Congratulations to Eleni for her new role as Book Reviews Editor for the Journal of Agricultural, Biological and Environmental Statistics.
Invited talks at the RSS Conference 2020
Oscar and Alex presented their work at the (virtual) RSS conference 2020 during the invited session on “Challenges and advances of spatial modelling in ecology” organised by Rachel.
Oscar’s talk, titled “The Importance of spatio-temporal modelling in Ecology” described the importance spatio-temporal models to understand the relationship between species in a common area. Oscar explains the problem caused due to the wolf eradication in Yellowstone National Park in 1920’s and how the landscape changed from this eradication to the reintroduction in 1990’s.
Alex’s talk, titled “Interaction point processes in spatially explicit capture-recapture models” described his work on a spatial capture-recapture model incorporating interactions within and between individuals of two species. The model relies on the theory of interaction point processes. As inference for these processes cannot be performed using standard techniques due to the intractability of the likelihood, specific MCMC methods have to be used. The model is applied to a capture-recapture data-set of leopards and tigers collected in India.
RSS meeting on eDNA: Challenges and Opportunities now virtual
The meeting, initially planned for May 2020, will now take place virtually on the 16th of October.
The timetable for the day is
9.30-10 Kerry Walsh, Environment Agency: “Challenges and opportunities: A regulator’s perspective.”
10-10.15 discussion/change over
10.15-10.45 Naomi Ewald, FreshWater Habitats Trust: “Analysis of eDNA data to inform conservation priorities: case studies of long term species monitoring and short term before-after surveys.”
10.45-11 discussion/change over
11-11.30 morning break
11.30-12 Francesco Ficetola, University of Milan: “Environmental DNA to track long-term changes of mountain ecosystem.”
12-12.15 discussion/change over
12.15-12.45 lunch break
12.45-13.15 Jim Griffin, University College London: “Modelling environmental DNA data; Bayesian variable selection accounting for false positive and false negative errors.”
13.15-13.30 discussion/change over
13.30-14 Doug Yu, University of East Anglia: “Managing wildlife with eDNA data: salmon, leeches, insects, and forests.”
14-14.30 discussion/close
Participants can register on the RSS website.
Rachel and Byron receive their RSS awards
Congratulations once again to Rachel, for receiving the bronze award, and Byron, for receiving the Barnett award. The virtual RSS 2020 conference has released a video honouring the recipients of its awards for this year
New paper: A Generic Method for Estimating and Smoothing Multispecies Biodiversity Indicators Using Intermittent Data
The paper, A Generic Method for Estimating and Smoothing Multispecies Biodiversity Indicators Using Intermittent Data, by Stephen Freeman, Nicholas Isaac, Panagiotis Besbeas, Emily Dennis and Byron Morgan has just been published in the Journal of Agricultural, Biological and Environmental Statistics
https://doi.org/10.1007/s13253-020-00410-6
Abstract
Biodiversity indicators summarise extensive, complex ecological data sets and are important in influencing government policy. Component data consist of time-varying indices for each of a number of different species. However, current biodiversity indicators suffer from multiple statistical shortcomings. We describe a state-space formulation for new multispecies biodiversity indicators, based on rates of change in the abundance or occupancy probability of the contributing individual species. The formulation is flexible and applicable to different taxa. It possesses several advantages, including the ability to accommodate the sporadic unavailability of data, incorporate variation in the estimation precision of the individual species’ indices when appropriate, and allow the direct incorporation of smoothing over time. Furthermore, model fitting is straightforward in Bayesian and classical implementations, the latter adopting either efficient Hidden Markov modelling or the Kalman filter. Conveniently, the same algorithms can be adopted for cases based on abundance or occupancy data—only the subsequent interpretation differs. The procedure removes the need for bootstrapping which can be prohibitive. We recommend which of two alternatives to use when taxa are fully or partially sampled. The performance of the new approach is demonstrated on simulated data, and through application to three diverse national UK data sets on butterflies, bats and dragonflies. We see that uncritical incorporation of index standard errors should be avoided.
New Paper: Predicting potential cambium damage and fire resistance in Pinus nigra Arn. ssp. salzmannii
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.
SE@K at vISEC
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.
Speed talks were given by Diana, Eleni and Ulrike. Diana talked about Inference with parameter redundant models: reparameterisation, constraints, robust design and integrated models. Eleni talked about Efficient Bayesian variable selection in ecological models. Ulrike’s talk was on Adjusting for misclassified sex observation in a capture recapture study of Telfair skinks.
Chloe presented the poster Statistical Modelling of Spatial and Temporal Patterns in Human-Elephant Conflict.
Rachel was co-chair of the scientific committee.
Congratulations to Alex!
Congratulations to Alex who passed his viva yesterday 22/06/20!
Dr Alex Diana is staying on at the University of Kent as a post-doc on the NERC-funded project Integrating new statistical frameworks into eDNA survey and analysis at the landscape scale.
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.
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
- 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.
- 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.
- 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.
- 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.
- 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.