Landscape Ecology

, 24:455 | Cite as

Identifying future research needs in landscape genetics: where to from here?

  • Niko Balkenhol
  • Felix Gugerli
  • Sam A. Cushman
  • Lisette P. Waits
  • Aurélie Coulon
  • J. W. Arntzen
  • Rolf Holderegger
  • Helene H. Wagner
  • Participants of the Landscape Genetics Research Agenda Workshop 2007
Perspectives

Abstract

Landscape genetics is an emerging interdisciplinary field that combines methods and concepts from population genetics, landscape ecology, and spatial statistics. The interest in landscape genetics is steadily increasing, and the field is evolving rapidly. We here outline four major challenges for future landscape genetic research that were identified during an international landscape genetics workshop. These challenges include (1) the identification of appropriate spatial and temporal scales; (2) current analytical limitations; (3) the expansion of the current focus in landscape genetics; and (4) interdisciplinary communication and education. Addressing these research challenges will greatly improve landscape genetic applications, and positively contribute to the future growth of this promising field.

Keywords

Landscape resistance Adaptive genetic variation Gene flow Single-nucleotide polymorphisms Spatial heterogeneity Spatio-temporal scale 

References

  1. Balkenhol N, Waits LP, Dezzani R (2009) Statistical approaches in landscape genetics: an evaluation of methods for linking landscape and genetic data. Ecography. doi:10.1111/j.1600-0587.2009.05807.x (in press)
  2. Bolnick DI, Fitzpatrick BM (2007) Sympatric speciation: models and empirical evidence. Annu Rev Ecol Evol Syst 38:459–487. doi:10.1146/annurev.ecolsys.38.091206.095804 CrossRefGoogle Scholar
  3. Brumfield RT, Beerli P, Nickerson DA, Edwards SV (2003) The utility of single nucleotide polymorphisms in inferences of population history. Trends Ecol Evol 18:249–256. doi:10.1016/S0169-5347(03)00018-1 CrossRefGoogle Scholar
  4. Chen C, Durand E, Forbes F, François O (2007) Bayesian clustering algorithms ascertaining spatial population structure: a new computer program and a comparison study. Mol Ecol Notes 7:747–756. doi:10.1111/j.1471-8286.2007.01769.x CrossRefGoogle Scholar
  5. Coulon A, Cosson JF, Angibault JM et al (2004) Landscape connectivity influences gene flow in a roe deer population inhabiting a fragmented landscape: an individual-based approach. Mol Ecol 13:2841–2850. doi:10.1111/j.1365-294X.2004.02253.x PubMedCrossRefGoogle Scholar
  6. Cushman SA (2006) Effects of habitat loss and fragmentation on amphibians: a review and prospectus. Biol Conserv 128:231–240. doi:10.1016/j.biocon.2005.09.031 CrossRefGoogle Scholar
  7. Cushman SA, McKelvey KS, Hayden J, Schwartz MK (2006) Gene flow in complex landscapes: testing multiple hypotheses with causal modeling. Am Nat 168:486–499. doi:10.1086/506976 PubMedCrossRefGoogle Scholar
  8. Cushman SA, McKelvey KS, Schwartz MK (2009) Using empirically derived source-destination models to map regional conservation corridors. Conserv Biol. doi:10.1111/j.1523-1739.2008.01111.x (in press)
  9. Davies KF, Gascon C, Margules CR (2001) Habitat fragmentation: consequences, management, and future research priorities. In: Soule ME, Orians G (eds) Conservation biology: research priorities for the next decade. Island Press, Washington, DC, pp 81–98Google Scholar
  10. Dupanloup I, Schneider S, Excoffier L (2002) A simulated annealing approach to define genetic structure of populations. Mol Ecol 11:2571–2581. doi:10.1046/j.1365-294X.2002.01650.x PubMedCrossRefGoogle Scholar
  11. Dyer RJ, Nason JD (2004) Population graphs: the graph-theoretic shape of genetic structure. Mol Ecol 13:1713–1728. doi:10.1111/j.1365-294X.2004.02177.x PubMedCrossRefGoogle Scholar
  12. Epps CW, Wehausen JD, Bleich VC et al (2007) Optimizing dispersal and corridor models using landscape genetics. J Appl Ecol 44:714–724. doi:10.1111/j.1365-2664.2007.01325.x CrossRefGoogle Scholar
  13. Faubet P, Gaggiotti OE (2008) A new Bayesian method to identify the environmental factors that influence recent migration. Genetics 178:1491–1504. doi:10.1534/genetics.107.082560 PubMedCrossRefGoogle Scholar
  14. Foll M, Gaggiotti OE (2006) Identifying the environmental factors that determine the genetic structure of populations. Genetics 174:875–891. doi:10.1534/genetics.106.059451 PubMedCrossRefGoogle Scholar
  15. François O, Ancelet S, Guillot G (2006) Bayesian clustering using hidden Markov random fields in spatial population genetics. Genetics 174:805–816. doi:10.1534/genetics.106.059923 PubMedCrossRefGoogle Scholar
  16. Futuyma DJ (1997) Evolutionary biology. Sinauer, SunderlandGoogle Scholar
  17. Geffen E, Anderson MJ, Wayne RK (2004) Climate and habitat barriers to dispersal in the highly mobile grey wolf. Mol Ecol 13:2481–2490. doi:10.1111/j.1365-294X.2004.02244.x PubMedCrossRefGoogle Scholar
  18. Holderegger R, Wagner HH (2006) A brief guide to landscape genetics. Landscape Ecol 21:793–796. doi:10.1007/s10980-005-6058-6 CrossRefGoogle Scholar
  19. Holderegger R, Wagner HH (2008) Landscape genetics. Bioscience 58:199–207. doi:10.1641/B580306 CrossRefGoogle Scholar
  20. Holderegger R, Kamm U, Gugerli F (2006) Adaptive versus neutral genetic diversity: implications for landscape genetics. Landscape Ecol 21:797–807. doi:10.1007/s10980-005-5245-9 CrossRefGoogle Scholar
  21. Holderegger R, Hermann D, Poncet B et al (2008) Land ahead: using genome scans to identify molecular markers of adaptive relevance. Plant Ecol Div 1:273–283CrossRefGoogle Scholar
  22. Holzhauer S, Ekschmitt K, Sander A-C et al (2006) Effect of historic landscape change on the genetic structure of the bush-cricket Metrioptera roeseli. Landscape Ecol 21:891–899. doi:10.1007/s10980-005-0438-9 CrossRefGoogle Scholar
  23. Joost S, Bonin A, Bruford MW et al (2007) A spatial analysis method (SAM) to detect candidate loci for selection: towards a landscape genomics approach to adaptation. Mol Ecol 16:3955–3969. doi:10.1111/j.1365-294X.2007.03442.x PubMedCrossRefGoogle Scholar
  24. Kamm U (2008) Landscape genetics of a rare, naturally scattered, temperate forest tree (Sorbus domestica). PhD-thesis, ETH Zürich, Zürich, SwitzerlandGoogle Scholar
  25. Keyghobadi N, Roland J, Matter S, Strobeck C (2005) Among- and within-patch components of genetic diversity respond at different rates to habitat fragmentation: an empirical demonstration. Proc R Soc Ser B 272:553–560. doi:10.1098/rspb.2004.2976 CrossRefGoogle Scholar
  26. Landergott U, Holderegger R, Kozlowski G, Schneller JJ (2001) Historical bottlenecks decrease genetic diversity in natural populations of Dryopteris cristata. Heredity 87:344–355. doi:10.1046/j.1365-2540.2001.00912.x PubMedCrossRefGoogle Scholar
  27. Latch E, Dharmarajan G, Glaubitz JC, Rhodes OE Jr (2006) Relative performance of Bayesian clustering software for inferring population substructure and individual assignment at low levels of population differentiation. Conserv Genet 7:295–302. doi:10.1007/s10592-005-9098-1 CrossRefGoogle Scholar
  28. Manel S, Schwartz MK, Luikart G, Taberlet P (2003) Landscape genetics: combining landscape ecology and population genetics. Trends Ecol Evol 18:189–197. doi:10.1016/S0169-5347(03)00008-9 CrossRefGoogle Scholar
  29. Mayr E (1954) Change of genetic environment and evolution. In: Huxley J, Hardy AC, Ford EB (eds) Evolution as a process. Allen and Unwin, London, pp 157–180Google Scholar
  30. Mayr E (1988) Processes of speciation in animals. In: Mayr E (ed) Towards a new philosophy of biology: observations of an evolutionist. Harvard University Press, Cambridge, pp 364–382Google Scholar
  31. McRae BH (2006) Isolation by resistance. Evol Int J Org Evol 60:1551–1561Google Scholar
  32. McRae BH, Beier P (2007) Circuit theory predicts gene flow in plant and animal populations. Proc Natl Acad Sci USA 104:19885–19890. doi:10.1073/pnas.0706568104 PubMedCrossRefGoogle Scholar
  33. McRae BH, Dickson BG, Keitt TH (2008) Using circuit theory to model connectivity in ecology and conservation. Ecology 89:2712–2724. doi:10.1890/07-1861.1 PubMedCrossRefGoogle Scholar
  34. Meudt HM, Clarke AC (2007) Almost forgotten or latest practice? AFLP applications, analyses and advances. Trends Plant Sci 12:106–117. doi:10.1016/j.tplants.2007.02.001 PubMedCrossRefGoogle Scholar
  35. Morin PA, Luikart G, Wayne RK et al (2004) SNPs in ecology, evolution and conservation. Trends Ecol Evol 19:208–216. doi:10.1016/j.tree.2004.01.009 CrossRefGoogle Scholar
  36. Orsini L, Corander J, Alasentie A, Hanski I (2008) Genetic spatial structure in a butterfly metapopulation correlates better with past than present demographic structure. Mol Ecol 17:2629–2642. doi:10.1111/j.1365-294X.2008.03782.x PubMedCrossRefGoogle Scholar
  37. Ouborg NJ, Vriezen WH (2007) An ecologist’s guide to ecogenomics. J Ecol 95:8–16. doi:10.1111/j.1365-2745.2006.01197.x CrossRefGoogle Scholar
  38. Pascual-Hortal L, Saura S (2007) Impact of spatial scale on the identification of critical habitat patches for the maintenance of landscape connectivity. Landsc Urban Plan 83:176–186. doi:10.1016/j.landurbplan.2007.04.003 CrossRefGoogle Scholar
  39. Petit R, Vendramin GG (2007) Plant phylogeography based on organelle genes: an introduction. In: Weiss S, Ferrand N (eds) Phylogeography of Southern European refugia—evolutionary perspectives on the origins and conservation of European biodiversity. Springer, Dordrecht, pp 23–97Google Scholar
  40. Petit RJ, Duminil J, Fineschi S et al (2005) Comparative organization of chloroplast, mitochondrial and nuclear diversity in plant populations. Mol Ecol 14:689–701. doi:10.1111/j.1365-294X.2004.02410.x PubMedCrossRefGoogle Scholar
  41. Pritchard JK, Stephens M, Peter D (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedGoogle Scholar
  42. Rico Y, Lorenzo C, González-Cózatl FX et al (2008) Phylogeography and population structure of the endangered Tehuantepec jackrabbit Lepus flavigularis: implications for conservation. Conserv Genet 9:1467–1477. doi:10.1007/s10592-007-9480-2 CrossRefGoogle Scholar
  43. Rousset F (2000) Genetic differentiation between individuals. J Evol Biol 13:58–62. doi:10.1046/j.1420-9101.2000.00137.x CrossRefGoogle Scholar
  44. Scandura M, Iacolina L, Crestanello B et al (2008) Ancient versus recent processes as factors shaping the genetic variation of the European wild boar: are the effects of the last glaciation still detectable? Mol Ecol 17:1745–1762. doi:10.1111/j.1365-294X.2008.03703.x PubMedCrossRefGoogle Scholar
  45. Schlesinger WH, Clark JS, Mohan JE, Reid CD (2001) Global environmental change: effects on biodiversity. In: Soule ME, Orians G (eds) Conservation biology: research priorities for the next decade. Island Press, Washington, DC, pp 175–224Google Scholar
  46. Schwartz MK, McKelvey KS (2009) Why sampling scheme matters: the effect of sampling scheme on landscape genetic results. Conserv Genet. doi:10.1007/s10592-008-9622-1 Google Scholar
  47. Selkoe KA, Toonen RJ (2006) Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. Ecol Lett 9:615–629. doi:10.1111/j.1461-0248.2006.00889.x PubMedCrossRefGoogle Scholar
  48. Spear SF, Peterson CR, Matoq MD, Storfer A (2005) Landscape genetics of the blotched tiger salamander (Ambystoma tigrinum melanostictum). Mol Ecol 14:2553–2564. doi:10.1111/j.1365-294X.2005.02573.x PubMedCrossRefGoogle Scholar
  49. Stephens PA, Buskirk SW, del Rio CM (2007) Inference in ecology and evolution. Trends Ecol Evol 22:192–197. doi:10.1016/j.tree.2006.12.003 PubMedCrossRefGoogle Scholar
  50. Storfer A, Murphy MA, Evans JS et al (2007) Putting the “landscape” in landscape genetics. Heredity 98:128–142. doi:10.1038/sj.hdy.6800917 PubMedCrossRefGoogle Scholar
  51. Vandergast AG, Bohonak AJ, Weissman DB, Fisher RN (2007) Understanding the genetic effects of recent habitat fragmentation in the context of evolutionary history: phylogeography and landscape genetics of a southern California endemic jerusalem cricket (Orthoptera: Stenopelmatidae: Stenopelmatus). Mol Ecol 16:977–992. doi:10.1111/j.1365-294X.2006.03216.x PubMedCrossRefGoogle Scholar
  52. Vasemägi A, Primmer CR (2005) Challenges for identifying functionally important genetic variation: the promise of combining complementary research strategies. Mol Ecol 14:3623–3642. doi:10.1111/j.1365-294X.2005.02690.x PubMedCrossRefGoogle Scholar
  53. Via S (2001) Sympatric speciation in animals: the ugly duckling grows up. Trends Ecol Evol 16:381–390. doi:10.1016/S0169-5347(01)02188-7 PubMedCrossRefGoogle Scholar
  54. Wagner H, Fortin M-J (2005) Spatial analysis of landscapes: concepts and statistics. Ecology 86:1975–1987. doi:10.1890/04-0914 CrossRefGoogle Scholar
  55. Whitham TG, Bailey JK, Schweitzer JA et al (2006) A framework for community and ecosystem genetics: from genes to ecosystems. Nat Rev Genet 7:510–523. doi:10.1038/nrg1877 PubMedCrossRefGoogle Scholar
  56. Wright S (1977) Evolution and the genetics of populations. University of Chicago Press, ChicagoGoogle Scholar
  57. Wu J (2007) Scale and scaling: a cross-disciplinary perspective. In: Wu J, Hobbs RJ (eds) Key topics in landscape ecology. Cambridge University Press, Cambridge, pp 115–142Google Scholar

Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  • Niko Balkenhol
    • 1
  • Felix Gugerli
    • 2
  • Sam A. Cushman
    • 3
  • Lisette P. Waits
    • 1
  • Aurélie Coulon
    • 4
  • J. W. Arntzen
    • 5
  • Rolf Holderegger
    • 2
  • Helene H. Wagner
    • 6
  • Participants of the Landscape Genetics Research Agenda Workshop 2007
  1. 1.Department of Fish & Wildlife ResourcesUniversity of IdahoMoscowUSA
  2. 2.WSL Eidgenössische ForschungsanstaltBirmensdorfSwitzerland
  3. 3.Rocky Mountain Research StationMissoulaUSA
  4. 4.Cornell Laboratory of OrnithologyIthacaUSA
  5. 5.Research DepartmentNational Museum of Natural HistoryLeidenThe Netherlands
  6. 6.Department of Ecology and Evolutionary BiologyUniversity of TorontoMississaugaCanada

Personalised recommendations