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Landscape Ecology

, Volume 21, Issue 6, pp 809–820 | Cite as

Integrating patterns across multiple genetic markers to infer spatial processes

  • Robert G. LattaEmail author
Research Article

Abstract

Landscape geneticists can take considerable advantage of differences in the action of evolutionary forces (mutation, migration, selection, and drift) on different loci within the genome. Appropriate comparisons among loci allow researchers to isolate and study the effects of these processes. For example, the organelles are typically inherited maternally (but occasionally paternally), and so will experience migration only when females or seeds disperse (males or pollen in the paternally inherited organelles). Thus, the comparison with biparentally inherited loci allows inferences about the differential migration rates of male vs. female animals or of seeds vs. pollen in plants. Conversely, all biparentally inherited nuclear loci should experience the same levels of migration and drift. Thus, loci that show unusually large levels of variation across the landscape (as compared with the bulk of loci) may be reflecting the action of spatially varying natural selection (local adaptation). Such comparisons are conceptually straightforward, but are complicated by the high intrinsic variability of stochastic neutral processes. Careful statistical analysis is needed to avoid over-interpreting differences among loci. Inferences will be most robust when both genetic and non-genetic data can be integrated, and the collaboration of landscape ecologists with geneticists promises to be particularly fruitful.

Keywords

Coalescent Fst Migration-Drift Equilibrium Ponderosa Pine Qst Selection 

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References

  1. Allendorf, F.W., Seeb, L.W. 2000Concordance of genetic divergence among sockeye salmon populations at allozymenuclear DNA and mitochondrial DNA markersEvolution54640651PubMedCrossRefGoogle Scholar
  2. Austerlitz, F., Dick, C.W., Dutech, C., Klein, E.K., Oddou-Muratorio, S., Smouse, P.E., Sork, V.L. 2004Using genetic markers to estimate the pollen dispersal curveMolecular Ecology13937954PubMedCrossRefGoogle Scholar
  3. Beaumont, M.A., Balding, D.J. 2004Identifying adaptive genetic divergence among populations from genome scansMolecular Ecology13969980PubMedCrossRefGoogle Scholar
  4. Beaumont, M.A., Nichols, R.A. 1996Evaluating loci for use in the genetic analysis of population structureProceedings of the Royal Society of London Series B26316191626Google Scholar
  5. Black, W.C.,IV, Baer, C.F., Antolin, M.F., DuTeau, N.M. 2001Population genomics: Genome-wide sampling of insect populationsAnnual Review of Entomology46441469PubMedCrossRefGoogle Scholar
  6. Conkle, M.T., Critchfield, W.B. 1988Genetic variation and hybridization of ponderosa pineBaumgartner, D.M.Lotan, J.E. eds. Ponderosa Pine: the Species and its ManagementWashington State Univ. PressPullman, Washington, USA2743Google Scholar
  7. Crandall, K.A., Bininda-Emonds, O.R.P., Mace, G.M., Wayne, R.K. 2000Considering evolutionary processes in conservation biologyTrends in Ecology and Evolution15290295PubMedCrossRefGoogle Scholar
  8. Innocentis, S., Sola, L., Cataudella, S., Bentzen, P. 2001Allozyme and microsatellite loci provide discordant estimates of population differentiation in the endangered dusky grouper (Epinephelus marginatus) within the Mediterranean SeaMolecular Ecology1021632175CrossRefGoogle Scholar
  9. Dhuyvetter, H., Gaublomme, E., Desender, K. 2004Genetic differentiation and local adaptation in the salt-marsh beetle Pogonus chalceus: a comparison between allozyme and microsatellite lociMolecular Ecology1310651074PubMedCrossRefGoogle Scholar
  10. Dong, J., Wagner, D.B. 1994Paternally inherited chloroplast polymorphism in Pinus: estimation of diversity and population subdivision and tests of disequilibrium with a maternally inherited mitochondrial polymorphismGenetics13611871194PubMedGoogle Scholar
  11. Drake, J.W., Charlesworth, B., Charlesworth, D., Crow, J.F. 1998Rates of spontaneous mutationGenetics14816671686PubMedGoogle Scholar
  12. Eanes, W. 1999Analysis of selection on enzyme polymorphismsAnnual Review of Ecology and Systematics30301326CrossRefGoogle Scholar
  13. Ennos, R.A. 1994Estimating the relative rates of pollen and seed migration among plant populationsHeredity72250259Google Scholar
  14. Ennos, R.A., Sinclair, W.T., Hu, X.-S., Langdon, A. 1999Using organelle markers to elucidate the history, ecology and evolution of plant populationsHollingsworth, P.M.Bateman, R.M.Gornall, R.J. eds. Molecular Systematics and Plant EvolutionTaylor and FrancisLondon UK119Google Scholar
  15. Estoup, A., Wilson, I.J., Sullivan, C., Cornuet, J.M., Moritz, C. 2001Inferring population history from microsatellite and enzyme data in serially introduced cane toads, Bufo marinus Genetics15916711687PubMedGoogle Scholar
  16. Excoffier, L., Novembre, J., Schneider, S. 2000SIMCOAL: A general coalescent program for the simulation of molecular data in interconnected populations with arbitrary demographyJournal of Heredity91506510PubMedCrossRefGoogle Scholar
  17. Falconer, D.S., MacKay, T.F.C. 1996Introduction to Quantitative GeneticsLongmanNew York, New York, USAGoogle Scholar
  18. Hamrick, J.L., Godt, M.J., Sherman-Broyles, S.L. 1992Factors influencing levels of genetic diversity in woody plant speciesAdams, W.T.Strauss, S.H.Copes, D.L.Griffen, A.R. eds. Population Genetics of Forest TreesKluwerBoston, Massachusetts, USA95124Google Scholar
  19. Hedrick, P.W. 1999Highly variable loci and their interpretation in evolution and conservationEvolution53313318CrossRefGoogle Scholar
  20. Holderegger, R. 2006The meaning of genetic diversityLandscape Ecol.21797807Google Scholar
  21. Hong, Y.P., Hipkins, V.D., Strauss, S.H. 1994Chloroplast DNA diversity among trees, populations and species in the California closed cone pines (Pinus radiata, P.muricata and P. attenuata)Genetics13511871196Google Scholar
  22. Hudson, R.R. 1990Gene genealogies and the coalescent processOxford Reviews in Evolutionary Biology7144Google Scholar
  23. Jaramillo-Correa, J.P., Beaulieu, J., Bousquet, J. 2001Contrasting evolutionary forces driving population structure at expressed sequence tag polymorphisms, allozymes and quantitative traits in white spruceMolecular Ecology1027292740PubMedCrossRefGoogle Scholar
  24. Johansen, A.D., Latta, R.G. 2003Mitochondrial haplotype distribution, seed dispersal and patterns of post glacial expansion of ponderosa pineMolecular Ecology12293298PubMedCrossRefGoogle Scholar
  25. Karl, S.A., Avise, J.C. 1992Balancing selection at allozyme loci in oysters: implications from nuclear RFLP'sScience256100102PubMedGoogle Scholar
  26. Kohn, M.H., Pelz, H.-J., Wayne, R.K. 2000Natural selection mapping of the warfarin resistance geneProceedings of the National Academy of Sciences USA9779117915CrossRefGoogle Scholar
  27. Lascoux, M., Palme, A.E., Cheddadi, R., Latta, R.G. 2004Impact of the Ice Ages on the genetic structure of trees and shrubsPhilosophical Transactions of the Royal Society359197207CrossRefGoogle Scholar
  28. Latta, R.G. 2004Gene flow and adaptive population divergenceNew Phytologist1516368Google Scholar
  29. Latta, R.G., Mitton, J.B. 1997A comparison of population structure across four classes of gene marker in limber pineGenetics14611531163PubMedGoogle Scholar
  30. Latta, R.G., Mitton, J.B. 1999Historical separation and present gene flow through a zone of secondary contact in ponderosa pineEvolution53769776CrossRefGoogle Scholar
  31. Latta, R.G., Linhart, Y.B., Fleck, D., Elliot, M. 1998Direct and indirect estimates of seed versus pollen movement in ponderosa pineEvolution526167CrossRefGoogle Scholar
  32. Normand, T., Bourguet, D., Guillemaud, T., Raymond, M. 1999Tracking the evolution of insecticide resistance in the mosquito Culex pipiens Nature400861864CrossRefGoogle Scholar
  33. Lewontin, R.C. 1991Twenty-five years ago in Genetics. Electrophoresis in the development of evolutionary genetics: Milestone or millstone?Genetics128657662PubMedGoogle Scholar
  34. Lewontin, R.C., Krakauer, J. 1973Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphismsGenetics74175195PubMedGoogle Scholar
  35. Lynch, M., Pfrender, M., Spitze, K., Lehman, N., Hicks, J., Allen, D., Latta, L., Ottene, M., Bogue, F., Colbourn, J. 1999The quantitative and molecular genetic architecture of a subdivided speciesEvolution53100110CrossRefGoogle Scholar
  36. Manel, S., Schwartz, M.K., Luikhart, G., Taberlet, P. 2003Landscape genetics: combining landscape ecology and population geneticsTrends in Ecology and Evolution18189197CrossRefGoogle Scholar
  37. McCauley, D.E. 1994Contrasting the distribution of chloroplast DNA and allozyme polymorphism among local populations of Silene alba: implications for studies of gene flow in plantsProceedings of the National Academy of Sciences USA9181278131CrossRefGoogle Scholar
  38. McCauley, D.E., Stevens, J.E., Peroni, P.A., Raveill, J.A. 1996The spatial distribution of chloroplast DNA and allozyme polymorphisms within a population of Silene alba (Caryophyllaceae)American Journal of Botany83727731CrossRefGoogle Scholar
  39. McKay, J.K., Latta, R.G. 2002Adaptive population divergence: Markers, QTL and traitsTrends in Ecology and Evolution17285291CrossRefGoogle Scholar
  40. Merilä, J., Crnokrak, P. 2001Comparison of genetic differentiation at marker loci and quantitative traitsJournal of Evolutionary Biology14892903CrossRefGoogle Scholar
  41. Milligan, B.G. 1991Chloroplast DNA diversity within and among populations of Trifolium pratense Current Genetics19411416CrossRefGoogle Scholar
  42. Mitton, J.B., Duran, K.L. 2004Genetic variation in piñon pinePinus edulisassociated with summer precipitationMolecular Ecology1312591264PubMedCrossRefGoogle Scholar
  43. Mitton, J.B., Kreiser, B.R., Latta, R.G. 2000Glacial refugia of limber pine (Pinus flexilis James) inferred from the population structure of mitochondrial DNAMolecular Ecology99197PubMedCrossRefGoogle Scholar
  44. Neigel, J.E. 1997A comparison of alternative strategies for estimating gene flow from genetic markersAnnual Review of Ecology and Systematics28105128CrossRefGoogle Scholar
  45. Niebling, C.R., Conkle, M.T. 1990Diversity of Washoe pine and comparisons with allozymes of ponderosa pine racesCanadian Journal of Forest Research20298308CrossRefGoogle Scholar
  46. Nordborg, M. 2001Coalescent theoryBalding, D.J.Bishop, M.Cannings, C. eds. Handbook of Statistical GeneticsJohn WileyNew York, New York, USA179238Google Scholar
  47. Oakshott, J.G., Gibson, J.B., Anderson, P.R., Knibb, W.R., Anderson, D.G., Chambers, G.K. 1982Alcohol dehydrogenase and glycerol-3-phosphate dehydrogenase clines in Drosopholia melanogaster on different continentsEvolution368696CrossRefGoogle Scholar
  48. Oddou-Muratorio, S., Petit, R.J., Le Guerroue, B., Guesnet, D., Demesure, B. 2001Pollen- versus seed-mediated gene flow in a scattered forest tree speciesEvolution5511231135PubMedCrossRefGoogle Scholar
  49. Pannell, J.R., Dorken, M.E. 2006Colonization as a common denominator in plant metapopulations: effects on genetic diversity and sexual systemsLandsc. Ecol.21837847Google Scholar
  50. Petit, R.J., Kremer, A., Wagner, D.B. 1993Finite island model for organelle and nuclear genes in plantsHeredity71630641Google Scholar
  51. Petit, E., Balloux, F., Excoffier, L. 2002Mammalian population genetics: why not Y?Trends in Ecology and Evolution172833CrossRefGoogle Scholar
  52. Podolsky, R.H., Holtsford, T.P. 1995Population structure of morphological traits in Clarkia dudleyana I. Comparison of F st between allozymes and morphological traitsGenetics140733744PubMedGoogle Scholar
  53. Pogson, G.H., Mesa, K.A., Boutilier, R.G. 1995Genetic population structure and gene flow in the Atlantic cod Gadus morhua: A comparison of allozyme and nuclear RFLP lociGenetics139375385PubMedGoogle Scholar
  54. Powers, D.A., Smith, M., Gonzalez-Villasenor, I., DiMichele, L., Crawford, D., Bernardi, G., Lauerman, T. 1993A multidisciplinary approach to the selectionist/neutralist controversy using the model teleostFundulus heteroclitusFutuyma, D.Antonovics, J. eds. Oxford Surveys in Evolutionary BiologyOxford University PressOxford, UK49109Google Scholar
  55. Rehfeldt, G.E., Ying, C.C., Spittlehouse, D.L., Hamilton, D.A.,Jr. 1999Genetic responses to climate in Pinus contorta: niche breadthclimate change and reforestationEcological Monographs69375407CrossRefGoogle Scholar
  56. Rice, S.H. 2004Evolutionary Theory: Mathematical and Conceptual FoundationsSinauerSunderland, Massachusetts, USAGoogle Scholar
  57. Richardson, B.A., Brunsfeld, S.J., Klopfenstein, N.B. 2002DNA from bird-dispersed seed and wind-disseminated pollen provides insights into postglacial colonization and population genetic structure of whitebark pine (Pinus albicaulis)Molecular Ecology11215227PubMedCrossRefGoogle Scholar
  58. Richardson, D.M. 1998Ecology and Biogeography of PinusCambridge University PressCambridge, UKGoogle Scholar
  59. Rosenberg, N.A., Nordborg, M. 2002Genealogical trees, coalescent theory, and the analysis of genetic polymorphismsNature Reviews Genetics3380390PubMedCrossRefGoogle Scholar
  60. Ross, K.G. 2001How to measure dispersal: the genetic approach. The example of fire antsClobert, J.Danchin, E.Dhondt, A.A.Nichols, J.D. eds. DispersalOxford University PressNew York, New York, USA2942Google Scholar
  61. Scribner, K.T., Arntzen, J.W., Burke, T. 1994Comparative analysis of intra- and interpopulation genetic diversity in Bufo bufousing allozymesingle-locus microsatelliteminisatellite and multilocus minisatellite dataMolecular Biology and Evolution11737748PubMedGoogle Scholar
  62. Slatkin, M. 1995A measure of population subdivision based on microsatellite allele frequenciesGenetics139457462PubMedGoogle Scholar
  63. Slatkin, M. 2001A coalescent view of population structureSing, R.SKrimbas, K.B. eds. Evolutionary Genetics: From Molecules to MorphologyCambridge University PressCambridge, UK418429Google Scholar
  64. Sork, V.L., Smouse, P.E. 2006Genetic analysis of landscape connectivity in tree populationsLandsc. Ecol.21821836Google Scholar
  65. Spitze, K. 1993Population structure in Daphnia obtusa: quantitative genetic and allozyme variationGenetics135367374PubMedGoogle Scholar
  66. Squirrell, J., Hollingsworth, P.M., Bateman, R.M., Dickson, J.H., Light, M.H.S., MacConaill, M., Tebbitt, M.C. 2001Partitioning and diversity of nuclear and organelle markers in native and introduced populations of Epipactis helleborine (Orchidaceae)American Journal of Botany8814091418Google Scholar
  67. Storz, J.F. 2005Using genome scans of DNA variability to infer the genetic basis of adaptive population divergenceMolecular Ecology14671688PubMedCrossRefGoogle Scholar
  68. Vitalis, R., Dawson, K., Boursot, P. 2001Interpretation of variation across marker loci as evidence of selectionGenetics15818111823PubMedGoogle Scholar
  69. Wagner, D.B. 1992Nuclearchloroplast and mitochondrial DNA polymorphisms as biochemical markers in population genetic analyses of forest treesAdams, W.T.Strauss, S.H.Copes, D.L.Griffen, A.R. eds. Population Genetics of Forest TreesKluwerBoston, Massachusetts, USA373390Google Scholar
  70. Watt, W.B., Wheat, C.W., Meyer, E.H., Martin, J.-F. 2003Adaptation at specific loci. VII. Natural selection, dispersal and the diversity of molecular – functional variation patterns among butterfly species complexes (Colias: LepidopteraPieridae)Molecular Ecology1212651275PubMedCrossRefGoogle Scholar
  71. Weir, B.S. 1991Genetic Data AnalysisSinauerSunderland, Massachusetts, USAGoogle Scholar
  72. Whitlock, M.C., McCauley, D.E. 1999Indirect measures of gene flow and migration F st≠ 1/(4Nm+1)Heredity82117125PubMedCrossRefGoogle Scholar
  73. Wright, S. 1951The genetical structure of populationsAnnals of Eugenics15323354Google Scholar
  74. Wright, S. 1952The theoretical variance within and among subdivisions of a population that is in a steady stateGenetics37312321PubMedGoogle Scholar
  75. Zouros, E. 2000The exceptional mitochondrial DNA system of the mussel family MytilidaeGenes and Genetic Systems75313318PubMedCrossRefGoogle Scholar

Copyright information

© Springer 2006

Authors and Affiliations

  1. 1.Department of BiologyDalhousie UniversityHalifax, Nova ScotiaCanada

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