The geographical dimension of genetic diversity

In its natural framework, genetic information is embedded within a geographic context. Plants and animals are directly influenced by the specific characteristics of their surrounding environment. Therefore, spatial information is a potentially important element to be considered in trying to understand genetic resources. For many years, Geographical Information Science (GIScience) turned toward environmental modelling, generally to demonstrate how GIS basic features could be efficiently applied to fields related to the natural sciences. However, despite its current predominance in life sciences and its direct application to concerns of public society (health, food), genetics had heretofore remained outside the scope of research by the GIScience community while biologists were developing approaches based on GIS, which conducted to the elaboration of "landscape genetics". The present GIScience approach to linking genetics and geographics obviously places emphasis on geographic information, unlike most studies in this domain. This perspective is developed through an application to two case studies to assess the potential contribution of GIScience to conservation biology. The main one is provided by Econogene, a European research project aiming at promoting the sustainable conservation of genetic resources in sheep and goats. These small ruminants have considerable economic importance in marginal agrosystems in Europe. The surveying of their genetic resources makes it possible to highlight endangered breeds having high distinctiveness and priority for conservation. The second case study is complementary and supplies wild species data to demonstrate how genetic information is used to assess conservation measures applied to the endangered Scandinavian Brown Bear. Advanced molecular technologies make it possible to efficiently measure genetic information. In parallel, considerable advancements in computer science have led to the development of sophisticated GIS software and methods. The joining of molecular biology and GIScience enables novel and complementary methods of tackling some of the challenging issues related to evolutionary processes. This tentative application of diverse facets of GIScience to molecular biology addresses three distinct issues. Firstly, considering the vast quantity of information collected within the Econogene project, exploratory data analysis methods are applied to extract useful information from large spatially explicit genetic data sets. This category of GIS tools facilitates investigations to understand the geographic distribution of genetic diversity among sheep and goat breeds as well as its variation according to environmental parameters. Secondly, a review of population genetics literature having revealed weaknesses about the way spatial genetic data are generally represented on maps, the semiology of graphics is used to produce improved thematic maps representing patterns of genetic diversity. The recourse to high-performance cartography improves the interpretation of data, and facilitates the transmission of the results as well as their communication between researchers, or between researchers and the general public. Thirdly, this combination of GIScience with molecular biology mainly leads to the development of a spatial analysis method to detect signatures of natural selection within the genome. The method is adapted to a precise conception of environmental modelling, advocating the implementation of simple models in order to better grasp the functioning of natural processes, and recognizing an inescapable uncertainty. To find out these signatures, spatial analysis takes advantage of the evolution of genetics toward genomics and of the subsequent availability of large data sets generated by large genome scans. This permits to compute many simultaneous univariate logistic regression models and to identify specific regions of the genome which are selected by environmental parameters. These are identical to the ones detected by a standard approach developed in population genomics.

Advances in farm animal genomic resources

Stéphane Joost

The history of livestock started with the domestication of their wild ancestors: a restricted number of species allowed to be tamed and entered a symbiotic relationship with humans. In exchange for food, shelter and protection, they provided us with meat, eggs, hides, wool and draught power, thus contributing considerably to our economic and cultural development. Depending on the species, domestication took place in different areas and periods. After domestication, livestock spread over all inhabited regions of the earth, accompanying human migrations and becoming also trade objects. This required an adaptation to different climates and varying styles of husbandry and resulted in an enormous phenotypic diversity. Approximately 200 years ago, the situation started to change with the rise of the concept of breed. Animals were selected for the same visible characteristics, and crossing with different phenotypes was reduced. This resulted in the formation of different breeds, mostly genetically isolated from other populations. A few decades ago, selection pressure was increased again with intensive production focusing on a limited range of types and a subsequent loss of genetic diversity. For short-term economic reasons, farmers have abandoned traditional breeds. As a consequence, during the 20th century, at least 28% of farm animal breeds became extinct, rare or endangered. The situation is alarming in developing countries, where native breeds adapted to local environments and diseases are being replaced by industrial breeds. In the most marginal areas, farm animals are considered to be essential for viable land use and, in the developing world, a major pathway out of poverty. Historic documentation from the period before the breed formation is scarce. Thus, reconstruction of the history of livestock populations depends on archaeological, archeo-zoological and DNA analysis of extant populations. Scientific research into genetic diversity takes advantage of the rapid advances in molecular genetics. Studies of mitochondrial DNA, microsatellite DNA profiling and Y-chromosomes have revealed details on the process of domestication, on the diversity retained by breeds and on relationships between breeds. However, we only see a small part of the genetic information and the advent of new technologies is most timely in order to answer many essential questions. High-throughput single-nucleotide polymorphism genotyping is about to be available for all major farm animal species. The recent development of sequencing techniques calls for new methods of data management and analysis and for new ideas for the extraction of information. To make sense of this information in practical conditions, integration of geo-environmental and socio-economic data are key elements. The study and management of farm animal genomic resources (FAnGR) is indeed a major multidisciplinary issue. The goal of the present Research Topic was to collect contributions of high scientific quality relevant to biodiversity management, and applying new methods to either new genomic and bioinformatics approaches for characterization of FAnGR, to the development of FAnGR conservation methods applied ex-situ and in-situ, to socio-economic aspects of FAnGR conservation, to transfer of lessons between wildlife and livestock biodiversity conservation, and to the contribution of FAnGR to a transition in agriculture (FAnGR and agro-ecology).

Frontiers2016

Conception et évaluation d'un prototype de simulation de la morphogenèse urbaine par agents vecteurs multi-échelles

Vitor Silva

The research work of this PhD thesis was carried out in the context of an interdisciplinary project related to the study of urban morphogenesis. A team composed of architects and engineers specialized in GIS technologies have worked together in this project during three years, sharing their knowledge in order to understand and simulate the evolution of the urban environment of cities. The fundamental hypothesis that conducted this research is that the city can be seen as a self-organizing system governed by a set of morphogenesis rules, which can for example, determine the location of new architectural programs and induce the city's organization, from local to global scales. Architectural programs themselves are supposed to determine city's development. In this PhD thesis a simulation prototype of the urban growth based on the use of multi-agents systems was carried out. This prototype is a computer tool that allows the analysis and representation of the growth of the built environment. Nowadays, the ability to understand and simulate urban evolution proves to be essential in order to control the evolution of a city in a sustainable development view. Furthermore, this tool should facilitate the understanding and decision-making of those concerned with problems related to urban development. The urban system has been modeled as a set of space objects, such as buildings and networks, which interact between themselves. These interactions are carried out at different levels, from local to global scales, being controlled by behavioral rules or laws of growth. The result of their interaction can be figures or emergent phenomena represented at several scales. The approach using multi-agents vector systems was chosen in order to model a geographical complex system like a city, which integrates a vectorial modeling of space. Hence, each spatial agent does not possess a limit of form and size. The interest of using multi-agents vector systems also lies in their ability to manage various models of individuals, from simple entities to more complex ones. Thus, various levels of representation, such as individuals and groups of individuals, can be managed, which is not easily feasible, for example, with cellular agents. The development platform used is GeOxygene (Java computer programming language), which is an open-source platform developed at IGN (Institut Géographique National, France), by COGIT laboratory. This platform provides several GIS functions, allowing the development and implementation of the prototype here presented. An interaction model between agents was defined and the type of scenarios of each of these interactions was detailed. A set of methods and associated classes was developed. Agent's architecture was conceived in order to allow manipulation (sending, receiving and treatment) of exchanged messages. In order to show the relevance of the multi-agent multi-scale methodology, examples of buildings creation in a case study zone were carried out. Using the multi-scale vector simulation prototype here presented, the development of cities can be computed in a very innovative way. However, the developed prototype still lacks some accuracy, mostly due to the fact that the specified laws adopted for simulation do not reflect the whole reality, which is obviously much more complex to traduce. We have not yet validated the model for other cities – nevertheless, the model could already be used as a decision support tool, particularly as a planning support instrument for architects and urban planners. With regards to future work this prototype shall be integrated in a global approach of urban simulation, allowing the analysis of environmental risks, demographic and economic growth and transports simulation at different scales of analysis and 2D/3D visualization output, such as district and city.

EPFL2010

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