SE@K members Oscar and Rachel have published a paper reviewing the current state-of-the-art in modelling removal data. This work is part of the the EPSRC project EP/S020470/1 “Modelling removal and re-introduction data for improved conservation”.

The paper is available in full here: https://journals.plos.org/plosone/article/authors?id=10.1371/journal.pone.0229965

Removal modelling in ecology: A systematic review

Oscar Rodriguez de Rivera and Rachel McCrea

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.

Former SE@K PhD student Anita Jeyam, Rachel and Roger Pradel (Montpellier) have had a paper published presenting a new test for determining the underlying state structure of Hidden Markov models.  This is an exciting piece of work which provides the foundation for addressing a complex topic for general HMMs.

The full paper is available open access here: https://www.frontiersin.org/articles/10.3389/fevo.2021.598325/full

A Test for the Underlying State-Structure of Hideen 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.

Rachel McCrea and co-authors from St Andrews and Edinburgh have published a paper on modelling the recruitment process of gray seals.

The full paper is available open access here: https://www.frontiersin.org/articles/10.3389/fevo.2021.600967/full

Modeling Recruitment of Birth Cohorts to the Breeding Population: A Hidden Markov Approach

Worthington, King, McCrea, Smout and Pomeroy

Long-term capture-recapture studies provide an opportunity to investigate the population dynamics of long-lived species through individual maturation and adulthood and/or
time. We consider capture-recapture data collected on cohorts of female gray seals
(Halichoerus grypus) born during the 1990s and later observed breeding on the Isle
of May, Firth of Forth, Scotland. Female gray seals can live for 30+ years but display
individual variability in their maturation rates and so recruit into the breeding population
across a range of ages. Understanding the partially hidden process by which individuals
transition from immature to breeding members, and in particular the identification of
any changes to this process through time, are important for understanding the factors
affecting the population dynamics of this species. Age-structured capture-recapture
models can explicitly relate recruitment, and other demographic parameters of interest,
to the age of individuals and/or time. To account for the monitoring of the seals from
several birth cohorts we consider an age-structured model that incorporates a specific
cohort-structure. Within this model we focus on the estimation of the distribution of
the age of recruitment to the breeding population at this colony. Understanding this
recruitment process, and identifying any changes or trends in this process, will offer
insight into individual year effects and give a more realistic recruitment profile for the
current UK gray seal population model. The use of the hidden Markov model provides an
intuitive framework following the evolution of the true underlying states of the individuals.
The model breaks down the different processes of the system: recruitment into the
breeding population; survival; and the associated observation process. This model
specification results in an explicit and compact expression for the model with associated
efficiency in model fitting. Further, this framework naturally leads to extensions to more
complex models, for example the separation of first-time from return breeders, through
relatively simple changes to the mathematical structure of the model.

The paper: Predicting potential cambium damage and fire resistance in Pinus nigra Arn. ssp. salzmannii by: ESPINOSA, J.; RODRÍGUEZ DE RIVERA, O.; MADRIGAL, J.; GUIJARRO, M; HERNANDO, C. , has just been published in Forest Ecology and Management.

Abstract:

Fire management can play a key role in ensuring stand maintenance in future scenarios of global change, particularly in Pinus nigra stands, which are known to be adapted to low-intensity surface fires through characteristics such as thick bark. In this study, laboratory tests were carried out to quantify cambium damage and fire resistance in P. nigra, by using a mass loss colorimeter device in a vertical configuration for the first time. In addition, low-intensity prescribed burning treatments were conducted in the field, and the field and laboratory data were compared. The following variables were used as proxy measures to assess cambium damage: time that temperature remained above 60 °C, heating rate and maximum absolute temperature in the inner bark area. The data were analysed using a Bayesian hierarchical approach (generalized linear mixed model). A threshold heat flux (25 kW m^-2) for the time to ignition of bark was identified. A critical temperature of 60 °C was reached in the cambium during the combustion phase, after the flame was extinguished. The laboratory experiments showed, for the first time, the influence of flame residence time on the potential cambium damage. A bark thickness of 17 mm can be considered the threshold level for preventing critical temperatures being reached in Pinus nigra stands. The influence of bark thickness on protection against fire was confirmed, as was the importance of the coefficient of variation of bark thickness. The field results showed that flame characteristics (maximum temperature and residence time) were the most significant predictors of cambium damage. The combination of fire intensity and exposure time at low heat fluxes is more important than bark in determining cambium damage and may have important implications in the field of forest fuel management and in the ecology of pine forests.

The statistical ecology group from Kent (SE@K) attended the first virtual international statistical ecology conference (vISEC) from 22nd June to 26th June.

Fabian, Katie Oscar and James gave contributed talks. Fabian talked about Objective Priors from Scoring rules for N-mixture models. Katie  gave a talk on Mark-recapture modelling to inform conservation management in Mauritius. Oscar talked about Assessing the Spatio-Temporal distribution of invasive species. James gave the talk Modelling butterfly lifespans using citizen-science count data.

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.