Holderegger, Rolf

Wagner, Helene

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PrefaceA brief guide to Landscape GeneticsRolf Holderegger and Helene H. Wagner*WSL Swiss Federal Research Institute, Zu¨rcherstrasse 111, CH-8903 Birmensdorf, Switzerland; *Author forcorrespondence (e-mail: helene.wagner@wsl.ch)Received 30 November 2005; accepted in revised form 18 December 2005What is landscape genetics?In their inaugural paper, Manel et al. (2003) de-ﬁned landscape genetics as a combination oflandscape ecology and population genetics. Inmore detail, these authors stated that landscapegenetics ‘aims at providing information about theinteraction between landscape features andmicroevolutionary processes, such as gene ﬂow,genetic drift and selection’ (Manel et al. 2003,p. 189). The ﬁrst lesson to learn from this is thatwe are dealing with microevolution, i.e., evolu-tionary processes within species. Second, we aretalking about gene ﬂow and selection, two eco-logical and evolutionary processes that need dif-ferent genetic approaches to be investigatedHolderegger et al. 2006). Third, Manel et al.(2003, p. 190) remarked that ‘the two key steps oflandscape genetics are the detection of geneticdiscontinuities and the correlation of these dis-continuities with landscape environmental fea-tures, such as barriers’, which provides relevantinformation for various scientiﬁc disciplines suchas evolution, ecology or conservation biology.Hence, we need two data sets, a genetic one and alandscape ecological one, and we look for breaks,gradients or transitions that coincide in these twodata sets. Manel et al. (2003) were less explicit intheir landscape deﬁnition, and landscape ecolo-gists are well aware that this is a diﬃcult task(Turner et al. 2001). Thus, the deﬁnition of land-scape genetics by Manel et al. (2003) was muchclearer on the population genetic than on thelandscape ecological side, including spatial scale.A pragmatic circumscription of landscapegenetics could be that landscape genetics endorsesthose studies that combine population genetic data,adaptive or neutral, with data on landscape com-position and conﬁguration, including matrix quality.A comparison with metapopulation biology andmetapopulation genetics may clarify the majorcharacteristic of landscape genetics. Classicalmetapopulation studies are spatially implicit, theyview the natural world as divided into cheerfulislands (patches) and hostile sea (matrix) (Baquette2004). Spatially realistic metapopulation modelstypically consider the geographic distance betweenpatches (Ovaskainen and Hanski 2004), but do notinclude matrix quality. In landscape genetics,however, the landscape with its composition, spa-tial conﬁguration and dynamics makes up half ofthe story beside genetics. Landscape geneticstherefore is much closer to the real world than theclassical metapopulation concept. For instance,the actual connectivity of populations in terms ofdispersal of organisms may deviate markedly froman abstract population genetic gene ﬂow index(Whitlock and McCauley 1999) or from a land-scape ecological connectivity index calculatedfrom a habitat map (Li and Wu 2004). Landscapegenetics provides powerful tools for quantifyingsuch processes in real landscapes. While popula-tion geneticists have eagerly adopted this ap-proach, landscape ecologists have only startedusing genetic methods.Landscape genetics is an important emergingresearch topic that integrates landscape patternwith population genetics. It is a new way of sci-Landscape Ecology (2006) 21:793–796  Springer 2006DOI 10.1007/s10980-005-6058-6entiﬁc thinking, whereas there exists neither aspeciﬁc landscape genetic theory nor speciﬁc con-cepts. While landscape ecology partly shares theselimitations (Wu and Hobbs 2002), the situation isdiﬀerent with population genetics, which has awell-founded theoretical basis (Hartl and Clark1997). However, no landscape genetic researchagenda has been deﬁned to date, and landscapegenetic data are still scarce.We believe that the beneﬁt of landscape geneticslies in its heuristic, as well as practical, values offorcing landscape ecologists to think more aboutprocesses rather than spatial patterns, and to re-mind population geneticists that processes are af-fected by the quality of a landscape and not just bypure spatial distance (Holderegger et al. in press).This is new, especially when it comes to scientiﬁcpractice.Special section on landscape geneticsThe following collection of papers, partly origi-nating from a symposium held at the 2005 US-IALE meeting in Syracuse, NY (USA), aims atproviding an introduction to the genetic back-ground of landscape genetics, giving examples oflandscape ecological applications and pointing tomethodological problems of landscape genetics.The papers address the broader audience of land-scape ecologists rather than specialists and shouldserve as an entry point to landscape genetics forlandscape ecologists.The ﬁrst two papers deal with basic genetictopics. The ﬁrst article by Holderegger et al. (2006)introduces some genetic principles as well as neu-tral and adaptive genetic diversity and furtherpoints to caveats and limitations of the use of ge-netic data. The properties of diﬀerent geneticmarkers that can be used to investigate diﬀerentprocesses at various spatio-temporal scales arethen discussed by Latta (2006). How populationgenetic methods can be applied to study twoprincipal ecological processes that are closely re-lated to landscape ecology, namely migration, orgene ﬂow in genetic terms, and metapopulationdynamics, is the topic of the following two con-tributions. Sork and Smouse (2006) provide a ge-netic analysis of landscape connectivity by meansof gene ﬂow assessment using tree populations asmodel systems, while Pannell and Dorken (2006)evaluate the role of colonization in plant meta-populations and its inﬂuence on range expansion.Subsequently, Wagner et al. (2006) give an exam-ple of a simulation approach in landscape geneticsusing both habitat data and genetic data of anepiphytic lichen in a dynamic landscape. Finally,Antolin et al. (2006) show how landscape featuresaﬀect the distribution of genetic variation in col-onies of prairie dogs. The special section is com-plemented by three contributed research papersdescribing applications of landscape genetics inanimals, (i.e.,) an insect (Holzhauer et al. 2006), aﬁsh (Neville et al. 2006) and a mammal (Broquetet al. 2006).PerspectiveLandscape genetics is a current scientiﬁc trend.During the last 15 years, the papers that inter-preted genetic data in relation to landscape fea-tures steadily increased in numbers (grey line inFigure 1). Since the seminal paper of Manel et al.05101520251990199119921993199419951996199719981999200020012002200320042005YearNumber of articlesFigure 1. Landscape genetics is a current scientiﬁc trend. Re-sults of an ISI Web of Science search for articles relating geneticresults to landscape features (search criterion: Landscape ANDGenetics; grey line) or explicitly referring to landscape genetics(search criterion: Landscape Genetics; black line) during theyears 1990–2005 (January–September). Note that the articleswithin the second category are included in those of the ﬁrstcategory. The asterisk denotes the publication year of theseminal article by Manel et al. (2003).794(2003), landscape genetic studies are strongly onthe rise (black line in Figure 1), although the termhad been used before. What makes landscapegenetics so attractive to researchers? We believethat the major driver of this interest is the possi-bility to investigate a process through genetic dataand to analyse how this process works in the realworld by assessing landscape ecological data.We hope that this special section will helplandscape ecologists to better understand and usemodern molecular genetic methods. It is new touse molecular genetic data to test speciﬁc land-scape ecological hypotheses concerning the eﬀectof landscape structure on the actual movement oforganisms, the connectivity of habitats from anorganism’s perspective or the eﬀect of disturbanceand landscape dynamics on metapopulationdynamics. Thus we provide a list of suggestions forlandscape ecologists who want to conduct suchlandscape genetics research (Table 1). On theother hand, we also believe that it is necessary toexplain to population geneticists the wealth ofanalyses that can be done with landscape ecolog-ical data. Table 2 summarizes some key issues thatpopulation geneticists should consider whenincorporating landscape ecology in their analyses.Only if we combine concepts and methods fromboth ﬁelds correctly and to their full potential willlandscape genetics become a fruitful scientiﬁc ap-proach of the future.AcknowledgementsWe thank Felix Gugerli and Jingle Wu for com-ments on this manuscript and the many refereesthat reviewed the articles of this special section.This work was partly funded by the Swiss Na-tional Science Foundation within the NCCR PlantSurvival.ReferencesAntolin M.F., Savage L.T. and Eisen R.J. 2006. Landscapefeatures inﬂuence genetic structure of Black-Tailed PrairieDogs (Cynomys ludovicianus). Landsc. Ecol. 21: 867–875.Table 1. Dos and don’ts for landscape ecologists who want to use genetics.(1) Do not try to do it all alone: collaborate with population geneticists and invest time in developing a common ground, as it isnecessary in any interdisciplinary project (Holderegger et al. 2006)(2) Be aware of what genetic data mean; do not confound neutral and adaptive genetic variation (Holderegger et al. 2006)(3) Population genetics oﬀers the possibility to investigate diﬀerent time scales (from evolutionary time spans to the current year);do not confound recent and historic gene ﬂow (Latta 2006; Pannell and Dorken 2006; Sork and Smouse 2006)(4) Distinguish between biparentally inherited DNA and uniparentally inherited DNA that come from either the father, the motheror both, and consider their respective mode of dispersal by seed and/or pollen (Latta 2006; Sork and Smouse 2006)(5) Test hypotheses; make it a truly landscape-related hypothesis, e.g., the eﬀect of landscape structure or landscape dynamics onconnectivity (Neville et al. 2006; Wagner et al. 2006)(6) Make sure you choose the appropriate landscape and organism to test your hypothesis; check whether suitable genetic markersalready exist or can easily be developed (Antolin et al. 2006; Latta 2006)Table 2. Landscape ecological advice for population geneticists.(1) A GIS is more than a tool for mapping populations; GIS combines a spatial data base with tools for data management,analysis and visualisation. For example, it contains ﬂexible methods for calculating cost-distance functions, i.e., modifyingEuclidean distance estimates with information on matrix traversability or resistance based on environmental data(Broquet et al. 2006)(2) A landscape approach should go beyond testing the eﬀect of distance (e.g., isolation by distance); use pure distance as a nullmodel and then test for quantitative or qualitative matrix eﬀects (Antolin et al. 2006; Neville et al. 2006)(3) Landscapes can rarely be assumed constant; disturbance and landscape change can be incorporated into the study design(Holzhauer et al. 2006; Wagner et al. 2006)(4) Replication at the landscape level is often problematic or simply not possible; simulation modelling may help establishing amechanistic link (Wagner et al. 2006)(5) The spatial and temporal variability of site conditions may be as important for explaining quantitative traits as are diﬀerencesin their mean (Antolin et al. 2006; Holzhauer et al. 2006)795Baquette M. 2004. The classical metapopulation theory and thereal, natural world: a critical appraisal. Basic Appl. Ecol. 5:213–224.Broquet T., Ray N., Petit E., Fryxell J.M. and Burel F. 2006.Genetic isolation by distance and landscape connectivity inthe American Marten (Martes americana). Landsc. Ecol. 21:877–889.Hartl D.L. and Clark A.G. 1997. Principles of PopulationGenetics. Sinauer, Sunderland.Holderegger R., Gugerli F., Scheidegger F. and Taberlet P. Inpress. Integrating population genetics with landscape ecologyto infer spatio-temporal processes. In: Kienast F., Gosh R.and Wildi O. (eds), A Changing World: Challenges forLandscape Research. Kluwer, Dordrecht.Holderegger R., Kamm U. and Gugerli F. 2006. Adaptiveversus neutral genetic diversity: implications for landscapegenetics. Landsc. Ecol. 21: 797–807.Holzhauer S.I.J., Ekschmitt K., Sander A.-C., Dauber J. andWolters V. 2006. Eﬀect of historic landscape change on thegenetic structure of the bush-cricket Metrioptera roeseli.Landsc. Ecol. 21: 891–899.Latta R. 2006. Integrating patterns across multiple geneticmarkers to infer spatial processes. Landsc. Ecol. 21: 809–820.Li H. and Wu J. 2004. Use and misuse of landscape indices.Landsc. Ecol. 19: 389–399.Manel S., Schwartz M.K., Luikart G. and Taberlet P. 2003.Landscape genetics: combining landscape ecology and pop-ulation genetics. Trends Ecol. Evol. 18: 189–197.Neville H.M., Dunham J.B. and Peacock M.M. 2006. Land-scape attributes and life history variability shape geneticstructure of trout populations in a stream network. Landsc.Ecol. 21: 901–916.Ovaskainen O. and Hanski I. 2004. Metapopulation dynamicsin highly fragmented landscapes. In: Hanski I.A. andGaggiotti O.E. (eds), Ecology, Genetics and Evolution ofMetapopulations. Academic Press, Amsterdam, pp. 73–103.Pannell J.R. and Dorken M. 2006. Colonisation as a commondenominator in plant metapopulations and range expansions:eﬀects on genetic diversity and sexual systems. Landsc. Ecol.21: 837–848.Sork V.L. and Smouse P.E. 2006. Genetic analysis of landscapeconnectivity in tree populations. Landsc. Ecol. 21: 821–836.Turner M.G., Gardner R.H. and O’Neill R.V. 2001. LandscapeEcology in Theory and Practice. Springer, New York.Wagner H.H., Werth S., Kalwij J.M., Bolli J.C. and Sche-idegger C. 2006. Modelling forest recolonization by an epi-phytic lichen using a landscape genetic approach. Landsc.Ecol. 21: 849–865.Whitlock M.C. and McCauley D.E. 1999. Indirect measures ofgene ﬂow and migration: FST „ 1/(4Nm + 1). Heredity 82:117–125.Wu J. and Hobbs R. 2002. Key issues and research priorities inlandscape ecology: an idiosyncratic synthesis. Landsc. Ecol.17: 355–365.796

A brief guide to Landscape Genetics

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