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New paper: Duration of female parental care and their survival in the little auk Alle alle – are these two traits linked?

The paper: Duration of female parental care and their survival in the little auk Alle alle – are these two traits linked? by: Katarzyna Wojczulanis-Jakubas, Marina Jiménez-Muñoz, Dariusz Jakubas, Dorota Kidawa, Nina Karnovsky, Diana Cole and Eleni Matechou, has just been published in Behavioral Ecology and Sociobiology.

Abstract:

Desertion of offspring before its independence by one of the parents is observed in a number of avian species with bi-parental care but reasons for this strategy are not fully understood. This behaviour is particularly intriguing in species where bi-parental care is crucial to raise the brood successfully. Here, we focus on the little auk, Alle alle, a small seabird with intensive bi-parental care, where the female deserts the brood at the end of the chick rearing period. The little auk example is interesting as most hypotheses to explain desertion of the brood by females (e.g. “re-mating hypothesis”, “body condition hypothesis”) have been rejected for this species. Here, we analysed a possible relationship between the duration of female parental care over the chick and her chances to survive to the next breeding season. We performed the study in two breeding colonies on Spitsbergen with different foraging conditions – more favourable in Hornsund and less favourable in Magdalenefjorden. We predicted that in Hornsund females would stay for shorter periods of time with the brood and would have higher survival rates in comparison with birds from Magdalenefjorden. We found that indeed in less favourable conditions of Magdalenefjorden, females stay longer with the brood than in the more favourable conditions of Hornsund. Moreover, female survival was negatively affected by the length of stay in the brood. Nevertheless, duration of female parental care over the chick was not related to their parental efforts, earlier in the chick rearing period, and survival of males and females was similar. Thus, although females brood desertion and winter survival are linked, the relationship is not straightforward.

 

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Papers

New Paper: Size‐ and stage‐dependence in cause‐specific mortality of migratory brown trout

The paper Size‐ and stage‐dependence in cause‐specific mortality of migratory brown trout by Chloé R. Nater, Yngvild Vindenes, Per Aass, Diana Cole, Øystein Langangen, S. Jannicke Moe, Atle Rustadbakken, Daniel Turek, Leif Asbjørn Vøllestad and Torbjørn Ergon was published in Journal of Animal Ecology.

Abstract

  1. Evidence‐based management of natural populations under strong human influence frequently requires not only estimates of survival but also knowledge about how much mortality is due to anthropogenic vs. natural causes. This is the case particularly when individuals vary in their vulnerability to different causes of mortality due to traits, life history stages, or locations.
  2. Here, we estimated harvest and background (other cause) mortality of landlocked migratory salmonids over half a century. In doing so, we quantified among‐individual variation in vulnerability to cause‐specific mortality resulting from differences in body size and spawning location relative to a hydropower dam.
  3. We constructed a multistate mark–recapture model to estimate harvest and background mortality hazard rates as functions of a discrete state (spawning location) and an individual time‐varying covariate (body size). We further accounted for among‐year variation in mortality and migratory behaviour and fit the model to a unique 50‐year time series of mark–recapture–recovery data on brown trout (Salmo trutta) in Norway.
  4. Harvest mortality was highest for intermediate‐sized trout, and outweighed background mortality for most of the observed size range. Background mortality decreased with body size for trout spawning above the dam and increased for those spawning below. All vital rates varied substantially over time, but a trend was evident only in estimates of fishers’ reporting rate, which decreased from over 50% to less than 10% throughout the study period.
  5. We highlight the importance of body size for cause‐specific mortality and demonstrate how this can be estimated using a novel hazard rate parameterization for mark–recapture models. Our approach allows estimating effects of individual traits and environment on cause‐specific mortality without confounding, and provides an intuitive way to estimate temporal patterns within and correlation among different mortality sources.
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Parameter Redundancy and Identifiability Book Published

Diana Cole’s book Parameter Redundancy and Identifiability has been publish by Chapman and Hall/CRC

Book Synopsis

Statistical and mathematical models are defined by parameters that describe different characteristics of those models. Ideally it would be possible to find parameter estimates for every parameter in that model, but, in some cases, this is not possible. For example, two parameters that only ever appear in the model as a product could not be estimated individually; only the product can be estimated. Such a model is said to be parameter redundant, or the parameters are described as non-identifiable. This book explains why parameter redundancy and non-identifiability is a problem and the different methods that can be used for detection, including in a Bayesian context. Key features of this book:

  • Detailed discussion of the problems caused by parameter redundancy and non-identifiability
  • Explanation of the different general methods for detecting parameter redundancy and non-identifiability, including symbolic algebra and numerical methods
  • Chapter on Bayesian identifiability
  • Throughout illustrative examples are used to clearly demonstrate each problem and method. Maple and R code are available for these examples
  • More in-depth focus on the areas of discrete and continuous state-space models and ecological statistics, including methods that have been specifically developed for each of these areas

This book is designed to make parameter redundancy and non-identifiability accessible and understandable to a wide audience from masters and PhD students to researchers, from mathematicians and statisticians to practitioners using mathematical or statistical models.

Book website: https://www.routledge.com/Parameter-Redundancy-and-Identifiability/Cole/p/book/9781498720878

Code for book available at: https://www.kent.ac.uk/smsas/personal/djc24/parameterredundancy.html

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New publication: Statistical Development of Animal Density Estimation Using Random Encounter Modelling

New publication in JABES: Statistical Development of Animal Density Estimation Using Random Encounter Modelling by Natoya Jourdain, Diana Cole, Martin Ridout and Marcus Rowcliffe.

Abstract:

Camera trapping is widely used in ecological studies to estimate animal density, although these studies are largely restricted to animals that can be identified to the individual level. The random encounter model, developed by Rowcliffe et al. (J Anal Ecol 45(4):1228–1236, 2008), estimates animal density from camera-trap data without the need to identify animals. Although the REM can provide reliable density estimates, it lacks the potential to account for the multiple sources of variance in the modelling process. The density estimator in REM is a ratio, and since the variance of a ratio estimator is intractable, we examine and compare the finite sample performance of many approaches for obtaining confidence intervals via simulation studies. We also propose an integrated random encounter model as a parametric alternative, which is flexible and can incorporate covariates and random effects. A data example from Whipsnade Wild Animal Park, Bedfordshire, south England, is used to demonstrate the application of these methods.

 

 

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Prizes

Congratulation to Marina whose poster won silver at STEM for Britain.

On 13th March Marina went to Parliament to present her poster on How do bird populations vary across Britain? Spatially-explicit integrated population models, as part of STEM for Britain competition. As stated on the STEM for Britain website, “STEM for BRITAIN Awards are made on the basis of the very best research work and results by an early-stage or early-career researcher together with their ability to communicate their work to a lay audience.” Marina’s poster won silver in the Mathematics category. Well done Marina on this amazing achievement.

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Paper – Estimating age‐dependent survival from age‐aggregated ringing data

The paper Estimating age‐dependent survival from age‐aggregated ringing data—extending the use of historical records, by Marina, Diana, Stephen Freeman (Centre for Ecology and Hydrology), Rob Robinson (BTO), Stephen Baillie (BTO) and Eleni, has been published in Ecology and Evolution.

Open access paper

Abstract:

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.

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NERC Advanced Training Course

Statistical models for wildlife population assessment and conservation

 

Dates and Location: 7-11 January 2019, University of Kent, Canterbury Campus

Deadline for Applications: (Extended) 5pm on Wednesday 31st October 2018, by emailing advancedtraining@kent.ac.uk with a completed application form

Specifications: We have 30 fully-funded places (inc. travel within the UK and accommodation); priority will be given to NERC-funded PhD students but if spaces remain we are able to offer the funded places to other UK-based PhD students and early-career researchers.

Description:

Within the environmental sector there is currently a shortage of practitioners equipped with the statistical modelling skills to carry out reliable population assessments. Consequently, environmental impact assessments (EIAs) and development mitigation projects often use population assessment protocols that are not fit-for-purpose. The skills shortage arises because (1) recent advances in statistical models for population assessment are largely confined to the academic sector with little penetration to the end-users; and (2) although many postgraduate programmes have a statistical modelling training component, this often fails to expose PhD students to new models in the area and the potential applications these have for conservation practice. This training programme will provide a cohort of PhD students and early career researchers/practitioners with the relevant modelling skills required for a career that involves wildlife population assessment for conservation.

The workshop will focus on ecological questions that arise in conservation practice and use real case study data. Training will include individual-based models, such as capture-recapture, but will also embrace scenarios more frequently used in EIA, such as batch-marked, presence/absence, site occupancy and counts. Applications will include newts, butterflies, birds, bees, beetles, ibex and bats. Each module will be accompanied by a practical computer session using R and each module builds on the last so that delegates build a portfolio of statistical skills.

More detailed information about the workshop timetable and training outcomes is available here.

Trainers: Dr Rachel McCrea, Dr Eleni Matechou, Dr Diana Cole, Richard Griffiths.

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Paper: Removal models accounting for temporary emigration

The paper Removal models accounting for temporary emigration by Ming Shou, Rachel McCrea, Eleni Matechou , Diana Cole and Richard Griffiths has just been published online early in Biometrics.

Open access link to paper.

Summary:

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.

 

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International Biometric Conference

From 8th-13th July Byron and Marina attended the International Biometric Conference in Barcelona.

Marina gave a talk on Integrated Population Modelling Incorporating Spatial Information.

Byron gave a talk on Hidden Markov modelling for a multi-species index.

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