- Dealing with Varying Detection Probability, Unequal Sample Sizes and Clumped Distributions in Count Data (2012)
- Temporal variation in the detectability of a species can bias estimates of relative abundance if not handled correctly. For example, when effort varies in space and/or time it becomes necessary to take variation in detectability into account when data are analyzed. We demonstrate the importance of incorporating seasonality into the analysis of data with unequal sample sizes due to lost traps at a particular density of a species. A case study of count data was simulated using a spring-active carabid beetle. Traps were ‘lost’ randomly during high beetle activity in high abundance sites and during low beetle activity in low abundance sites. Five different models were fitted to datasets with different levels of loss. If sample sizes were unequal and a seasonality variable was not included in models that assumed the number of individuals was log-normally distributed, the models severely under- or overestimated the true effect size. Results did not improve when seasonality and number of trapping days were included in these models as offset terms, but only performed well when the response variable was specified as following a negative binomial distribution. Finally, if seasonal variation of a species is unknown, which is often the case, seasonality can be added as a free factor, resulting in well-performing negative binomial models. Based on these results we recommend (a) add sampling effort (number of trapping days in our example) to the models as an offset term, (b) if precise information is available on seasonal variation in detectability of a study object, add seasonality to the models as an offset term; (c) if information on seasonal variation in detectability is inadequate, add seasonality as a free factor; and (d) specify the response variable of count data as following a negative binomial or over-dispersed Poisson distribution.
- On the setting of environmental noise and the performance of population dynamical models (2010)
- Background: Environmental noise is ubiquitous in population growth processes, with a well acknowledged potential to affect populations regardless of their sizes. It therefore deserves consideration in population dynamics modelling. The usual approach to incorporating noise into population dynamical models is to make some model parameter(s) (typically the growth rate, the carrying capacity, or both) stochastic and responsive to environment fluctuations. It is however still unclear whether including noise in one or/and another parameter makes a difference to the model performance. Here we investigated this issue with a focus on model fit and predictive accuracy. To do this, we developed three population dynamical models of the Ricker type with the noise included in the growth rate (Model 1), in the carrying capacity (Model 2), and in both (Model 3). We generated several population time series under each model, and used a Bayesian approach to fit the three models to the simulated data. We then compared the model performances in fitting to the data and in forecasting future observations. Results: When the mean intrinsic growth rate, r, in the data was low, the three models had roughly comparable performances, irrespective of the true model and the level of noise. As r increased, Models 1 performed best on data generated from it, and Model 3 tended to perform best on data generated from either Models 2 or Model 3. Model 2 was uniformly outcompeted by the other two models, regardless of the true model and the level of noise. The correlation between the deviance information criterion (DIC) and the mean square error (MSE) used respectively as measure of fit and predictive accuracy was broadly positive. Conclusion: Our results suggested that the way environmental noise is incorporated into a population dynamical model may profoundly affect its performance. Overall, we found that including noise in one or/and another parameter does not matter as long as the mean intrinsic growth rate, r, is low. As r increased, however, the three models performed differently. Models 1 and 3 broadly outperformed Model 2, the first having the advantage of being simple and more computationally tractable. A comforting result emerging from our analysis is the broad positive correlation between MSEs and DICs, suggesting that the latter may also be informative about the predictive performance of a model.
- Hierarchical modelling of temperature and habitat size effects on population dynamics of North Atlantic cod (2010)
- Understanding how temperature affects cod (Gadus morhua) ecology is important for forecasting how populations will develop as climate changes in future. The effects of spawning-season temperature and habitat size on cod recruitment dynamics have been investigated across the North Atlantic. Ricker and Beverton and Holt stock–recruitment (SR) models were extended by applying hierarchical methods, mixed-effects models, and Bayesian inference to incorporate the influence of these ecosystem factors on model parameters representing cod maximum reproductive rate and carrying capacity. We identified the pattern of temperature effects on cod productivity at the species level and estimated SR model parameters with increased precision. Temperature impacts vary geographically, being positive in areas where temperatures are <5°C, and negative for higher temperatures. Using the relationship derived, it is possible to predict expected changes in population-specific reproductive rates and carrying capacities resulting from temperature increases. Further, carrying capacity covaries with available habitat size, explaining at least half its variability across stocks. These patterns improve our understanding of environmental impacts on key population parameters, which is required for an ecosystem approach to cod management, particularly under ocean-warming scenarios. Key words: carrying capacity , cod , hierarchical models , North Atlantic , temperature , uncertainty
- Variable strength of forest stand attributes and weather conditions on the questing activity of Ixodes ricinus ticks over years in managed forests (2013)
- Given the ever-increasing human impact through land use and climate change on the environment, we crucially need to achieve a better understanding of those factors that influence the questing activity of ixodid ticks, a major disease-transmitting vector in temperate forests. We investigated variation in the relative questing nymph densities of Ixodes ricinus in differently managed forest types for three years (2008–2010) in SW Germany by drag sampling. We used a hierarchical Bayesian modeling approach to examine the relative effects of habitat and weather and to consider possible nested structures of habitat and climate forces. The questing activity of nymphs was considerably larger in young forest successional stages of thicket compared with pole wood and timber stages. Questing nymph density increased markedly with milder winter temperatures. Generally, the relative strength of the various environmental forces on questing nymph density differed across years. In particular, winter temperature had a negative effect on tick activity across sites in 2008 in contrast to the overall effect of temperature across years. Our results suggest that forest management practices have important impacts on questing nymph density. Variable weather conditions, however, might override the effects of forest management practices on the fluctuations and dynamics of tick populations and activity over years, in particular, the preceding winter temperatures. Therefore, robust predictions and the detection of possible interactions and nested structures of habitat and climate forces can only be quantified through the collection of long-term data. Such data are particularly important with regard to future scenarios of forest management and climate warming.
- Host genotype shapes the foliar fungal microbiome of balsam poplar (Populus balsamifera) (2013)
- Foliar fungal communities of plants are diverse and ubiquitous. In grasses endophytes may increase host fitness; in trees, their ecological roles are poorly understood. We investigated whether the genotype of the host tree influences community structure of foliar fungi. We sampled leaves from genotyped balsam poplars from across the species' range, and applied 454 amplicon sequencing to characterize foliar fungal communities. At the time of the sampling the poplars had been growing in a common garden for two years. We found diverse fungal communities associated with the poplar leaves. Linear discriminant analysis and generalized linear models showed that host genotypes had a structuring effect on the composition of foliar fungal communities. The observed patterns may be explained by a filtering mechanism which allows the trees to selectively recruit fungal strains from the environment. Alternatively, host genotype-specific fungal communities may be present in the tree systemically, and persist in the host even after two clonal reproductions. Both scenarios are consistent with host tree adaptation to specific foliar fungal communities and suggest that there is a functional basis for the strong biotic interaction.