Dispersal modelling | EPFL Graph Search

In human-dominated landscapes, populations and species extinctions are directly related to habitat destruction and fragmentation. To provide genetic diversity as well as population viability, individual exchanges among isolated populations must be maintained. Therefore, animal dispersal processes in fragmented landscape become an important topic for ecologists, and ecological networks planning has become one of the major challenges for landscape planners. Identification of habitat patches as well as assessment of the effect of ecological networks is badly needed. Since little information on the effect of landscape heterogeneities on animal dispersal is available, simulation models are being developed. As dispersal pattern and success strongly depend on the spatial context, species' interactions with landscapes, species behaviour and species ability to disperse, these models must be able to simulate them explicitly. This research work therefore aims first at developing methods and models that allow realistic animal dispersal simulations in fragmented landscapes. Second it aims at evaluating the effect of landscape heterogeneities and animal behaviour on dispersal and on species persistence. Additionally, the ability of such a model to estimate gene flow is analysed. To carry on this research, the following fields have been explored: landscape ecology, metapopulation dynamic, animal behaviour, genetics, Geographical Information Systems, modelling approaches and programming. A method, based on properties provided by Geographical Information Systems software, is first proposed to generate ecological networks by simulating animal dispersal according to animal movement constraints induced by human infrastructures. The resulting maps provide a spatial identification of ecological networks, corridors and conflicting areas. This model has proved to be a useful and straightforward tool for landscape planning, even if this model, similar to other present-day models used in dispersal simulations, presents numerous technical and scientific limitations. To improve models for animal dispersal, a feature-oriented landscape model associated with an expert system has been developed. Its conceptualisation, its formalism, its data structure and its object-oriented design implementation provide a very accurate representation of landscape features and simulation of complex interactions between model entities (individuals and landscape features) based on simple rules. It allows the spatial identification of simulated processes. The ability of this model to incorporate states, relations and transition rules between entities makes it applicable to simulate large ranges of dispersal processes according to specific behaviour and/or landscape uses. To analyse the influence of landscape heterogeneities and species behaviour on dispersal and their incidence on metapopulation dynamics, the proposed feature-oriented model has been coupled with an animal model. The latter assigns different cognitive and dispersal abilities to individuals. Based on simulations according to three movement strategies (corresponding to the cognitive abilities of the simulated species), two measures evaluate the effect of cognitive abilities on dispersal: the colonisation probability between habitat patches and the ecological distance (due to landscape heterogeneities). These measures give an estimation of metapopulation structures (the habitat patches belonging to the metapopulation) and metapopulation dynamics induced by the landscape heterogeneities (for example, the habitat patches which release individuals). The complexity of dispersal processes, considering species behaviours and dispersal abilities, can therefore be reproduced and analysed at different levels. This application has shown the importance of animal behaviour on metapopulation dynamics and structure. Since tracking animals and providing sufficient data remain difficult, calibration and validation procedures of dispersal models are difficult to perform. One approach proposed here is to measure one of the consequences of dispersal: genetic differentiation among populations. Geographical distances are in general used to explain a part of the genetic differentiations. But as our fundamental assumption states that landscape heterogeneities and spatial arrangements of landscape features may strongly affect dispersal successes, genetic distance between populations must be better explained by the estimate of a model which considers these factors. We have tested this assumption with the greater white-toothed shrew (Crocidura russula). Scenarios considering various behaviours and dispersal abilities of C. russula have been performed. Relating measures of genetic, geographical and ecological distances (the latter emerge from scenario simulation results) highlights the model capability to reproduce dispersal of C. russula by explaining a greater part of the genetic differentiation than that explained by the geographical distances. This application has not only pointed out the ability of the model to quantify connectivity between habitat patches but also the difficulty to relate gene dispersal and individual dispersal.

Species conservation in the face of global environmental changes: surface-based modelling of geo-environmental data to identify vulnerable populations

Estelle Rochat

Human activities are resulting in many land-use changes, particularly due to urbanisation and intensification of agricultural practices. Because of these changes, in addition to climate change, many species are facing habitat degradation. In order to avoid extinction under these conditions, they can either move to more favourable areas or adapt to their new environment. To develop appropriate conservation measures, it is essential to identify vulnerable populations that may not be able to disperse or adapt. In this context, modelling tools can be used to predict the potential impact of environmental changes on species and populations. However, to date, few approaches take into account the degree of exposure, the possibility of dispersal and the potential for adaptation. In this thesis, we present modelling approaches based on geo-environmental data to integrate these three elements. First, we use ecological niche models to estimate the distribution of suitable habitats for a given species as a function of environmental conditions. We propose an improvement of commonly used models by developing an approach to integrate spatio-temporal variability of environmental predictors. In addition, we develop a nested model to predict the distribution of vector-borne pathogens. This model can be used to identify populations that may be threatened by an increasing presence of pathogens in their habitat. We use it to model the evolution of the distribution of Ixodes ricinus ticks and their Chlamydiales bacterial pathogen. We then use landscape graphs to analyse the connectivity between habitats and estimate the possibilities for threatened species to move to more favourable areas. Connectivity is also essential for maintaining gene flow and genetic diversity, which is necessary for greater adaptive capacity. We propose here an approach combining landscape graphs, simulations and empirical genetic data to identify the impact of reduced connectivity on population persistence and genetic diversity. We use it to identify butterfly populations that are threatened by increasing fragmentation in an urban landscape. Finally, we develop the concept of "Spatial Areas of Genotypes Probability" (SPAG) to better analyse the adaptive potential of populations. SPAGs make it possible to model the probability of finding locally adapted genetic variants in a given territory, as well as to identify vulnerable populations lacking in genetic variants that would favour adaptation to future climate conditions. We use it to highlight populations of Moroccan and European goats that are poorly adapted to the climatic conditions predicted under a climate change scenario for 2070 (strong variations in precipitation or increased drought). To conclude, we show how the three modelling approaches presented can be combined and integrated into a more general conservation framework to identify vulnerable populations facing high exposure to environmental changes, low dispersal possibilities and reduced adaptive capacity.

EPFL2020

Amphibian conservation in human shaped environments

Flavio Zanini

Global biodiversity is experiencing a worrying decline. Habitats destruction, associated to their degradation and fragmentation are among the greatest causes. Amphibians are particularly interesting because they are more threatened and decline more rapidly than either birds or mammals. In this context, the objective of our research is to improve some methodological approaches and offer practical scientific bases for decision making in landscape management and amphibian conservation. Our study focuses on fragmented Swiss landscapes. We developed a method that uses land-cover data and expert knowledge to enable a spatially explicit assessment of 1) the temporal changes in the nature conservation value of the landscape and 2) the rehabilitation potential of the landscape. We applied this Geographical Information Systems (GIS) based approach in the Swiss Rhone plain and we used the years 1900 as the reference state. The method constitutes a helpful tool for communication, decision-making and biological conservation management in landscape planning. Effective and optimal species management strategies can only be formulated after relationships between species distribution and environmental factors have been identified. Concerning amphibians, several approaches exist but they generally suffer from two limitations: 1) the spatial autocorrelation (i.e. the dependency between two observations) in data is rarely explicitly analyzed, even if it may affect the accuracy of species-habitat relationships models. We showed how this spatial autocorrelation can be measured and included in logistic models with the example of the agile frog (Rana dalmatina) in north-eastern Switzerland. We used the Moran's I and the autologistic model (i.e. a logistic model including a measure of the spatial arrangement of the response variables). We found that if spatial autocorrelation is not considered, then conclusions on species-habitat relationships can be incorrect. 2) The effect of landscape on amphibian occurrence in ponds is often assumed to be equal in every direction (isotropic). However, barriers and inhospitable surfaces may reduce movement patterns and the area around ponds accessible to species. This implies that the ideal circular area has in reality a shape depending on the surrounding landscape. We developed a method to determine the effect of habitat variables on amphibian species distribution, considering physical barriers in their movement around ponds. We studied two amphibian species: the common toad (Bufo bufo) and the common frog (Rana temporaria) in the Rhone plain. We demonstrated that reducing the boundaries of circular area following barriers, allowed to compute landscape predictors which better explained species distribution. These results suggested that the proposed approach is more pertinent than the traditional circular buffers analysis. Our results stress the necessity to consider barriers and ecological corridors in species distribution models in order to avoid incorrect inferences. Species distribution models are usually established for a single region. It is generally unknown whether the identified relationships between species distribution and environmental variables can be directly transferred to another geographical area. We examined landscape-level habitat relationships for six amphibian species by measuring correlations with their presence in 655 ponds of five different regions. We analyzed several models by using the information-theoretic approach and the Akaike Information criterion (AIC). For five out of six species, the best models predict that site occupation probability depends on region. Our results suggest that caution is needed when predictions of species occurrence and species management strategies are done using models built in other geographic regions. We also observed that connectivity was generally more explicative than landscape variables. In addition, we found that the spatial scale at which habitat affected species occurrence varied from pond to several km around ponds. Management strategies for amphibian conservation should be conducted taking into account the geographic context, connectivity of ponds and habitat characteristics at multiple spatial scales. Finally, we demonstrated that the landscape, separating patches in metapopulation models, has to be considered in order to avoid incorrect conclusions on population viability analyses. We explored how patch occupancy is sensitive to Euclidean (shortest) versus a landscape-based distance (least-cost). We found: 1) from a theoretical standpoint, that inter-patch landscape affects patch occupancy; 2) from a practical and conservation standpoints, which patches should be considered in priority for landscape management. The approach was illustrated in the case of two metapopulations of the Yellow-bellied Toad in the Rhone plain. We applied successfully the developed practical approaches to the case of several amphibian species, but they can doubtlessly be extended to any species functioning on a spatially defined patch basis (e.g. pond, nesting place, den …), structured as a metapopulation and affected by landscape structure during movement. By improving and combining spatially explicit approaches, we are more likely to provide wildlife managers with tools for valuable decision making.

EPFL2006

Beyond the patch: on landscape-explicit metapopulation dynamics

Jonathan Giezendanner

Climate change threatens biodiversity and species distribution all over the world at unprecedented rates. Human induced changes to landscape structure and habitat are redefining the relation between species and their environment. Understanding, characterizing and modeling the relation between complex landscape features and geographical species presence, the subject of this thesis, have thus gained paramount importance in order to make informed decisions on near- and far-term management strategies for species and landscape protection. The present thesis pays particular attention to the understanding of how mountain landscapes, described as heterogeneous habitat matrices, govern the presence of a species in space and time. To this end, throughout this thesis a metapopulation model is considered, a spatially-explicit model based on the balance between colonization and extinction events in areas of different suitability. The classical patch-based modelling approach is extended here in various ways in order to incorporate landscape-explicit information about the habitat matrix. A first theoretical study is performed on geometric, realistic, and real landscapes which highlights how different levels of connectivity, the degree to which different areas of similar habitat are actually linked together in the landscape (say, derived from geomorphic structures, such as valleys and peaks or emerging structures shaped by fluvial erosion and tectonic uplift) impact the dynamic of mountain species under climate change. A second, applied, study investigates how different landscape descriptors derived from Earth Observation data can be used in order to dynamically model the spatial, landscape-explicit, presence of two carabid species (Pterostichus flavofemoratus and Carabus depressus) in the Gran Paradiso National Park. In a final study, the consistency of the metapopulation model is investigated when considering different resolutions of the landscape matrix, i.e. different levels of coarse-graining. This last part is fundamental to the understanding of how conclusions drawn from local studies can be made general and extrapolated to larger regions. Overall, this thesis bridges the fields of population and landscape ecology, focusing on modelling metapopulation dynamics in complex landscapes seen as the substrate for ecological interactions. The result from the three studies show that metapopulation ecology can profit from the insights of landscape ecology. The combination of the two fields can be a useful tool in furthering the understanding and monitoring of mountain species.

EPFL2020

Beyond the patch: on landscape-explicit metapopulation dynamics

Jonathan Giezendanner

EPFL2020

Species conservation in the face of global environmental changes: surface-based modelling of geo-environmental data to identify vulnerable populations

Estelle Rochat

EPFL2020

Amphibian conservation in human shaped environments

Flavio Zanini

EPFL2006