Landscape Genetics

by

Andrew Storfer

• LAST REVIEWED: 31 August 2015
• LAST MODIFIED: 31 August 2015
• DOI: 10.1093/obo/9780199941728-0066

Introduction

Landscape genetics emerged in 2003 as a field that integrates population genetics, landscape ecology, and spatial statistics to test the influence of landscape characteristics on the spatial distribution of genetic variation. At that time, rapid increases in our ability to obtain high-resolution genetic data, together with advances in remote sensing and geographic information systems (GIS), allowed statistical tests of spatial population structure. In contrast to population genetics studies that assessed isolation-by-distance (IBD), or essentially a test for a positive correlation between genetic distance and (Euclidean) distance, landscape genetics offered a means to test the influence of actual landscape processes, such as mountains, rivers, and weather patterns, on genetic population structure. As a result, landscape genetics has been refined to refer to studies that quantify the effects of landscape characteristics on gene flow and genetic variation in an explicitly spatial framework. This area of inquiry has met with early success, as landscape genetic models generally provide a more complete picture of population genetic structure by typically explaining a significantly higher proportion of variation in gene flow than classic IBD models. Consequently, landscape genetics studies can provide insight into fundamental biological processes such as: metapopulation dynamics, (ecological) speciation, and ultimately limits to species’ geographic distributions.

General Overviews

Since the term “landscape genetics” was coined in 2003 (Manel, et al. 2003), landscape genetics has been reviewed extensively. Researchers new to landscape genetics will quickly note that there are numerous ways to design a study as well as multiple analytical frameworks and methods. Basic introductions to the field and associated conceptual frameworks include papers such as Holderegger and Wagner 2006; Holderegger and Wagner 2008; Storfer, et al. 2007; and Wagner and Fortin 2013. A review of landscape genetics in plants was written by Holderegger and colleagues (Holderegger, et al. 2010), and a ten-year retrospective has been provided in Manel and Holderegger 2013. A review of empirical studies is found in Storfer, et al. 2010. As with any rapidly growing field that integrates previously disparate (sub)disciplines, landscape genetics has faced challenges with: interdisciplinary communication and the integration of rapidly developing new analytical techniques and software, as well as integrating and interpreting multiple analysis methods in a single study. Opinion pieces on how to move forward have included Balkenhol, et al. 2009; Manel and Segelbacher 2009; and Sork and Waits 2010. In addition, the entire 2010 Molecular Ecology, Volume 19, Issue 17 is a special issue devoted to landscape genetics and provides overviews of several aspects of landscape genetics studies—from sampling design to computer simulations, to empirical studies and theoretical considerations. Further, a special section in an issue of Evolution (Volume 67, Issue 12) has several articles that review landscape genetics, provide empirical examples, and discuss recent empirical results. Most recently, a useful guide to designing, conducting, and analyzing landscape genetics studies is provided in Hall and Beissinger 2014.

• Balkenhol, N., F. Gugerli, S. A. Cushman, et al. 2009. Identifying future research needs in landscape genetics: Where to from here? Landscape Ecology 24:455–463.

  DOI: 10.1007/s10980-009-9334-z

  Meeting overview and perspective piece on future directions in landscape genetics. Identifies future challenges with scale, analytical limitations, and communication.

• Hall, L. A., and S. R. Beissinger. 2014. A practical toolbox for design and analysis of landscape genetics studies. Landscape Ecology 29:1487–1504.

  DOI: 10.1007/s10980-014-0082-3

  Outlines a stepwise framework for designing, conducting, and analyzing a landscape genetics study.

• Holderegger, R., D. Buehler, and F. Gugerli. 2010. Landscape genetics of plants. Trends in Plant Science 15:675–683.

  DOI: 10.1016/j.tplants.2010.09.002

  Provides an overview of landscape genetics studies in plants along with insights into generalities.

• Holderegger, R., and H. H. Wagner. 2006. A brief guide to landscape genetics. Landscape Ecology 21:793–796.

  DOI: 10.1007/s10980-005-6058-6

  Brief, nontechnical overview of landscape genetics.

• Holderegger, R., and H. H. Wagner. 2008. Landscape genetics. BioScience 58:199–207.

  DOI: 10.1641/B580306

  Nontechnical overview of landscape genetics. Provides a clear summary of the objectives of landscape genetics studies.

• Manel, S., and R. Holderegger. 2013. Ten years of landscape genetics. Trends in Ecology and Evolution 28:614–621.

  DOI: 10.1016/j.tree.2013.05.012

  Reviews the first ten years of the field.

• Manel, S., M. K. Schwartz, G. Luikart, and P. Taberlet. 2003. Landscape genetics: Combining landscape ecology and population genetics. Trends in Ecology & Evolution 18:189–197.

  DOI: 10.1016/S0169-5347(03)00008-9

  Well-cited paper that coined the term “landscape genetics” and introduced the field in a formal way.

• Manel, S., and G. Segelbacher. 2009. Perspectives and challenges in landscape genetics. Molecular Ecology 18:1821–1822.

  DOI: 10.1111/j.1365-294X.2009.04151.x

  Brief perspective piece.

• Sork, V. L., and L. P. Waits. 2010. Contributions of landscape genetics—approaches, insights, and future potential. In Special issue: Special issue on landscape genetics. Edited by V. L. Sork and L. Waits. Molecular Ecology 19:3489–3495.

  DOI: 10.1111/j.1365-294X.2010.04786.x

  Introduces special issue on landscape genetics.

• Storfer, A., M. A. Murphy, J. S. Evans, et al. 2007. Putting the “landscape” in landscape genetics. Heredity 98:128–142.

  DOI: 10.1038/sj.hdy.6800917

  Overview of the field that introduces basics of how to do a landscape genetics study, including sampling design, analyses, and types of questions that can be addressed.

• Storfer, A., M. A. Murphy, S. F. Spear, R. Holderegger, and L. P. Waits. 2010. Landscape genetics: Where are we now? Molecular Ecology 19:3496–3514.

  DOI: 10.1111/j.1365-294X.2010.04691.x

  Review of empirical landscape genetics studies from 1999 to 2008. Synthesizes study organisms, locations, analysis types, and general insights.

• Wagner, H. H., and M. -J. Fortin. 2013. A conceptual framework for the spatial analysis of landscape genetic data. Conservation Genetics 14:253–261.

  DOI: 10.1007/s10592-012-0391-5

  Proposes a nice framework for understanding landscape genetics studies under four major research categories. Under each category, challenges and recommendations are discussed.