Biology subjects

Barraquand, F.

Publications and source records attributed to Barraquand, F..

3 recordsLinked to original sources

bioRxiv2017

Predator-prey feedback in a gyrfalcon-ptarmigan system?

Specialist predators with oscillating dynamics are often strongly affected by the population dynamics of their prey, yet they do not always participate in a predator-prey cycle. Only those that exert strong population regulation of their prey do so. Inferring the strength and direction of the predator-prey coupling from time series therefore requires contrasting models with top-down versus bottom-up predator-prey dynamics. We examine such population-level coupling using multivariate autoregressive models. The models translate several hypotheses for the joint dynamics of population densities of the Icelandic gyrfalcon Falco rusticolus, and its prey, the rock ptarmigan Lagopus muta. The dynamics of both species are likely not only linked to each other but also to stochastic weather variables acting as confounding factors on the joint dynamics. The classical MAR(1) model, used most often in ecology, predicts that the times series exhibit predator-prey feedback (i.e., Granger causality): the predator helps to explain prey dynamics and the prey helps to explain predator dynamics. Weather, in the form of spring temperature, influences gyrfalcon population growth but not ptarmigan population growth, despite individual-level evidence that ptarmigan chicks can be strongly affected by weather. MAR(2) models, allowing for species to cycle independently from each other, further suggests alternative scenarios where a cyclic prey influence its predator but not the other way around; such bottom-up models produce a better fit but less realistic cross-correlation patterns. Simulations of MAR(1) and MAR(2) models further demonstrate that the top-down MAR(1) models are most likely to be misidentified as bottom-up dynamics than vice-versa. We therefore conclude that predator-prey feedback in the gyrfalcon-ptarmigan system is very likely, though bottom-up dynamics cannot be excluded with certainty. We finally discuss what sort of information is needed to advance the characterization of joint predator-prey dynamics in birds and other vertebrates.

ecology↗

bioRxiv2017

Goodness of fit checks for binomial N-mixture models

O_LIBinomial N-mixture models are commonly applied to analyze population survey data. By estimating detection probabilities, N-mixture models aim at extracting information about abundances in terms of actual and not just relative numbers. This separation of detection probability and abundance relies on parametric assumptions about the distribution of individuals among sites and of detections of individuals among repeat visits to sites. Current methods for checking assumptions are limited, and their computational complexity have hindered evaluations of their performances.\nC_LIO_LIWe develop computationally efficient graphical goodness of fit checks and measures of overdispersion for binomial N-mixture models. These checks are illustrated in a case study, and evaluated in simulations under two scenarios. The two scenarios assume overdispersion in the abundance distribution via a negative binomial distribution or in the detection probability via a beta-binomial distribution. We evaluate the ability of the checks to detect lack of fit, and how lack of fit affects estimates of abundances.\nC_LIO_LIThe simulations show that if the parametric assumptions are incorrect there can be severe biases in estimated abundances: negatively if there is overdispersion in abundance relative to the fitted model and positively if there is overdispersion in detection. Our goodness of fit checks performed well in detecting lack of fit when the abundance distribution is overdispersed, but struggled to detect lack of fit when detections were overdispersed. We show that the inability to detect lack of fit due to overdispersed detection is caused by a fundamental similarity between N-mixture models with beta-binomial detections and N-mixture models with negative binomial abundances.\nC_LIO_LIThe strong biases in estimated abundances that can occur in the binomial N-mixture model when the distribution of individuals among sites, or the detection model, is mis-specified implies that checking goodness of fit is essential for sound inference in ecological studies that use these methods. To check the assumptions we provide computationally efficient goodness of fit checks that are available in an R-package nmixgof. However, even when a binomial N-mixture model appears to fit the data well, estimates are not robust in the presence of overdispersion unless additional information about detection is collected.\nC_LI

ecology↗

bioRxiv2017

Weak interactions between groups and physical drivers of community dynamics in coastal phytoplankton

Phytoplanktonic communities maintain a high diversity in a seemingly homogeneous environment, competing for the same set of resources. Many theories have been proposed to explain this coexistence despite likely competition, such as contrasted responses to temporal environmental variation. However, theory has developed at a faster pace than its empirical evaluation using field data, that requires to infer biotic and abiotic drivers of community dynamics from observational time series. Here, we combine autoregressive models with a data set spanning more than 20 years of biweekly plankton counts and abiotic variables, including nutrients and physical variables. By comparing models dominated by nutrients or physical variables (hydrodynamics and climate), we first explore which abiotic factors contribute more to phytoplankton growth and decline. We find that physical drivers - such as irradiance, wind, and salinity - explain some of the variability in abundances unexplained by biotic interactions. In contrast, responses to nutrients explain less of phytoplankton variability. Concerning biotic drivers of community dynamics, multivariate autoregressive models reveal that competition between different groups (at the genus level for most) has a much weaker effect on population growth rates than competition within a group. In fact, the few biotic interactions between genera that are detected are frequently positive. Hence, our system is unlikely to be best represented as a set of competitors whose differing responses to fluctuating environments allow coexistence, as in \"paradox of the plankton\" models with a storage effect or a relative nonlinearity of competition. Coexistence is more likely to result from stabilizing niche differences, manifested through high intragroup density-dependence. Competition between planktonic groups and nutrients are often invoked as drivers of phytoplankton dynamics; our findings suggest instead that more attention should be given to the physical structure of the environment and natural enemies, for coastal phytoplankton at least.

ecology↗