Biology subjects

Moulherat, S.

Publications and source records attributed to Moulherat, S..

4 recordsLinked to original sources

bioRxiv2025

When does temporal resolution matter? Including detection covariates in discrete- versus continuous-time occupancy and N-mixture models

Camera traps and other sensors allow continuous-time biodiversity observation, raising new questions and opportunities for modelling detection in hierarchical models such as occupancy (for species presence) and N-mixture models (for abundance). We focused on a rarely considered aspect: how the temporal treatment of detection covariates affects inference. Through simulations and a five-month case study on an research center, we examined the effects of covariate temporal resolution, discretisation scale in discrete-time (DT) models, and interpolation methods in continuous-time (CT) models. While occupancy and abundance estimates were largely unaffected by these choices, detection estimates were more sensitive to them. DT models with fine temporal discretisation closely matched CT models. Simulations showed that when detection covariates had no effect on detectability, the considered modelling choices had little impact. But when covariates did influence detection, bias and error increased if their temporal variation was not accurately retained. The case study revealed more complex patterns, highlighting the consequences of temporally simplifying both observations and detection covariates. Overall, our results suggest that when detectability is of ecological interest, exploring a range of temporal treatments of detection covariates, from fine-scale to coarser resolutions, can reveal complementary insights into scale-dependent patterns in detection.

ecology↗

bioRxiv2023

Analysing biodiversity observation data collected in continuous time: Should we use discrete or continuous-time occupancy models?

O_LIBiodiversity monitoring is undergoing a revolution, with fauna observations data being increasingly gathered continuously over extended periods, through sensors like camera traps and acoustic recorders, or via opportunistic observations. These data are often analysed with discrete-time ecological models, requiring the transformation of continuously collected data into arbitrarily chosen non-independent discrete time intervals. To overcome this issue, ecologists are increasingly turning to the existing continuous-time models in the literature. Closer to the real detection process, they are lesser known than discrete-time models, not always easily accessible, and can be more complex. Focusing on occupancy models, a type of species distribution models, we asked ourselves: Should we dedicate time and effort to learning and using these continuous-time models, or can we go on using discrete-time models? C_LIO_LIWe conducted a comparative simulation study using data generated within a continuous-time framework. We assessed the performance of five static occupancy models with varying detection processes: discrete detection/non-detection process, discrete count process, continuous-time Poisson process, and two types of modulated Poisson processes. Our goal was to assess their abilities to estimate occupancy probability with continuously collected data. We applied all models to empirical lynx data as an illustrative example. C_LIO_LIIn scenarios with easily detectable animals, we found that all models accurately estimated occupancy. All models reached their limits with highly elusive animals. Variation in discretisation intervals had minimal impact on the discrete models capacity to estimate occupancy accurately. C_LIO_LIOur study underscores that opting for continuous-time models with an increased number of parameters, aiming to get closer to the sensor detection process, may not offer substantial advantages over simpler models when the sole aim is to accurately estimate occupancy. Model choice can thus be driven by practical considerations such as data availability or implementation time. However, occupancy models can encompass goals beyond estimating occupancy probability. Continuous-time models, particularly those considering temporal variations in detection, can offer valuable insights into specific species behaviour and broader ecological inquiries. We hope that our findings offer valuable guidance for researchers and practitioners working with continuously collected data in wildlife monitoring and modelling. C_LI

ecology↗

bioRxiv2020

MetaConnect, a new platform for population viability modelling to assist decision makers in conservation and urban planning

In a context of global change, scientists and policy-makers require tools to address the issue of biodiversity loss. Population viability analysis (PVA) has been the main tool to deal with this problem. However, the tools developed during the 90s poorly integrate recent scientific advances in landscape genetics and dispersal. We developed a flexible and modular modelling platform for PVA that addresses many of the limitations of existing software. MetaConnect is an individual-based, process-based and PVA-oriented modelling platform which could be used as a research or a decision-making tool. Here, we present the core base modelling of MetaConnect. We demonstrate its potential use through a case study illustrating the platforms capability for performing integrated PVA including extinction probability estimation, genetic differentiation and landscape connectivity analysis. We used MetaConnect to assess the impact of infrastructure works on the natterjack toad metapopulation functioning.

ecology↗

bioRxiv2019

Patterns of gene flow across multiple anthropogenic infrastructures: insights from a multi-species approach

1.Large-scale Transportation Infrastructures (LTIs) are among the main determinants of landscape fragmentation, with strong impacts on animal dispersal movements and metapopulation functioning. Although the detection of LTIs impacts is now facilitated by landscape genetic tools, studies are often conducted on a single species, although different species might react differently to the same obstacle. Multi-specific approaches are thus required to get a better overview of the impacts of human-induced fragmentation. We surveyed four species (a snake, an amphibian, a butterfly and a ground-beetle) in a landscape fragmented by six LTIs: a motorway, a railway, a country road, a gas pipeline, a power line and a secondary road network. We showed that half of the overall explained genetic variability across all species was due to LTIs. While the butterfly was seemingly not impacted by any LTI, the genetic structure of the three other species was mostly influenced by roads, motorway and railway. The power line did not affect any species and the gas pipeline only impacted gene flow in the ground-beetle through forest fragmentation, but other LTIs systematically affected at least two species. LTIs mostly acted as barriers but we showed that some LTIs could somehow promote gene flow, embankments probably providing favourable habitats for vertebrate species. Considering the high variability in species response to LTIs, we argue that drawing general conclusions on landscape connectivity from the study of a single species may lead to counterproductive mitigation measures and that multi-species approaches should be more systematically considered in conservation planning.

ecology↗