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Obtaining robust estimates of population abundance is a central challenge hindering the conservation and management of many threatened and exploited species. Close-kin mark-recapture (CKMR) is a genetics-based approach that has strong potential to improve monitoring of data-limited species by enabling estimates of abundance, survival, and other parameters for populations that have been challenging to assess. However, CKMR models have received limited sensitivity testing under realistic population dynamics and sampling scenarios, impeding application of the method in population monitoring programs and stock assessments. Here, we use individual-based simulation to examine how unmodeled population dynamics and sampling strategy affect the accuracy and precision of CKMR parameter estimates, and present adapted models that correct the biases that arise from model misspecification. Our results demonstrate that a relatively simple CKMR model produces robust estimates of population abundance when key assumptions including annual breeding and stable population size are met; however, if strong population declines or non-annual breeding dynamics are present, a more complex CKMR model must be constructed to avoid biased parameter estimates. In addition, we show that CKMR can generate reliable abundance estimates for adults from a variety of sampling strategies, including juvenile-focused sampling where adults are never directly observed. Finally, we apply our adapted CKMR model to two decades of genetic data from juvenile lemon sharks (Negaprion brevirostris) in Bimini, Bahamas to demonstrate how juvenile-focused CKMR can be used to expand monitoring efforts for highly mobile populations. Overall, this study expands our understanding of the biological factors and sampling decisions that cause bias in CKMR models, and provides recommendations for sampling design and model construction that can aid biologists in planning and implementing an effective CKMR experiment, particularly for long-lived data-limited species.

Migration of ungulates (hooved mammals) is a fundamental ecological process that promotes abundant herds, whose effects cascade up and down terrestrial food webs. Migratory ungulates provide the prey base that maintains large carnivore and scavenger populations and underpins terrestrial biodiversity (fig. S1). When ungulates move in large aggregations, their hooves, feces, and urine create conditions that facilitate distinct biotic communities. The migrations of ungulates have sustained humans for thousands of years, forming tight cultural links among Indigenous people and local communities. Yet ungulate migrations are disappearing at an alarming rate (1). Efforts by wildlife managers and conservationists are thwarted by a singular challenge: Most ungulate migrations have never been mapped in sufficient detail to guide effective conservation. Without a strategic and collaborative effort, many of the world's great migrations will continue to be truncated, severed, or lost in the coming decades. Fortunately, a combination of animal tracking datasets, historical records, and local and Indigenous knowledge can form the basis for a global atlas of migrations, designed to support conservation action and policy at local, national, and international levels.

Aim To develop a more ecologically realistic approach for estimating the population size of cetaceans and other highly mobile species with dynamic spatial distributions. Location California Current Ecosystem, USA. Methods Conventional spatial density models assume a constant relationship between densities and habitat covariates over some time period, typically a survey season. The estimated population size must change whenever total habitat availability changes. For highly mobile long-lived species, however, density–habitat relationships likely adjust more rapidly than population size. We developed an integrated population-redistribution model based on a more ecologically plausible alternative hypothesis: (1) population size is effectively constant over each survey season; (2) if habitat availability changes, then the population redistributes itself following an ideal free distribution process. Thus, the estimated relationship between densities and habitat covariates adjusts rather than population size. We constructed Bayesian hierarchical models corresponding to the conventional and alternative hypotheses and applied them to distance sampling data for Dall's porpoise (Phocoenoides dalli), a highly mobile cetacean with distribution patterns closely tied to cool sea-surface temperatures. Results The Dall's porpoise data provided strong support for the hypothesis based on an ideal free redistribution process. Our results indicate that the population size of Dall's porpoise within the survey region was relatively stable over each summer/fall survey season, but the distribution expanded and contracted with the extent of suitable habitat. Over multiple survey seasons, the model partitioned variation in observed densities among three sources: variation in population size, the density–habitat relationship and measurement error, leading to lower and more ecologically plausible estimates of interannual variation in population size. Main conclusions We conclude that the integrated population-redistribution model (IPRM) presented here represents an ecologically plausible model for use in future assessments of the population size and dynamics of cetaceans and other highly mobile long-lived species with variable spatial distributions.

Effective conservation and management of animal populations requires knowledge of abundance and trends. For many species, these quantities are estimated using systematic visual surveys. Additional individual-level data are available for some species. Integrated population modeling (IPM) offers a mechanism for leveraging these data sets into a single estimation framework. IPMs that incorporate both population- and individual-level data have previously been developed for birds, but have rarely been applied to cetaceans. Here, we explore how IPMs can be used to improve the assessment of cetacean populations. We combined three types of data that are typically available for cetaceans of conservation concern: population-level visual survey data, individual-level capture-recapture data, and data on anthropogenic mortality. We used this IPM to estimate the population dynamics of the Cook Inlet population of beluga whales (CIBW; Delphinapterus leucas) as a case study. Our state-space IPM included a population process model and three observational submodels: (1) a group detection model to describe group size estimates from aerial survey data; (2) a capture-recapture model to describe individual photographic capture-recapture data; and (3) a Poisson regression model to describe historical hunting data. The IPM produces biologically plausible estimates of population trajectories consistent with all three data sets. The estimated population growth rate since 2000 is less than expected for a recovering population. The estimated juvenile/adult survival rate is also low compared to other cetacean populations, indicating that low survival may be impeding recovery. This work demonstrates the value of integrating various data sources to assess cetacean populations and serves as an example of how multiple, imperfect data sets can be combined to improve our understanding of a population of interest. The model framework is applicable to other cetacean populations and to other taxa for which similar data types are available.

We combined field data and the output from a climate-to-fish coupled biophysical model to calculate weekly climatologies and 1971–2009 time series of physical and biological drivers for 16 distinct regions of the eastern Bering Sea shelf and slope. We focus on spatial trends and physical-biological interactions as a framework to compare model output to localized or season-specific observations. Data on pollock (≥8 cm) diet were used to evaluate energy flows and zooplankton dynamics predicted by the model. Model validation shows good agreement to sea-ice cover albeit with a one month delay in ice retreat. Likewise, the timing of spring phytoplankton blooms in the model were delayed approximately one month in the south and extend further into summer, but the relative timing between the spring and fall bloom peaks was consistent with observations. Ice-related primary producers may shift the timing of the spring bloom maximum biomass earlier in years when sea ice was still present after mid-March in the southern regions. Including the effects of explicit, dynamic fish predation on zooplankton in the model shifts the seasonal spring peak and distribution of zooplankton later in the year relative to simulations with implicit predation dependent only on zooplankton biomass and temperature; the former capturing the dynamic demand on zooplankton prey by fish. Pollock diets based on stomach samples collected in late fall and winter from 1982–2013 show overwintering euphausiids and small pollock as key prey items in the outer and southern Bering Sea shelf; a characteristic not currently present in the model. The model captured two large-scale gradients, supported by field data, characterizing the overall dynamics: 1) inshore to off-shelf physical and biological differences with a gradient in inter-annual variability from higher frequency inshore to lower frequency offshore; and 2) latitudinal gradients in the timing of events. The combined effects of length of day, bathymetry, and tides, which are consistent from year to year, and the two large-scale gradients, characterize the environment on which regional differences were based and restrict their inter-annual and seasonal variability. Thus, the relative timing and sequence of events remained consistent within regions. The combination of model outputs and observational data revealed specific ecosystem processes: (1) The spatial progression in the timing, peaks and sequence of events over the shelf is driven by wind, sea ice, and stratification and creates a seasonal expansion and contraction of the warmer pelagic and bottom habitat suitable to pollock. (2) The seasonal warming of air temperature and the spring-summer expansion of the warm pelagic and bottom habitats influence the ice retreat and the associated ice edge and open water spring blooms, as well as subsequent production/abundance of copepods and euphausiids. (3) These warmer conditions favor pelagic energy flows to pollock (≥10 cm) and allow their distribution to expand shoreward and northward along the shelf break. (4) The fall-winter expansion of the seasonal ice cover drives the contraction of warmer waters towards the outer and southwest shelf and favors benthic energy flows over most of the shelf. There, fall blooms allow for additional lipid storage by large copepods and euphausiids that sink close to the bottom where they either go into diapause or have a restricted diel migration over winter. (5) During these cold months, the preferred pollock habitat shifts and contracts towards the outer and southwest shelf where their increased density and reduced prey availability leads to winter pollock cannibalism and consumption of overwintering euphausiids. Our project highlights the benefits of linking continuous and long-term field work with the development and implementation of highly complex models. In the face of uncertainty, simulations such as these, tightly coupled to field programs, will be instrumental as testbeds for process exploration and management evaluation, increasing their relevance for future fisheries and ecosystem management and strategic planning.

Identifying species at risk of extinction is essential for effective conservation priority-setting in the face of accelerating biodiversity loss. However, the levels of risk that lead to endangered or threatened listing decisions under the United States Endangered Species Act (ESA) are not well defined. We used a Bayesian population modeling approach to estimate levels of risk consistently for 14 marine species previously assessed under the ESA. For each species, we assessed the risks of declining below various abundance thresholds over various time horizons. We found that high risks of declining below 250 mature individuals within five generations matched well with ESA endangered status, while number of populations was useful for distinguishing between threatened and “not warranted” species. The risk assessment framework developed here could enable more consistent, predictable, and transparent ESA status assessments in the future.

Limit reference points (LRPs) for catch, which correspond to thresholds to undesirable population or ecosystem states, offer a consistent, objective approach to management evaluation and prioritization across fisheries, species, and jurisdictions. LRPs have been applied successfully to manage catch of some marine megafauna (elasmobranchs, marine reptiles, seabirds, and marine mammals) in some jurisdictions, such as the use of Potential Biological Removal (PBR) to manage incidental mortality of marine mammals under the U.S. Marine Mammal Protection Act. However, implementation of ecosystem-based management is still in its infancy globally, and LRPs have not yet been widely adopted for marine megafauna, particularly for incidental catch. Here, guidelines are proposed for estimating catch LRPs for marine megafauna, with particular attention to resolving common technical and political challenges, including (1) identifying management units, population thresholds, and risk tolerances that align with common conservation goals and best practices, (2) choosing catch LRP estimators, (3) estimating input parameters such as abundance and productivity, (4) handling uncertainty, and (5) dealing with mismatches between management jurisdictions and population boundaries. The problem of cumulative impacts across sectors is briefly addressed. These guidelines, grounded in marine policy, science, precedent, and lessons learned, should facilitate wider application of catch LRPs in evaluation and management of fisheries impacts on marine megafauna, in support of global commitments to conserve biodiversity and manage fisheries responsibly.

Worldwide, in recent years capture fisheries targeting lower-trophic level forage fish and euphausiid crustaceans have been substantial (similar to 20 million metric tons [MT] annually). Landings of forage species are projected to increase in the future, and this harvest may affect marine ecosystems and predator-prey interactions by removal or redistribution of biomass central to pelagic food webs. In particular, fisheries targeting forage fish and euphausiids may be in competition with seabirds, likely the most sensitive of marine vertebrates given limitations in their foraging abilities (ambit and gape size) and high metabolic rate, for food resources. Lately, apparent competition between fisheries and seabirds has led to numerous high-profile conflicts over interpretations, as well as the approaches that could and should be used to assess the magnitude and consequences of fisheries sea-bird resource competition. In this paper, we review the methods used to date to study fisheries competition with seabirds, and present "best practices" for future resource competition assessments. Documenting current fisheries competition with seabirds generally involves addressing two major issues: 1) are fisheries causing localized prey depletion that is sufficient to affect the birds? (i.e., are fisheries limiting food resources?), and 2) how are fisheries-induced changes to forage stocks affecting seabird populations given the associated functional or numerical response relationships? Previous studies have been hampered by mismatches in the scale of fisheries, fish, and seabird data, and a lack of causal understanding due to confounding by climatic and other ecosystem factors (e.g., removal of predatory fish). Best practices for fisheries-seabird competition research should include i) clear articulation of hypotheses, ii) data collection (or summation) of fisheries, fish, and seabirds on matched spatio-temporal scales, and integration of observational and experimental (including numerical simulation) approaches to establish connections and causality between fisheries and seabirds. As no single technique can provide all the answers to this vexing issue, an integrated approach is most promising to obtain robust scientific results and in turn the sustainability of forage fish fisheries from an ecosystem perspective.

The spatial scale of conservation necessary to avoid species extinctions is one of the most vigorous debates in conservation biology. One approach holds that protecting sites should be the primary level for action on the ground, the other that conservation action targeting broader seascapes and landscapes is more important. We address this debate systematically by assessing the appropriate spatial scales of conservation for all 4,239 threatened mammals, birds, tortoises and turtles, and amphibians. We find that, in the short- to medium term, 20% of these species are dependent on conservation at single sites, 62% on multiple sites, 18% on both sites and sea- or landscape-scale efforts, and

Summary 1.Seabirds and pinnipeds are vulnerable to reductions in prey availability, especially during the breeding season when spatial constraints limit their adaptive capacity. There are growing concerns about the effects of fisheries on prey availability in regions where large commercial fisheries target forage fish. 2.For breeding seabirds and pinnipeds, prey availability depends on a combination of abundance, accessibility, patchiness, and distance from the colony. An understanding of the aspects of prey availability that determine foraging success is essential for the design of effective management responses. 3.We used a mechanistic individual-based foraging model (IBFM) based on observed data for two seabird species, the Peruvian Booby Sula variegata and Guanay Cormorant Phalacrocorax bougainvilliorum, to simulate the foraging patterns of seabirds feeding on schooling fish. We ran the model over simulated prey fields representing eight possible combinations of high or low prey abundance, shallow or deep prey, and broadly-distributed or spatially-concentrated prey. 4.The results highlight the importance of the accessibility of prey. Depth distribution was the primary factor determining modelled foraging success for both species, followed by abundance, and then spatial configuration. 5. Synthesis and applications. The individual-based foraging model (IBFM) provides a spatially-explicit framework for assessing the effects of fisheries on the foraging success of seabirds and other central place foragers (CPFs), and for evaluating the potential effectiveness of marine protected areas and other fisheries management strategies for safeguarding CPFs in dynamic ecosystems. Our analysis indicates that broad-scale fisheries management strategies that maintain forage fish above critical biomass levels are essential, but may need to be supplemented by targeted actions, such as time-area closures, when environmental conditions lead to low prey abundance or reduce prey accessibility for seabirds or pinnipeds of conservation concern. The IBFM is adaptable and could be reconfigured for application to other species and systems. This article is protected by copyright. All rights reserved.

International audience; Small pelagic fish aggregate within areas of suitable habitat to form patchy distributions with localized peaks in abundance. This presents challenges for geostatistical methods designed to investigate the processes underpinning the spatial distribution of stocks and simulate distributions for further analysis. In two-stage models, presence-absence is treated as separable and independent from the process explaining nonzero densities. This is appropriate where gaps in the distribution are attributable to one process and conditional abundance to another, but less so where patchiness is attributable primarily to the strong schooling tendencies of small pelagic fish within suitable habitat. We therefore developed a new modelling framework based on a truncated Gaussian random field (GRF) within a Bayesian framework. We evaluated this method using simulated test data and then applied it to acoustic survey data for Peruvian anchoveta (Engraulis ringens). We assessed the method's performance in terms of posterior densities of spatial parameters, and the density distribution, spatial pattern, and overall spatial distribution of posterior predictions. We conclude that Bayesian posterior prediction based on a truncated GRF is effective at reproducing the patchiness of the observed spatial distribution of anchoveta.

© 2015 British Ecological Society. Understanding the ecological processes that underpin species distribution patterns is a fundamental goal in spatial ecology. However, developing predictive models of habitat use is challenging for species that forage in marine environments, as both predators and prey are often highly mobile and difficult to monitor. Consequently, few studies have developed resource selection functions for marine predators based directly on the abundance and distribution of their prey. We analysed contemporaneous data on the diving locations of two seabird species, the shallow-diving Peruvian Booby (Sula variegata) and deeper diving Guanay Cormorant (Phalacrocorax bougainvilliorum), and the abundance and depth distribution of their main prey, Peruvian anchoveta (Engraulis ringens). Based on this unique data set, we developed resource selection functions to test the hypothesis that the probability of seabird diving behaviour at a given location is a function of the relative abundance of prey in the upper water column. For both species, we show that the probability of diving behaviour is mostly explained by the distribution of prey at shallow depths. While the probability of diving behaviour increases sharply with prey abundance at relatively low levels of abundance, support for including abundance in addition to the depth distribution of prey is weak, suggesting that prey abundance was not a major factor determining the location of diving behaviour during the study period. The study thus highlights the importance of the depth distribution of prey for two species of seabird with different diving capabilities. The results complement previous research that points towards the importance of oceanographic processes that enhance the accessibility of prey to seabirds. The implications are that locations where prey is predictably found at accessible depths may be more important for surface foragers, such as seabirds, than locations where prey is predictably abundant. Analysis of the relative importance of abundance and accessibility is essential for the design and evaluation of effective management responses to reduced prey availability for seabirds and other top predators in marine systems.

a b s t r a c t Ecology and conservation depend on an understanding of how animals adjust their behaviour patterns in response to changes in their environment. Central place foragers (CPFs) are well-suited for developing ecological models of adaptive processes because their objective functions and operational constraints can be reasonably inferred. Central place foraging and provisioning theory provide the theoretical frame- work for this analysis. Analysis of CPF time allocation and energy budgets can provide insights into their strategies for responding to environmental variation. However, until recently, suitable high-resolution data on the behaviour of seabirds and other CPFs at sea have not been available. Previous studies of breeding seabirds have investigated variation in foraging trip duration and colony attendance, but few studies have analyzed variation in time allocation within foraging trips. Here, we develop a concep- tual energy-based model for analysing variation in the time allocation of CPFs during foraging trips, and apply it to the movement patterns of Peruvian boobies (Sula variegata). Foraging trips of Peruvian boobies, recorded using high-resolution global positioning systems (GPS), were first partitioned into movement modes consistent with travel and foraging behaviours using a hidden Markov model (HMM) adapted to account for gaps in the GPS tracks associated with diving behaviour. Analysis of the HMM results based on the conceptual model indicated that differences in foraging effort between two treatments were best explained by a combination of differences in travel time and in time spent searching for prey. The con- ceptual model provides the basis for an integrated approach to analysis of variation in foraging strategies in which identification of various behaviours is coupled with assessments of time and energy budgets. This integrated approach can contribute to greater understanding of the processes determining foraging strategies and the limits to these strategies in the context of competition for resources and global climate change.

Common pool resources are those which contribute to livelihoods but are not privately owned. They can be managed through common property arrangements, or be appropriated opportunistically through open access. The acronym CPR is used here to designate the common pool resource, not the management arrangements, and our interest is in managed, not open-access, arrangements. Given the impracticality and undesirability in many settings of physical fencing, joint action is required to protect CPRs. It is also required to define and enforce the responsibilities that individuals have for managing the resource and their rights over access to products generated by it. This article argues that

Minimizing seabird by-catch requires fisheries management strategies that will ensure the effective implementation of best practices and achieve by-catch reduction targets. This is the major current challenge. In their featured paper, Maree and colleagues conclude that their results provide ‘a strong case for the mandatory adoption of bird-scaring lines in trawl fisheries with high densities of scavenging seabirds’ (Maree et al., 2014, p.1). However, there are two broad approaches to managing fisheries for by-catch reduction: command-andcontrol approaches based on mandatory area/seasonal closures, fishing practices, gear modifications and by-catch reduction devices (BRDs); and incentive-based approaches designed to motivate fishers to minimize by-catch through a combination of incentives to reduce by-catch and penalties for failure. Below, I discuss the advantages of incentive-based approaches over command-and-control, and summarize the lessons learned from successful strategies. Incentive-based approaches are designed to align fishers’ incentives with societal goals, and have several advantages for by-catch reduction in fisheries (Hall & Mainprize, 2005; Pascoe et al., 2010). Management is focused directly on by-catch reduction targets, such as reducing the number of seabird mortalities, rather than the technical details of specific by-catch reduction measures, such as the material, length and colour of bird-scaring lines. Regulations can be simpler and adjusted more easily, allowing for stronger targets over time and adaptive management of changing fisheries in dynamic ecosystems. In most fisheries, single by-catch reduction measures are insufficient, and a combination of changes in fishing practices, gear modifications and BRDs is required. Incentive-based approaches are flexible, enabling captains and vessel owners to decide on the specific suite of by-catch reduction measures that will be most cost-effective for a given set of conditions. This can stimulate innovation and collaborative experimental research aimed at improving the cost-effectiveness of by-catch reduction measures (Melvin et al., 2001). Indeed, the most cost-effective by-catch solutions are often identified by fishers themselves (Hall, Alverson & Metuzals, 2000). Incentive-based approaches can also foster information-sharing on best practices and areas with high by-catch rates, and investment in compensatory mitigation including contributions to by-catch reduction in lower-value fisheries. In contrast, command-and-control approaches do not provide incentives for further innovation, and are often poorly implemented because fishers are not motivated to implement them effectively (Branch et al., 2006; Pascoe et al., 2010). Industrial fisheries that have already achieved substantial reductions in seabird by-catch can provide insights into the key elements of successful strategies. Successful strategies integrate clear objectives and targets, a range of accepted best practices, appropriate incentives, and effective monitoring. Leadership may be provided by government agencies, major wholesale seafood buyers like Walmart or sustainable seafood certification programmes such as the Marine Stewardship Council. The broad goal of minimizing seabird by-catch needs to be translated into more specific management objectives and measurable targets, such as the reduction of seabird mortalities in each fleet below a predefined number per unit of fishing effort. For threatened species, targets may be designed to reduce by-catch below levels that would have a measurable effect on population dynamics. These targets can be strengthened over time. There is a growing body of research on best practice in seabird by-catch in industrial fisheries (see Agreement on the Conservation of Albatrosses and Petrels by-catch mitigation fact sheets, available at http://www.acap.aq). In industrial trawl fisheries, bird-scaring lines are accepted best practice and are mandatory in some fisheries, including the South African deep-water hake trawl fishery. While birdscaring lines can be highly effective, they do not eliminate seabird by-catch entirely and may have unintended consequences, such as shifting by-catch from one species group to another (Maree et al., 2014). In contrast, avoiding discards and offal discharge can reduce by-catch of all seabird groups to negligible levels by removing the feature that attracts seabirds during fishing operations (ACAP, 2013). While several options for reducing discharges have been identified, including onboard fish meal plants and batch processing, these can be costly and are rarely implemented on smaller and older vessels. The challenge remains to develop management frameworks that will motivate fishers to bs_bs_banner

Effective long-term species conservation requires a conservation approach targeted at all scales at which biodiversity occurs, from the scale of species occurrences to the scale of populations and the ecological processes needed to sustain them (Noss, 2002). Protected areaand site-level initiatives have proven to be effective at protecting habitat, even when resources for effective management are lacking (Bruner et al., 2001), but protected areas alone are often of insufficient size to sustain viable populations of the species they are designed to protect (see, for example, Newmark, 1995). The total area accessible to conservation target species can be increased by connecting protected areas through biological corridors and stepping stones of habitat (Beier and Noss, 1998). But even with large protected areas and effective connectivity networks, human population pressures and incompatible land and resource use in surrounding areas can compromise biodiversity conservation goals (Wiens, 1996). In order to achieve the effective conservation of species, populations and ecological processes, a regional-scale biodiversity conservation corridor approach is necessary. Biodiversity conservation corridors have two objectives—the primary objective is the conservation or restoration of naturally functioning landscapes and the species diversity naturally present within the landscape; the secondary objective is the reconciliation of biodiversity conservation with the livelihood aspirations of human communities in the region and national development goals. Within biodiversity conservation corridors, irreplaceable biodiversity areas are put under strict protection, areas that can support both conservation and development goals through sustainable use and direct incentives for conservation are also identified, while economically important areas are targeted for more intensive development. A biodiversity conservation corridor is therefore a landscape in which land use, incentives, and policies are designed to achieve conservation objectives while contributing to economic development (Sanderson et al., 2003). Chapter 9 Approaches to Corridor Planning: Transitioning TAMARIN from Mata Atlantica to Madagascar