Fast Bayesian inference for large occupancy datasets.

In recent years, the study of species' occurrence has benefited from the increased availability of large-scale citizen-science data. While abundance data from standardized monitoring schemes are biased toward well-studied taxa and locations, opportunistic data are available for many taxonomic groups, from a large number of locations and across long timescales. Hence, these data provide opportunities to measure species' changes in occurrence, particularly through the use of occupancy models, which account for imperfect detection. These opportunistic datasets can be substantially large, numbering hundreds of thousands of sites, and hence present a challenge from a computational perspective, especially within a Bayesian framework. In this paper, we develop a unifying framework for Bayesian inference in occupancy models that account for both spatial and temporal autocorrelation. We make use of the Pólya-Gamma scheme, which allows for fast inference, and incorporate spatio-temporal random effects using Gaussian processes (GPs), for which we consider two efficient approximations: subset of regressors and nearest neighbor GPs. We apply our model to data on two UK butterfly species, one common and widespread and one rare, using records from the Butterflies for the New Millennium database, producing occupancy indices spanning 45 years. Our framework can be applied to a wide range of taxa, providing measures of variation in species' occurrence, which are used to assess biodiversity change.

A general modeling framework for open wildlife populations based on the Polya tree prior.

Wildlife monitoring for open populations can be performed using a number of different survey methods. Each survey method gives rise to a type of data and, in the last five decades, a large number of associated statistical models have been developed for analyzing these data. Although these models have been parameterized and fitted using different approaches, they have all been designed to either model the pattern with which individuals enter and/or exit the population, or to estimate the population size by accounting for the corresponding observation process, or both. However, existing approaches rely on a predefined model structure and complexity, either by assuming that parameters linked to the entry and exit pattern (EEP) are specific to sampling occasions, or by employing parametric curves to describe the EEP. Instead, we propose a novel Bayesian nonparametric framework for modeling EEPs based on the Polya tree (PT) prior for densities. Our Bayesian nonparametric approach avoids overfitting when inferring EEPs, while simultaneously allowing more flexibility than is possible using parametric curves. Finally, we introduce the replicate PT prior for defining classes of models for these data allowing us to impose constraints on the EEPs, when required. We demonstrate our new approach using capture-recapture, count, and ring-recovery data for two different case studies.

Reliability of environmental DNA surveys to detect pond occupancy by newts at a national scale.

The distribution assessment and monitoring of species is key to reliable environmental impact assessments and conservation interventions. Considerable effort is directed towards survey and monitoring of great crested newts (Triturus cristatus) in England. Surveys are increasingly undertaken using indirect methodologies, such as environmental DNA (eDNA). We used a large data set to estimate national pond occupancy rate, as well as false negative and false positive error rates, for commercial eDNA protocols. Additionally, we explored a range of habitat, landscape and climatic variables as predictors of pond occupancy. In England, 20% of ponds were estimated to be occupied by great crested newts. Pond sample collection error rates were estimated as 5.2% false negative and 1.5% false positive. Laboratory error indicated a negligible false negative rate when 12 qPCR replicates were used. Laboratory false positive error was estimated at 2% per qPCR replicate and is therefore exaggerated by high levels of laboratory replication. Including simple habitat suitability variables into the model revealed the importance of fish, plants and shading as predictors of newt presence. However, variables traditionally considered as important for newt presence may need more precise and consistent measurement if they are to be employed as reliable predictors in modelling exercises.

Parasites, Drugs and Captivity: Blastocystis-Microbiome Associations in Captive Water Voles.

(1) Background: Blastocystis is a microbial eukaryote inhabiting the gastrointestinal tract of a broad range of animals including humans. Several studies have shown that the organism is associated with specific microbial profiles and bacterial taxa that have been deemed beneficial to intestinal and overall health. Nonetheless, these studies are focused almost exclusively on humans, while there is no similar information on other animals. (2) Methods: Using a combination of conventional PCR, cloning and sequencing, we investigated presence of Blastocystis along with Giardia and Cryptosporidium in 16 captive water voles sampled twice from a wildlife park. We also characterised their bacterial gut communities. (3) Results: Overall, alpha and beta diversities between water voles with and without Blastocystis did not differ significantly. Differences were noted only on individual taxa with Treponema and Kineothrix being significantly reduced in Blastocystis positive water voles. Grouping according to antiprotozoal treatment and presence of other protists did not reveal any differences in the bacterial community composition either. (4) Conclusion: Unlike human investigations, Blastocystis does not seem to be associated with specific gut microbial profiles in water voles.

Optimising sampling and analysis protocols in environmental DNA studies.

Ecological surveys risk incurring false negative and false positive detections of the target species. With indirect survey methods, such as environmental DNA, such error can occur at two stages: sample collection and laboratory analysis. Here we analyse a large qPCR based eDNA data set using two occupancy models, one of which accounts for false positive error by Griffin et al. (J R Stat Soc Ser C Appl Stat 69: 377-392, 2020), and a second that assumes no false positive error by Stratton et al. (Methods Ecol Evol 11: 1113-1120, 2020). Additionally, we apply the Griffin et al. (2020) model to simulated data to determine optimal levels of replication at both sampling stages. The Stratton et al. (2020) model, which assumes no false positive results, consistently overestimated both overall and individual site occupancy compared to both the Griffin et al. (2020) model and to previous estimates of pond occupancy for the target species. The inclusion of replication at both stages of eDNA analysis (sample collection and in the laboratory) reduces both bias and credible interval width in estimates of both occupancy and detectability. Even the collection of > 1 sample from a site can improve parameter estimates more than having a high number of replicates only within the laboratory analysis.

Estimating age-dependent survival from age-aggregated ringing data-extending the use of historical records.

Bird ring-recovery data have been widely used to estimate demographic parameters such as survival probabilities since the mid-20th century. However, while the total number of birds ringed each year is usually known, historical information on age at ringing is often not available. A standard ring-recovery model, for which information on age at ringing is required, cannot be used when historical data are incomplete. We develop a new model to estimate age-dependent survival probabilities from such historical data when age at ringing is not recorded; we call this the historical data model. This new model provides an extension to the model of Robinson, 2010, Ibis, 152, 651-795 by estimating the proportion of the ringed birds marked as juveniles as an additional parameter. We conduct a simulation study to examine the performance of the historical data model and compare it with other models including the standard and conditional ring-recovery models. Simulation studies show that the approach of Robinson, 2010, Ibis, 152, 651-795 can cause bias in parameter estimates. In contrast, the historical data model yields similar parameter estimates to the standard model. Parameter redundancy results show that the newly developed historical data model is comparable to the standard ring-recovery model, in terms of which parameters can be estimated, and has fewer identifiability issues than the conditional model. We illustrate the new proposed model using Blackbird and Sandwich Tern data. The new historical data model allows us to make full use of historical data and estimate the same parameters as the standard model with incomplete data, and in doing so, detect potential changes in demographic parameters further back in time.

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.

Biclustering Models for Two-Mode Ordinal Data.

The work in this paper introduces finite mixture models that can be used to simultaneously cluster the rows and columns of two-mode ordinal categorical response data, such as those resulting from Likert scale responses. We use the popular proportional odds parameterisation and propose models which provide insights into major patterns in the data. Model-fitting is performed using the EM algorithm, and a fuzzy allocation of rows and columns to corresponding clusters is obtained. The clustering ability of the models is evaluated in a simulation study and demonstrated using two real data sets.