Landscape Genetics

Abstract

I nterdisciplinarity lies at the heart of landscape genetics, a field described as an "amalgamation of molecular population genetics and landscape ecology" (Manel et al. 2003). Storfer and colleagues (2007) proposed a more distinct definition of landscape genetics, stating that the field comprises "research that explicitly quantifies the effects of landscape composition, configuration and matrix quality on gene flow and spatial genetic variation. " In a broader sense, landscape genetics builds from those studies that combine population genetic data, adaptive or neutral, with data on landscape structure (Holderegger and Wagner 2006). The matrix in the quotation above defines the often-hostile space that separates the patches of a species' habitat in a given landscape (figure 1; Turner et al. 2001).The incorporation of the matrix into landscape genetics is a discriminating difference between landscape genetics and population genetics. At most, the latter includes the stretches of land between occupied habitat patches as a simple function of geographical distance; in contrast, in landscape genetics the matrix is seen as a major determinant of biological and ecological processes at the landscape level, and the different quantities and qualities of the areas that separate habitat patches are quite important. For instance, a strip of woodland might not hinder the movement of a ground-breeding bird found in open grasslands, but it could severely limit the migration of meadow butterflies or even form a complete barrier to the dispersal of meadow-plant seeds by wind. Landscape genetics does not possess its own conceptual methodological framework or its own analytical or statistical tool kit, but combines approaches and methods from landscape ecology, population genetics, and spatial statistics. We argue that landscape genetics is not a scientific discipline in itself but rather provides a perspective for examining spatio temporal processes such as habitat fragmentation (Fahrig 2003). The spatial scale and extent at which landscape genetic research occurs are predefined by the species-specific biological and ecological process under study, and by the spatial dimension at which operational practical measures can be taken. The "landscape" of landscape genetics therefore often consists of catchments, one or several valleys, hundreds of square kilometers of forest area, a part of a motorway and its hinterland, or an area of urban sprawl around a city center. A current question of landscape genetics: Inferring and testing landscape connectivityLandscape ecology and population genetics naturally converge in the exploration of how habitat loss and the spatial isolation or fragmentation of habitats affect the movement of species across landscapes. The constraints that landscape patterns and the matrix impose on dispersal-and thus on the distribution of animals, plants, and their genes in a land-

Coastal pollution limits pelagic larval dispersal

“…This is most likely because of the fact that the majority of landscape genetics studies have been on vertebrates and plants in the terrestrial systems 22 in which effective population sizes are small and genetic variation may be difficult to find. However, in an organism with high genetic diversity and a large effective population size, such as P. miniata, this is likely not the case and the crucial factor becomes not the mutation rate of the marker but whether or not there is enough variation within the landscape 36 . Recently isolated populations (< 50 generations) that were previously very diverse and well connected will not have time to accumulate much differentiation by mutation, even in fast-evolving markers 37 .…”

Towards modelling persistence of woodland birds: the role of genetics

“…Perhaps the most straightforward of these is identifying patterns of spatial population structure, important for maintaining populations, and for focussing pest control and eradication (Abdelkrim et al 2005;. Some recent in-depth reviews of spatial genetic approaches include Manel et al (2003), Holderegger and Wagner (2008), Storfer et al (2007) and Guillot et al (2009). Excoffier and Heckel (2006) review 13 commonly used programs: Arlequin, FSTAT, GDA, Genepop, Genetix, MSA, SPAGeDi, Hickory, Structure, BAPS, Geneland, DnaSP and MEGA.…”

“…Within the last decade, these approaches have developed very rapidly and been dubbed landscape genetics (Manel et al 2003;Storfer et al 2007;Holderegger and Wagner 2008;Balkenhol et al 2009aBalkenhol et al , 2009b.…”

Open computational landscape genetics

“…CDPOP requires the Python2.7.x interpreter and uses the NumPy and SciPy packages. And finally, one can also mention least-cost modelling approaches to provide functional landscape models, which have been a central component in the development of landscape genetics (Holderegger and Wagner, 2008). An example is «gdistance», an R package providing functionalities to calculate different distance measures and routes in heterogeneous geographic spaces represented as grids (https://cran.r-project.org/web/packages/gdistance/).…”