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Ecosystems are the stage on which the play of evolution is acted, and ecosystems are complex, spatially structured and temporally varying. The purpose of this Research Topic is to explore critical challenges and opportunities for the transition from landscape genetics to landscape genomics. Landscape genetics has focused on the spatial analysis of small genetic datasets, typically comprised of less than 20 microsatellite markers, taken from clusters of individuals in putative populations or distributed individuals across landscapes. The recent emergence of large scale genomic datasets produced by next generation sequencing methods poses tremendous challenge and opportunity to the field. Perhaps the greatest is to produce, process, curate, archive and analyze spatially referenced genomic datasets in a way such that research is led by a priori hypotheses regarding how environmental heterogeneity and temporal dynamics interact to affect gene flow and selection. The papers in the Research Topic cover a broad range of topics under this area of focus, from reviews of the emergence of landscape genetics, to best practices in spatial analysis of genetic data. The compilation, like the emerging field itself, is eclectic and illustrates the scope of both the challenges and opportunities of this emerging field.

landscape genomics --- gene flow --- next generation sequencing --- landscape genetics --- evolution

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Le chat forestier (Felis silvestris), après avoir subi un important déclin au 19ème siècle, semble être actuellement en expansion dans certains pays. L'espèce reste toutefois vulnérable à plusieurs menaces liées à l'activité humaine. En effet, l'omniprésence de l'homme dans le paysage européen provoque une perte et une fragmentation de l'habitat du chat forestier, isolant ainsi des noyaux de population où la diversité génétique finira par diminuer. Cette proximité accrue avec les constructions anthropiques engendre un second problème : l'hybridation avec le chat domestique (Felis catus). Dans cette étude, nous cherchions à approfondir les connaissances concernant l'ampleur de ces menaces dans deux pays : la Belgique (Wallonie) et le Luxembourg. Pour ce faire, nous avons récolté des échantillons de poils grâce à des pièges à poils enduits de teinture de valériane. Ceux-ci ont ensuite été analysés à l'aide de la méthode SNP. Nous avons utilisé 96 SNPs sélectionnés spécifiquement pour le chat forestier et pour ce type d'analyse. Un des objectifs principaux était de vérifier la présence d'hybrides. Nous avons calculé un taux d'hybridation de 6% (N = 63) en Wallonie (principalement la province de Liège) et de 8% (N = 117) au Luxembourg. Ces taux relativement bas concordent avec les résultats de récentes études sur le sujet dans l'ouest de l'Europe. Nous avons également mis en évidence l'existence de deux groupes génétiques distincts au sein des chats forestiers dont nous ne connaissons pas encore l'origine. La faible différentiation génétique (DJost = 0.005) entre ces groupes nous incite à penser qu’ils appartiennent effectivement à une même grande population d'Europe centrale occidentale. En analysant les coefficients de consanguinité, nous avons constaté un risque de dépression de consanguinité plus élevé en Wallonie (FIS = 0.32) qu'au Luxembourg (FIS = 0.07). Il convient de rester prudent quant à l'interprétation de ces résultats car les méthodes d'échantillonnage diffèrent dans les deux pays. Nous n'excluons pas la possibilité d'un biais d'échantillonnage en Wallonie. Le second objectif principal, centré sur le Luxembourg, consistait à identifier les éléments du paysage qui impactaient la connectivité des chats forestiers par une approche de génétique du paysage. Nous avons observé que les forêts et zones agricoles jouaient un rôle de corridor, tandis que les autoroutes et zones urbaines agissaient étaient des obstacles au flux génétique de l'espèce. The European wildcat (Felis silvestris), after having suffered a significant decline in the 19th century, seems to be currently expanding in some countries. However, the species remains vulnerable to several threats related to human activity. Indeed, the omnipresence of man in the European landscape is causing a loss and fragmentation of the European wildcat's habitat, thus isolating small populations where genetic diversity will eventually decrease. This increased proximity to man-made constructions creates a second problem: hybridization with the domestic cat (Felis catus). In this study, we wanted to improve our knowledge of the extent of these threats in two countries: Belgium (Wallonia) and Luxembourg. To do so, we collected hair samples using hair traps coated with valerian dye. These were then analysed using the SNP method. We used 96 SNPs selected specifically for the European wildcat and for this type of analysis. One of the main objectives was to check the presence of hybrids. We calculated a hybridization rate of 6% (N = 63) in Wallonia (mainly the province of Liège) and 8% (N = 117) in Luxembourg. These relatively low rates are in line with the results of recent studies on the subject in Western Europe. We have also highlighted the existence of two distinct genetic groups in European wildcats. However, we don’t know their origin yet. The low genetic differentiation (DJost = 0.005) between these groups leads us to believe that they do indeed belong to the same large population in Western Central Europe. By analysing the inbreeding coefficients, we found a higher risk of inbreeding depression in Wallonia (FIS = 0.32) than in Luxembourg (FIS = 0.07). We must be careful when interpreting these results as the sampling methods differ in the two countries. We do not exclude the possibility of sampling bias in Wallonia. The second main objective, focusing on Luxembourg, was to identify landscape elements that impacted European wildcat connectivity using a landscape genetics approach. We observed that forests and agricultural areas acted as corridors, while motorways and urban areas acted as barriers to the gene flow of the species.

felis silvestris --- snp --- hybridization --- landscape fragmentation --- landscape genetics --- conservation genetics --- Sciences du vivant > Génétique & processus génétiques

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This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact

Science: general issues --- Medical genetics --- Camelids --- genomics --- population and landscape genetics --- breeding strategies and sustainable management --- conservation genetics --- physiology and thermo tolerance --- response to pathogen

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