De Mita S.,CNRS Plant Diversity Adaptation and Development |
De Mita S.,French National Institute for Agricultural Research |
Thuillet A.-C.,CNRS Plant Diversity Adaptation and Development |
Gay L.,French National Institute for Agricultural Research |
And 4 more authors.
Molecular Ecology | Year: 2013
Thanks to genome-scale diversity data, present-day studies can provide a detailed view of how natural and cultivated species adapt to their environment and particularly to environmental gradients. However, due to their sensitivity, up-to-date studies might be more sensitive to undocumented demographic effects such as the pattern of migration and the reproduction regime. In this study, we provide guidelines for the use of popular or recently developed statistical methods to detect footprints of selection. We simulated 100 populations along a selective gradient and explored different migration models, sampling schemes and rates of self-fertilization. We investigated the power and robustness of eight methods to detect loci potentially under selection: three designed to detect genotype-environment correlations and five designed to detect adaptive differentiation (based on FST or similar measures). We show that genotype-environment correlation methods have substantially more power to detect selection than differentiation-based methods but that they generally suffer from high rates of false positives. This effect is exacerbated whenever allele frequencies are correlated, either between populations or within populations. Our results suggest that, when the underlying genetic structure of the data is unknown, a number of robust methods are preferable. Moreover, in the simulated scenario we used, sampling many populations led to better results than sampling many individuals per population. Finally, care should be taken when using methods to identify genotype-environment correlations without correcting for allele frequency autocorrelation because of the risk of spurious signals due to allele frequency correlations between populations. © 2013 Blackwell Publishing Ltd.
Manel S.,CNRS Alpine Ecology Laboratory |
Manel S.,CNRS Population, Environment, and Development Laboratory |
Poncet B.N.,CNRS Alpine Ecology Laboratory |
Legendre P.,University of Montréal |
And 2 more authors.
Molecular Ecology | Year: 2010
A major challenges facing landscape geneticists studying adaptive variation is to include all the environmental variables that might be correlated with allele frequencies across the genome. One way of identifying loci that are possibly under selection is to see which ones are associated with environmental gradient or heterogeneity. Since it is difficult to measure all environmental variables, one may take advantage of the spatial nature of environmental filters to incorporate the effect of unaccounted environmental variables in the analysis. Assuming that the spatial signature of these variables is broad-scaled, broad-scale Moran's eigenvector maps (MEM) can be included as explanatory variables in the analysis as proxies for unmeasured environmental variables. We applied this approach to two data sets of the alpine plant Arabis alpina. The first consisted of 140 AFLP loci sampled at 130 sites across the European Alps (large scale). The second one consisted of 712 AFLP loci sampled at 93 sites (regional scale) in three mountain massifs (local scale) of the French Alps. For each scale, we regressed the frequencies of each AFLP allele on a set of eco-climatic and MEM variables as predictors. Twelve (large scale) and 11% (regional scale) of all loci were detected as significantly correlated to at least one of the predictors (> 0.5), and, except for one massif, 17% at the local scale. After accounting for spatial effects, temperature and precipitation were the two major determinants of allele distributions. Our study shows how MEM models can account for unmeasured environmental variation in landscape genetics models. © 2010 Blackwell Publishing Ltd.
Holderegger R.,Swiss Federal Institute of forest |
Holderegger R.,ETH Zurich |
Buehler D.,Swiss Federal Institute of forest |
Buehler D.,ETH Zurich |
And 3 more authors.
Trends in Plant Science | Year: 2010
Landscape genetics is the amalgamation of landscape ecology and population genetics to help with understanding microevolutionary processes such as gene flow and adaptation. In this review, we examine why landscape genetics of plants lags behind that of animals, both in number of studies and consideration of landscape elements. The classical landscape distance/resistance approach to study gene flow is challenging in plants, whereas boundary detection and the assessment of contemporary gene flow are more feasible. By contrast, the new field of landscape genetics of adaptive genetic variation, establishing the relationship between adaptive genomic regions and environmental factors in natural populations, is prominent in plant studies. Landscape genetics is ideally suited to study processes such as migration and adaptation under global change. © 2010 Elsevier Ltd.
Schoville S.D.,CNRS Complex Medical Engineering Laboratory |
Schoville S.D.,CNRS Alpine Ecology Laboratory |
Bonin A.,CNRS Alpine Ecology Laboratory |
Francois O.,CNRS Complex Medical Engineering Laboratory |
And 4 more authors.
Annual Review of Ecology, Evolution, and Systematics | Year: 2012
There is a growing interest in identifying ecological factors that Influence adaptive genetic diversity patterns in both model and nonmodel species. The emergence of large genomic and environmental data sets, as well as the increasing sophistication of population genetics methods, provides an opportunity to characterize these patterns in relation to the environment. Landscape genetics has emerged as a flexible analytical framework that connects patterns of adaptive genetic variation to environmental heterogeneity in a spatially explicit context. Recent growth in this field has led to the development of numerous spatial statistical methods, prompting a discussion of the current benefits and limitations of these approaches. Here we provide a review of the design of landscape genetics studies, the different statistical tools, some important case studies, and perspectives on how future advances in this field are likely to shed light on important processes in evolution and ecology. © 2012 by Annual Reviews. All rights reserved.
Marco A.,CNRS Population, Environment, and Development Laboratory |
Lavergne S.,CNRS Alpine Ecology Laboratory |
Dutoit T.,French National Center for Scientific Research |
Bertaudiere-Montes V.,CNRS Population, Environment, and Development Laboratory
Biological Invasions | Year: 2010
To explain current ornamental plant invasions, or predict future ones, it is necessary to determine which factors increase the probability of an alien species becoming invasive. Here, we focused on the early phases of ornamental plant invasion in order to identify which plant features and cultivation practices may favor the escape of ornamental plants from domestic gardens to abandoned agricultural land sites in the Mediterranean Region. We used an original approach which consisted in visiting 120 private gardens in an urbanizing rural area of the French Mediterranean backcountry, and then visited surrounding old fields to determine which planted species had escaped out of the gardens. We built a database of 407 perennial ornamental alien species (most of which were animal-dispersed), and determined nineteen features that depicted the strength of species' propagule pressure within gardens, the match between species requirements and local physical environment, and each species' reproductive characteristics. Using standard and phylogenetic logistic regression, we found that ornamental alien plants were more likely to have escaped if they were planted in gardens' margins, if they had a preference for dry soil, were tolerant to high-pH or pH-indifferent, and if they showed a capacity for clonal growth. Focusing only on animal-dispersed plants, we found that alien plants were more likely to have escaped if they were abundant in gardens and showed preference for dry soil. This suggests that gardening practices have a primary impact on the probability of a species to escape from cultivation, along with species pre-adaptation to local soil conditions, and capacity of asexual reproduction. Our results may have important implications for the implementation of management practices and awareness campaigns in order to limit ornamental plants to becoming invasive species in Mediterranean landscapes. © Springer Science+Business Media B.V. 2009.
Barthelemy C.,CNRS Population, Environment, and Development Laboratory |
Armani G.,University Lumiere Lyon 2
Freshwater Biology | Year: 2015
Understanding social processes (trajectories of relationships among stakeholders), political constraints, cultural aspects and public opinions is essential for efficient design, sustainability and evaluation of restoration operations. However, few restoration projects involve the participation of social sciences. The ecological restoration of the Rhône River involved increasing flow below dams and better connecting floodplain channels at multiple sites along the river. Therefore, it provided a unique opportunity to identify the commonalities and differences among social processes associated with ecological restoration. We used qualitative analyses of speeches and interviews with stakeholders to understand their relationship to the Rhône. These analyses revealed that social values, relating local residents to the river, played a major role throughout the restoration projects. The comparison of social processes among three sites of the Rhône shows that they generally followed three stages: managing a crisis, transforming the relationship to the river and valuing the local social space (the territory). Consistent patterns emerging across sites included the following: (i) the role of a local public figure able to mobilise stakeholders in supporting the restoration project; (ii) the importance of the organisation of the stakeholder community and its commitment to the project; and (iii) the major role of interactions between local and national levels. Variation across sites also occurred and may be related to unforeseen events such as political changes and natural hazards (e.g. floods and pollution). Involving social science in restoration projects requires taking into account commonalities in social processes as well as the diversity of local experiences. © 2015 John Wiley & Sons Ltd.
Decout S.,IRSTEA |
Manel S.,CNRS Population, Environment, and Development Laboratory |
Manel S.,British Petroleum |
Miaud C.,British Petroleum |
Landscape Ecology | Year: 2012
Graph-based analysis is a promising approach for analyzing the functional and structural connectivity of landscapes. In human-shaped landscapes, species have become vulnerable to land degradation and connectivity loss between habitat patches. Movement across the landscape is a key process for species survival that needs to be further investigated for heterogeneous human-dominated landscapes. The common frog (Rana temporaria) was used as a case study to explore and provide a graph connectivity analysis framework that integrates habitat suitability and dispersal responses to landscape permeability. The main habitat patches influencing habitat availability and connectivity were highlighted by using the software Conefor Sensinode 2. 2. One of the main advantages of the presented graph-theoretical approach is its ability to provide a large choice of variables to be used based on the study's assumptions and knowledge about target species. Based on dispersal simulation modelling in potential suitable habitat corridors, three distinct patterns of nodes connections of differing importance were revealed. These patterns are locally influenced by anthropogenic barriers, landscape permeability, and habitat suitability. And they are affected by different suitability and availability gradients to maximize the best possible settlement by the common frog within a terrestrial habitat continuum. The study determined the key role of landscape-based approaches for identifying the "availability-suitability-connectivity" patterns from a local to regional approach to provide an operational tool for landscape planning. © 2011 Springer Science+Business Media B.V.
Dos Santos S.,CNRS Population, Environment, and Development Laboratory
Environnement, Risques et Sante | Year: 2012
According to the Millennium development goals (MDG), in 2012, 800 million people worldwide still had no access to safe drinking water. Sub-Saharan Africa records the lowest rate: two persons in five still lack this access. This article aims to demonstrate that theMDG drinking water target, both by its definition and the data used to define it, does not address the health risks related to water access, especially in sub-Saharan Africa. This statistic is based only on the source of water, but does not include aspects of accessibility related to distance and/or time required to collect water, the cost, or the quality and quantity used, although all of these affect health outcomes. In Ouagadougou, if only two aspects of accessibility are taken into account (the quantity available at homeand distance to thewater point), the rate of water access is half that of that used by the MDG. A relevant indicator of access to water is needed as leverage for the adoption of effective public health policies. Access to drinking water has been defined as a human right since 2010.
Genin D.,CNRS Population, Environment, and Development Laboratory |
Simenel R.,CNRS Population, Environment, and Development Laboratory
Human Ecology | Year: 2011
On the basis of two case studies in rural Morocco, one in a mountainous area of the Central High Atlas and the other in the argan tree area of the southwest Atlantic coast, we show how local Berber populations have actively shaped their forest areas through endogenous management systems at different scales: 1) at the individual tree level by differential cutting or trimming which lead to specific conformations of the tree, 2) at the tree stand level, by determining the type, structure and level of resources, and 3) at the landscape level in which complementary patches of forest areas with particular functions are consciously organized within the overall territory. These practices are strongly linked with the overall socioeconomic organization of the local communities, and mix individual with common rights of access and uses. Forests are viewed as part of the domestic sphere of local livelihoods. Hence, they typically constitute what we refer to as rural or domestic forests since they integrate production and conservation with social, political and spiritual dimensions. These features are of importance for considering forester-local community relationships, and for developing alternative forest management policies. © 2011 Springer Science+Business Media, LLC.
Mieulet E.,CNRS Population, Environment, and Development Laboratory |
Claeys C.,CNRS Population, Environment, and Development Laboratory
Health, Risk and Society | Year: 2014
In this article, we use an analytical framework based on the sociology of risk to provide a qualitative analysis of the implementation and reception of public risk-prevention policies for dengue epidemics in Martinique and French Guyana. The data are derived from 116 semi-structured interviews and direct observation conducted in 2012 and 2013. The two overseas departments studied provide an opportunity to draw on the social theory of risk and uncertainty in multicultural contexts. Our analysis highlights that the rise of several technical, economic, legal and entomological constraints has recently led to a public policy shift from biological and chemical mosquito control to awareness-raising campaigns focused on domestic spaces. This change involves a shift in responsibility from public authorities to the private sphere. However, there is strong demand from the local population for mosquito control and the involvement of public authorities. This reciprocal passing of responsibility is exacerbated by the colonial past and heritage of slavery in these multiethnic overseas territories located over 7000 km from the seat of the French government. © 2014 Taylor & Francis.