Navigating the pitfalls and promise of landscape genetics

Abstract

The field of landscape genetics has been evolving rapidly since its emergence in the early 2000s. New applications, techniques and criticisms of techniques appear like clockwork with each new journal issue. The developments are an encouraging, and at times bewildering, sign of progress in an exciting new field of study. However, we suggest that the rapid expansion of landscape genetics has belied important flaws in the development of the field, and we add an air of caution to this breakneck pace of expansion. Specifically, landscape genetic studies often lose sight of the fundamental principles and complex consequences of gene flow, instead favouring simplistic interpretations and broad inferences not necessarily warranted by the data. Here, we describe common pitfalls that characterize such studies, and provide practical guidance to improve landscape genetic investigation, with careful consideration of inferential limits, scale, replication, and the ecological and evolutionary context of spatial genetic patterns. Ultimately, the utility of landscape genetics will depend on translating the relationship between gene flow and landscape features into an understanding of long‐term population outcomes. We hope the perspective presented here will steer landscape genetics down a more scientifically sound and productive path, garnering a field that is as informative in the future as it is popular now.

Genomic and phenotypic analysis of Vavilov’s historic landraces reveals the impact of environment and genomic islands of agronomic traits

“…Such studies lend support to our broader findings of numerous genes for multiple phenotypes mostly co-localized to a single genomic region. Interestingly, while the evolution of this genomic region has taken place in the geographic region of primary domestication, the evolved genotypes have not gained widespread representation in Ethiopia, which represents an important location of chickpea’s secondary diversification 39, 40 .…”

Syntopic frogs reveal different patterns of interaction with the landscape: A comparative landscape genetic study of Pelophylax nigromaculatus and Fejervarya limnocharis from central China

“…Shifting from this approach are current comparative studies that are landscape‐focused (e.g., Amos et al., 2012; Poelchau & Hamrick, 2012), and seek for common impacts of landscape features on distinctly related species occurring in the same landscape. Such studies attempted to identify common elements, such as dispersal corridor, used by multiple species (e.g., Amos et al., 2012), and are particularly useful for land‐use management and identifying priority areas for conservation (Richardson et al., 2016). On the other hand, few studies are species‐focused, which compare closely related species occurring in the same landscape, examine interspecies intrinsic attributes, and seek how species‐specific attributes influence responses to the same landscape (Engler et al., 2014).…”

Multiple founder effects are followed by range expansion and admixture during the invasion process of the raccoon (Procyon lotor) in Europe

“…ResistanceGA is an approach to parameterize resistance surfaces to optimally fit genetic data (Richardson et al, 2016), circumventing typical issues of subjectivity in assigning resistance values and the usually associated assessment of only a limited parameter space in the process of optimization and also accounting for spatial autocorrelation Richardson et al, 2016). We used the R-package ResistanceGA, (Peterman, 2014) to optimize a resistance surface depicting waterways.…”