted and the fine-scale temporal resolution that is desired. Complementary surveys are one option for improving the accuracy of estimates. A pilot study was conducted in Perth, Western Australia, from April to June 2010 to test an expanded aerial–roving survey design that incorporated remotely operated cameras. Cameras recorded the distribution of shore-based fishing activity across a 24-h day, highlighting an afternoon peak as well as some nighttime activity, which is rarely captured in existing survey designs. This information was combined with instantaneous counts of shore fishers from aerial surveys and trip length data that were obtained from 1,194 incomplete trip interviews conducted during roving creel...

The population of Irrawaddy dolphins that occupies the Mekong River in southern Lao People's Democratic Republic and Cambodia is classified as Critically Endangered by the IUCN. Based on capture-recapture of photo-identified individuals, we estimated that the total population numbered 93 ± SE 3.90 individuals (95% CI 86-101), as of April 2007. The combined photo-identification and carcass recovery program undertaken from 2001 to 2007 established that the Irrawaddy dolphin population inhabiting the Mekong River has reached a critical point with regards to its continued survival, where immediate research and management actions are required to greatly reduce adult mortality, and establish the cause of newborn mortality. In addition, community consultation is required to initiate, and evaluate, urgently required conservation measures. An ongoing well-designed combined program of abundance estimation (i.e., photo-identification) and carcass recovery is required to monitor total population size and mortality rates, to inform and evaluate management initiatives. The conclusions of this paper are likely generic to river dolphin populations, particularly where photo-identification is possible.

Three common cross-sectional catch-curve methods for estimating total mortality rate (Z) are the Chapman–Robson, regression, and Heincke estimators. There are five unresolved methodological issues: (1) which is the best estimator, (2) how one should determine the first age-group to use in the analysis, (3) how the variance estimators perform; and, for regression estimators, (4) how the observations should be weighted, including (5) whether and how the oldest ages should be truncated. We used analytical methods and Monte Carlo simulation to evaluate the three catch-curve methods, including unweighted and weighted versions of the regression estimator. We evaluated four criteria for specifying the first age-class used. Regression estimators were evaluated with four different methods of right data truncation. Heincke's method performed poorly and is generally not recommended. The two-tailed χ2 test and one-tailed z-test for full selectivity described by Chapman and Robson did not perform as well as s...

The Smooth Marron Cherax cainii is endemic to south-western Australia and supports an iconic recreational fishery that exploits stocks in both lentic and lotic systems. This study is the first to determine and compare the population biology of a parastacid from both lentic and lotic systems and aimed to gather the information necessary for more effective management of the fishery. Modal progression demonstrated growth rates of juvenile C. cainii were greater in the lentic (Wellington Dam) compared to the lotic (Warren River) system, however, mark-recapture suggested the growth rate of the adult component of the lentic population was stunted whereas in the lotic population 60-90. mm OCL individuals were common and had a faster growth rate. The Wellington Dam stock appeared to be over-exploited and had very low productivity whereas the Warren River stock had relatively low fishing exploitation and a high productivity resulting from higher growth rates coupled with higher population densities (with the trappable population sizes estimated using the open POPAN formulation in the MARK software program). Comparisons of these biological parameters were made with populations elsewhere and there existed a considerable plasticity that is probably due to differences in thermal regimes, degree of habitat complexity, food resource availability and fisher accessibility. The findings demonstrate the need to determine the level of intraspecific biological plasticity in freshwater crayfish in order to sustainably manage their fisheries.

Coyotes (Canis latrans) may affect adult and neonate white-tailed deer (Odocoileus virginianus) survival and have been implicated as a contributor to the decline of deer populations. Additionally, coyote diet composition is influenced by prey availability, season, and region. Because coyote movement and diet vary by region, local data are important to understand coyote population dynamics and their impact on prey species. In southeast Minnesota, we investigated the effect of coyotes on white-tailed deer populations by doc- umenting movement rates, distances moved, and habitats searched by coyotes during fawning and non- fawning periods. Additionally, we determined survival, cause-specific mortality, and seasonal diet composition of coyotes. From 2001 to 2003, we captured and radiocollared 30 coyotes. Per-hour rate of movement averaged 0.87 km and was greater (P ¼ 0.046) during the fawning (1.07 km) than the non- fawning period (0.80 km); areas searched were similar (P ¼ 0.175) between seasons. Coyote habitat use differed during both seasons; habitats were not used in proportion to their availability (P < 0.001). Croplands were used more (P < 0.001) than their proportional availability during both seasons. Use of grasslands was greater during the fawning period (P ¼ 0.030), whereas use of cropland was greater in the nonfawning period (P < 0.001). We collected 66 fecal samples during the nonfawning period; coyote diets were primarily composed of Microtus spp. (65.2%), and consumption of deer was 9.1%. During the study, 19 coyotes died; annual survival rate range was 0.33-0.41, which was low compared with other studies. Consumption of deer was low and coyotes searched open areas (i.e., cropland) more than fawning areas with dense cover. These factors in addition to high coyote mortality suggested that coyote predation was not likely limiting white-tailed deer populations in southeast Minnesota. 2011 The Wildlife Society.

Models of infectious disease dynamics focus on describing the temporal and spatial variations in disease prevalence, and on understanding the factors that affect how many cases will occur in each time period and which individuals are likely to become infected. Classical methods for selecting and fitting models, mostly motivated by human diseases, are almost always based solely on raw counts of infected and uninfected individuals. We begin by reviewing the main classical approaches to parameter estimation, and some of their applications. We then review recently developed methods which enable representation of component processes such as infection and recovery, with observation models that acknowledge the complexities of the sampling and detection processes. We demonstrate the need to account for detectability in modeling disease dynamics, and explore a number of mark–recapture and occupancy study designs for estimating disease parameters while simultaneously accounting for variation in detectability. We highlight the utility of different modeling approaches and also consider the typically strong assumptions that may actually serve to limit their utility in general application to the study of disease dynamics (e.g., assignment of individuals to discrete disease states when underlying state space is more generally continuous; transitions assumed to be simple first-order Markov; temporal separation of hazard and transition events).

Summary. Ecologists applying capture–recapture models to animal populations sometimes have access to additional information about individuals’ populations of origin (e.g., information about genetics, stable isotopes, etc.). Tests that assign an individual’s genotype to its most likely source population are increasingly used. Here we show how to augment a superpopulation capture–recapture model with such information. We consider a single superpopulation model without age structure, and split each entry probability into separate components due to births in situ and immigration. We show that it is possible to estimate these two probabilities separately. We first consider the case of perfect information about population of origin, where we can distinguish individuals born in situ from immigrants with certainty. Then we consider the more realistic case of imperfect information, where we use genetic or other information to assign probabilities to each individual’s origin as in situ or outside the population. We use a resampling approach to impute the true population of origin from imperfect assignment information. The integration of data on population of origin with capture–recapture data allows us to determine the contributions of immigration and in situ reproduction to the growth of the population, an issue of importance to ecologists. We illustrate our new models with capture–recapture and genetic assignment data from a population of banner-tailed kangaroo rats Dipodomys spectabilis in Arizona.