Removal modelling in ecology: A systematic review

Removal models were proposed over 80 years ago as a tool to estimate unknown population size. More recently, they are used as an effective tool for management actions for the control of non desirable species, or for the evaluation of translocation management actions. Although the models have evolved over time, in essence, the protocol for data collection has remained similar: at each sampling occasion attempts are made to capture and remove individuals from the study area. Within this paper we review the literature of removal modelling and highlight the methodological developments for the analysis of removal data, in order to provide a unified resource for ecologists wishing to implement these approaches. Models for removal data have developed to better accommodate important features of the data and we discuss the shift in the required assumptions for the implementation of the models. The relative simplicity of this type of data and associated models mean that the method remains attractive and we discuss the potential future role of this technique

A Test for the Underlying State-Structure of Hidden Markov Models: Partially Observed Capture-Recapture Data

Hidden Markov models (HMMs) are being widely used in the field of ecological modeling, however determining the number of underlying states in an HMM remains a challenge. Here we examine a special case of capture-recapture models for open populations, where some animals are observed but it is not possible to ascertain their state (partial observations), whilst the other animals' states are assigned without error (complete observations). We propose a mixture test of the underlying state structure generating the partial observations, which assesses whether they are compatible with the set of states observed in the complete observations. We demonstrate the good performance of the test using simulation and through application to a data set of Canada Geese

Open models for removal data

Individuals of protected species, such as amphibians and reptiles, often need to be removed from sites before development commences. Usually, the population is considered to be closed. All individuals are assumed to i) be present and available for detection at the start of the study period and ii) remain at the site until the end of the study, unless they are detected. However, the assumption of population closure is not always valid. We present new removal models which allow for population renewal through birth and/or immigration, and population depletion through sampling as well as through death/emigration. When appropriate, productivity may be estimated and a Bayesian approach allows the estimation of the probability of total population depletion. We demonstrate the performance of the models using data on common lizards, Zootoca vivipara, and great crested newts, Triturus cristatus

A test of positive association for detecting heterogeneity in capture for capture-recapture data

The Cormack–Jolly–Seber (CJS) model assumes that all marked animals have equal recapture probabilities at each sampling occasion, but heterogeneity in capture often occurs and should be taken into account to avoid biases in parameter estimates. Although diagnostic tests are generally used to detect trap-dependence or transience and assess the overall fit of the model, heterogeneity in capture is not routinely tested for. In order to detect and identify this phenomenon in a CJS framework, we propose a test of positive association between previous and future encounters using Goodman–Kruskal’s gamma. This test is based solely on the raw capture histories and makes no assumption on model structure. The development of the test is motivated by a dataset of Sandwich terns (Thalasseus sandvicensis), and we use the test to formally show that they exhibit heterogeneity in capture. We use simulation to assess the performance of the test in the detection of heterogeneity in capture, compared to existing and corrected diagnostic goodness-of-fit tests, Leslie’s test of equal catchability and Carothers’ extension of the Leslie test. The test of positive association is easy to use and produces good results, demonstrating high power to detect heterogeneity in capture. We recommend using this new test prior to model fitting as the outcome will guide the model-building process and help draw more accurate biological conclusions. Supplementary materials accompanying this paper appear online

Removal models accounting for temporary emigration

Removal of protected species from sites scheduled for development is often a legal requirement in order to minimize the loss of biodiversity. The assumption of closure in the classic removal model will be violated if individuals become temporarily undetectable, a phenomenon commonly exhibited by reptiles and amphibians. Temporary emigration can be modeled using a multievent framework with a partial hidden process, where the underlying state process describes the movement pattern of animals between the survey area and an area outside of the study. We present a multievent removal model within a robust design framework which allows for individuals becoming temporarily unavailable for detection. We demonstrate how to investigate parameter redundancy in the model. Results suggest the use of the robust design and certain forms of constraints overcome issues of parameter redundancy. We show which combinations of parameters are estimable when the robust design reduces to a single secondary capture occasion within each primary sampling period. Additionally, we explore the benefit of the robust design on the precision of parameters using simulation. We demonstrate that the use of the robust design is highly recommended when sampling removal data. We apply our model to removal data of common lizards, Zootoca vivipara, and for this application precision of parameter estimates is further improved using an integrated model

Pond management enhances the local abundance and species richness of farmland bird communities

Agricultural intensification and the associated loss of non-cropped habitats have caused a major decline in UK farmland bird populations since the 1970s. As a consequence, there is an urgent need to implement effective conservation and habitat restoration measures in agricultural landscapes. Over the last 40–50 years, due to the cessation of traditional management practices, the majority of UK farmland ponds have become highly terrestrialised, resulting in major reductions in the diversity and abundance of aquatic plant and invertebrate assemblages. Recent research undertaken at farmland ponds in early summer, has shown restored open-canopy, macrophyte-dominated ponds support an increased abundance and diversity of farmland birds, compared to non-managed, overgrown ponds. Here, we expand on this previous research with a year-long field study to assess the implications of pond management for farmland birds by comparing bird diversity, abundance and activity at managed open-canopy ponds with those at unmanaged overgrown ponds. Driven strongly by pond management and connectivity to semi-natural landscape features such as hedgerows and woodland patches, bird abundance and species richness, as well as foraging and parental behaviour, were all significantly higher at managed open-canopy ponds. Further, a wider landscape analysis found that terrestrial land-use patterns in the vicinity of the ponds were not significant predictors of bird communities at the pond sites. In light of the numerous potential benefits to conservation-listed birds and other wildlife, we conclude that farmland pond management has been undervalued as a conservation measure to assist farmland birds. Consequently, we conclude that future agri-environment schemes, should more fully embrace farmland ponds

Estimation of population size when capture probability depends on individual state

We develop a multi-state model to estimate the size of a closed population from capture–recapture studies. We consider the case where capture–recapture data are not of a simple binary form, but where the state of an individual is also recorded upon every capture as a discrete variable. The proposed multi-state model can be regarded as a generalisation of the commonly applied set of closed population models to a multi-state form. The model allows for heterogeneity within the capture probabilities associated with each state while also permitting individuals to move between the different discrete states. A closed-form expression for the likelihood is presented in terms of a set of sufficient statistics. The link between existing models for capture heterogeneity is established, and simulation is used to show that the estimate of population size can be biased when movement between states is not accounted for. The proposed unconditional approach is also compared to a conditional approach to assess estimation bias. The model derived in this paper is motivated by a real ecological data set on great crested newts, Triturus cristatus. Supplementary materials accompanying this paper appear online

Lowe Syndrome Protein OCRL1 Supports Maturation of Polarized Epithelial Cells

Mutations in the inositol polyphosphate 5-phosphatase OCRL1 cause Lowe Syndrome, leading to cataracts, mental retardation and renal failure. We noted that cell types affected in Lowe Syndrome are highly polarized, and therefore we studied OCRL1 in epithelial cells as they mature from isolated individual cells into polarized sheets and cysts with extensive communication between neighbouring cells. We show that a proportion of OCRL1 targets intercellular junctions at the early stages of their formation, co-localizing both with adherens junctional components and with tight junctional components. Correlating with this distribution, OCRL1 forms complexes with junctional components α-catenin and zonula occludens (ZO)-1/2/3. Depletion of OCRL1 in epithelial cells growing as a sheet inhibits maturation; cells remain flat, fail to polarize apical markers and also show reduced proliferation. The effect on shape is reverted by re-expressed OCRL1 and requires the 5′-phosphatase domain, indicating that down-regulation of 5-phosphorylated inositides is necessary for epithelial development. The effect of OCRL1 in epithelial maturation is seen more strongly in 3-dimensional cultures, where epithelial cells lacking OCRL1 not only fail to form a central lumen, but also do not have the correct intracellular distribution of ZO-1, suggesting that OCRL1 functions early in the maturation of intercellular junctions when cells grow as cysts. A role of OCRL1 in junctions of polarized cells may explain the pattern of organs affected in Lowe Syndrome

Sufficient statistic likelihood construction for age- and time- dependent multi-state joint recapture and recovery data

Two closed-form likelihoods for multi-state joint recapture and recovery data were proposed in King and Brooks (2003); the first incorporated dependence on time and cohort whilst the second included dependence on age and cohort. However, when multi-state joint recapture and recovery data are modelled, it is likely that dependence on age and time will both be potentially of interest and therefore the most useful model formulation will incorporate both of these parameter structures. Within this article the likelihood function required for such a model is derived in terms of a set of sufficient statistics