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Landscape and ecological genomics

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Abstract

Landscape genomics is the modern version of landscape genetics, a discipline that arose approximately 10 years ago as a combination of population genetics, landscape ecology, and spatial statistics. It studies the effects of landscape variables on gene flow and other microevolutionary processes that determine genetic connectivity and variations in populations. In contrast to population genetics, it operates at the level of individual specimens rather than at the level of population samples. Another important difference between landscape genetics and genomics and population genetics is that, in the former, the analysis of gene flow and local adaptations takes quantitative account of landforms and features of the matrix, i.e., hostile spaces that separate species habitats. Landscape genomics is a part of population ecogenomics, which, along with community genomics, is a major part of ecological genomics. One of the principal purposes of landscape genomics is the identification and differentiation of various genome-wide and locus-specific effects. The approaches and computation tools developed for combined analysis of genomic and landscape variables make it possible to detect adaptation-related genome fragments, which facilitates the planning of conservation efforts and the prediction of species’ fate in response to expected changes in the environment.

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References

  1. Van Straalen, N.M. and Roelofs, D., An Introduction to Ecological Genomics, New York: Oxford Univ. Press, 2006.

    Google Scholar 

  2. Manel, S., Schwartz, M.K., Luikart, G., and Taberlet, P., Landscape genetics: combining landscape ecology and population genetics, Trends Ecol. Evol., 2003, vol. 18, no. 4, pp. 189–197.

    Article  Google Scholar 

  3. Tyutyunnik, Yu.G., About the origin and original meaning of the word “Landschaft”, Izv. Akad. Nauk, Ser. Geogr., 2004, no. 4, pp. 116–122.

    Google Scholar 

  4. Vinogradov, B.V., Osnovy landshaftnoi ekologii (Fundamentals of Landscape Ecology), Moscow: GEOS, 1998.

    Google Scholar 

  5. MacArthur, R.H. and Wilson, E.O., The Theory of Island Biogeography, Princeton: Princeton Univ. Press, 1967.

    Google Scholar 

  6. Levins, R., Some demographic and genetic consequences of environmental heterogeneity for biological control, Bull. Entomol. Soc. Am., 1969, vol. 15, pp. 237–240.

    Google Scholar 

  7. Altukhov, Yu.P., Geneticheskie protsessy v populyatsiyakh (Genetic Processes in Populations), Moscow: Akademkniga, 2003.

    Google Scholar 

  8. Holderegger, R. and Wagner, H.H., A brief guide to landscape genetics, Landscape Ecol., 2006, vol. 21, pp. 793–796.

    Article  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  10. Holderegger, R. and Wagner, H.H., Landscape genetics, BioScience, 2008, vol. 58, no. 3, pp. 199–207.

    Article  Google Scholar 

  11. McKelvey, K.S., Cushman, S.A., and Schwartz, M.K., Landscape Genetics: Spatial Complexity, Informatics, and Wildlife Conservation, Tokyo: Springer-Verlag, 2009.

    Google Scholar 

  12. Manel, S. and Segelbacher, G., Perspectives and challenges in landscape genetics, Mol. Ecol., 2009, vol. 18, pp. 1821–1822.

    Article  PubMed  Google Scholar 

  13. Schwartz, M.K., Luikart, G., McKelvey, K.S., and Cushman, S.A., Landscape Genomics: A Brief Perspectives: Spatial Complexity, Informatics, and Wildlife Conservation, Tokyo: Springer-Verlag, 2009.

    Google Scholar 

  14. Manel, S., Joost, S., Epperson, B.K., et al., Perspectives on the use of landscape genetics to detect genetic adaptive variation in the field, Mol. Ecol., 2010, vol. 19, pp. 3760–3772.

    Article  PubMed  CAS  Google Scholar 

  15. Sork, V.L. and Waits, L., Contributions of landscape genetics-approaches, insights, and future potential, Mol. Ecol., 2010, vol. 19, pp. 3489–3495.

    Article  PubMed  Google Scholar 

  16. Storfer, A., Murphy, M.A., Spear, S.F., et al., Landscape genetics: where are we now, Mol. Ecol., 2010, vol. 19, pp. 3496–3514.

    Article  PubMed  Google Scholar 

  17. Avise, J.C., Phylogeography: retrospect and prospect, J. Biogeogr., 2009, vol. 36, pp. 3–15.

    Article  Google Scholar 

  18. Wang, I.J., Recognizing the temporal distinctions between landscape genetics and phylogeography, Mol. Ecol., 2010, vol. 19, pp. 2605–2608.

    Article  PubMed  Google Scholar 

  19. Wang, I.J., Choosing appropriate genetic markers and analytical methods for testing landscape genetic hypothesis, Mol. Ecol., 2011, vol. 20, pp. 2480–2482.

    Article  Google Scholar 

  20. Ford, E.B., Ecological Genetics, London: Methuen, 1964.

    Google Scholar 

  21. Merrell, D., Ecological Genetics, Minneapolis: University of Minnesota Press, 1981.

    Google Scholar 

  22. Ecological Genetics, Real, L.A., Ed., Princeton: Princeton University Press, 1994.

    Google Scholar 

  23. Lowe, A., Harris, S., and Ashton, P., Ecological Genetics: Design, Analysis, and Application, Oxford: Blackwell, 2004.

    Google Scholar 

  24. Via, S., The ecological genetics of speciation, Am. Nat., 2002, vol. 159, pp. S1–S7.

    Article  PubMed  Google Scholar 

  25. Zhuchenko, A.A., Ekologicheskaya genetika kul’turnykh rastenii kak samostoyatel’naya nauchnaya distsiplina: Teoriya i praktika (Ecological Genetics of Cultivated Plants as an Independent Scientific Discipline: Theory and Practice), Krasnodar: Prosveshchenie-Yug, 2010.

    Google Scholar 

  26. Zhuchenko, A.A., Ecological genetics of cultivated plants: Theory and practice, in Ekologicheskaya genetika i evolyutsiya (Ecological Genetics and Evolution), Kishinev: Shtiintsa, 1987, pp. 50–73.

    Google Scholar 

  27. Inge-Vechtomov, S.G., Ecological genetics, what is it?, Sorosovskii Obrazovatel’nyi Zh., 1998, no. 2, pp. 59–65.

    Google Scholar 

  28. Antonovics, J., Toward community genetics, in Plant Resistance to Herbivores and Pathogens: Ecology, Evolution, and Genetics, Frite, R.S. and Simms, E.L., Eds., Chicago: University of Chicago Press, 1992, pp. 426–449.

    Google Scholar 

  29. Antonovics, J., Toward community genomics?, Ecology, 2003, vol. 84, no. 3, pp. 598–601.

    Article  Google Scholar 

  30. Agrawal, A.A., Community genetics: new insights into community ecology by integrating population genetics, Ecology, 2003, vol. 84, no. 3, pp. 543–544.

    Article  Google Scholar 

  31. Chase, J.M. and Knight, T.M., Community genetics: toward a synthesis, Ecology, 2003, vol. 84, no. 3, pp. 580–582.

    Article  Google Scholar 

  32. Wade, M.J., Community genetics and species interactions, Ecology, 2003, vol. 84, no. 3, pp. 583–585.

    Article  Google Scholar 

  33. Wilson, D.S. and Swenson, W., Community genetics and community selection, Ecology, 2003, vol. 84, no. 3, pp. 586–588.

    Article  Google Scholar 

  34. Johnson, M.T.J. and Stinchcombe, J.R., An emerging synthesis between community ecology and evolutionary biology, Trends Ecol. Evol., 2007, vol. 22, no. 5, pp. 250–257.

    Article  PubMed  Google Scholar 

  35. Silvertown, J., Biss, P.M., and Freeland, J., Community genetics: resource addition has opposing effects on genetic and species diversity in a 150-year experiment, Ecol. Lett., 2009, vol. 12, pp. 165–170.

    Article  PubMed  Google Scholar 

  36. Hersch-Green, E.I., Nash, E., Turley, N.E., and Johnson, M.T.J., Community genetics: what have we accomplished and where should we be going?, Philos. Trans. R. Soc., B, 2011, vol. 366, pp. 1453–1460.

    Article  Google Scholar 

  37. Collins, J.P., What can we learn from community genetics? Ecology, 2003, vol. 84, no. 3, pp. 574–577.

    Article  Google Scholar 

  38. Neuhauser, C., Andow, D.A., Heimpel, G.E., et al., Community genetics: expanding the synthesis of ecology and genetics, Ecology, 2003, vol. 84, no. 3, pp. 545–558.

    Article  Google Scholar 

  39. Ten Kate, L.P., Al-Gazali, L., Anand, S., et al., Community genetics: its definition 2010, J. Community Genet., 2010, vol. 1, pp. 19–22.

    Article  PubMed  Google Scholar 

  40. Tikhonovich, I.A., Symbiogenetics study in the system of biological education, Ekol. Genet., 2007, vol. 5, no. 1, pp. 8–17.

    Google Scholar 

  41. Inge-Vechtomov, S.G., Genetika s osnovami selektsii: Uchebnik dlya studentov vysshikh uchebnykh zavedenii (Genetics with the Basics of Breeding: Handbook for Students of Higher School), St. Petersburg: N-L, 2010.

    Google Scholar 

  42. Wade, M.J., The co-evolutionary genetics of ecological communities, Nat. Rev. Genet., 2007, vol. 8, pp. 185–195.

    Article  PubMed  CAS  Google Scholar 

  43. Vavilov, N.I., Etyudy po istorii genetiki (Etudes on the History of Genetics), Moscow: Novyi Khronograf, 2012.

    Google Scholar 

  44. Odum, E.P., Fundamentals of Ecology, Philadelphia: W.B. Saunders, 1959, 2nd ed.

    Google Scholar 

  45. Barabanova, L.V., Ecological Genetics, Ekol. Genet., 2007, vol. 5, no. 1, pp. 18–20.

    Google Scholar 

  46. Spitsyn, V.A., Ekologicheskaya genetika cheloveka (Human Ecological Genetics), Moscow: Nauka, 2008.

    Google Scholar 

  47. Lee, C.E. and Mitchell-Olds, T., Preface to the special issue: ecological and evolutionary genomics of populations in nature, Mol. Ecol., 2006, vol. 15, pp. 1193–1196.

    Article  PubMed  Google Scholar 

  48. Landry, C.R. and Aubin-Horth, N., Ecological annotation of genes and genomes through ecological genomics, Mol. Ecol., 2007, vol. 16, pp. 4419–4425.

    Article  PubMed  Google Scholar 

  49. Mitchell-Olds, T., Feder, M., and Wray, G., Evolutionary and ecological functional genomics, Heredity, 2008, vol. 100, pp. 101–102.

    Article  PubMed  CAS  Google Scholar 

  50. Whitham, T.G., DiFazio, S.P., Schweitzer, J.A., et al., Extending genomics to natural communities and ecosystems, Science, 2008, vol. 320, pp. 492–495.

    Article  PubMed  CAS  Google Scholar 

  51. Pennisi, E., Ecological genomics gets down to genes- and function, Science, 2009, vol. 326, pp. 1620–1621.

    Article  PubMed  CAS  Google Scholar 

  52. Lowry, D.B., Landscape evolutionary genomics, Biol. Lett., 2010. vol. 6, pp. 502–504. doi: 10.1098/rsbl.2009.0969

    Article  PubMed  Google Scholar 

  53. Renn, S.C.P. and Siemens, D.H., Ecological genomics-changing perspectives on Darwin’s basic concerns, Mol. Ecol., 2010, vol. 19, pp. 3025–3030.

    Article  PubMed  Google Scholar 

  54. Roelofsen, A., Broerse, J., de Cock Buning, T., and Bunders, J., Engaging with future technologies: how potential future users frame ecogenomics, Sci. Pub. Policy, 2010, vol. 37, no. 3, pp. 167–179.

    Article  Google Scholar 

  55. Roelofsen, A., Kloet, R.R., Broerse, J.E.W., et al., Guiding visions in ecological genomics: a first step to exploring the future, New Genet. Soc., 2010, vol. 29, no. 1, pp. 19–36.

    Article  Google Scholar 

  56. Stapley, J., Reger, J., Feulner, P.G.D., et al., Adaptation genomics: the next generation, Trends Ecol. Evol., 2010, vol. 25, no. 12, pp. 705–712.

    Article  PubMed  Google Scholar 

  57. Elmer, K.R. and Meyer, A., Adaptation in the age of ecological genomics: insights from parallelism and convergence, Trends Ecol. Evol., 2011, vol. 26, no. 6, pp. 298–306.

    Article  PubMed  Google Scholar 

  58. Kloet, K., de Cock Buning, T., and Bunders, J., An introduction to and a reflection on the “ecogenomics promise”, J. Integr. Environ. Sci., 2011, vol. 8, no. 1, pp. 23–38.

    Article  Google Scholar 

  59. Feder, M.E. and Mitchell-Olds, T., Evolutionary and ecological functional genomics, Nat. Rev. Genet., 2003, vol. 4, pp. 651–657.

    Article  PubMed  CAS  Google Scholar 

  60. Van Straalen, N.M. and Feder, M.E., Ecological and evolutionary functional genomics-how can it contribute to the risk assessment of chemicals?, Environ. Sci. Technol., 2012, vol. 46, pp. 3–9.

    Article  PubMed  Google Scholar 

  61. Lempe, J. and Weigel, D., Ecological genomics, from genes to ecosystems, in Research Perspectives of the Max Planck Society, 2010+, pp. 26–27. www.mpg.de/36246/bm07-Ecological.pdf

    Google Scholar 

  62. Bossdorf, O., Richards, C.L., and Pigliucci, M., Epigenetics for ecologists, Ecol. Lett., 2008, vol. 11, pp. 106–115.

    PubMed  Google Scholar 

  63. Galindo, H.M., Pfeiffer-Herbert, A.S., McManus, M.A., et al., Seascape genetics along a steep cline: using genetic patterns to test predictions of marine larval dispersal, Mol. Ecol., 2010, vol. 19, pp. 3692–3707.

    Article  PubMed  Google Scholar 

  64. Amaral, A.R., Beheregaray, L.B., Bilgmann, K., et al., Seascape genetics of a globally distributed, highly mobile marine mammal: The short-beaked common dolphin (genus Delphinus), PLoS One, 2012, vol. 7, no. 2, p. e31482. doi: 10.1371/journal.pone.0031482

    Article  PubMed  CAS  Google Scholar 

  65. Segelbacher, G., Cushman, S.A., Epperson, B.K., et al., Application of landscape genetics in conservation biology: concepts and challenges, Conserv. Genet., 2010, vol. 11, pp. 375–385.

    Article  Google Scholar 

  66. Luikart, G., England, P.R., Tallmon, D., et al., The power and promise of population genomics: from genotyping to genome typing, Nat. Rev. Genet., 2003, vol. 4, pp. 981–994.

    Article  PubMed  CAS  Google Scholar 

  67. Black, W.C., Baer, C.F., Antolin, M.F., and DuTeau, N.M., Population genomics: genome-wide sampling of insect populations, Ann. Rev. Entomol., 2001, vol. 46, pp. 441–469.

    Article  CAS  Google Scholar 

  68. Joost, S., Bonin, A., Bruford, M.W., et al., A spatial analysis method (SAM) to detect candidate loci for selection: towards a landscape genomics approach to adaptation, Mol. Ecol., 2007, vol. 16, pp. 3955–3969.

    Article  PubMed  CAS  Google Scholar 

  69. Paetkau, D., Calvert, W., Stirling, I., and Strobeck, C., Microsatellite analysis of population structure in Canadian polar bears, Mol. Ecol., 1995, vol. 4, pp. 347–354.

    Article  PubMed  CAS  Google Scholar 

  70. Pritchard, J.K., Stephens, M., and Donnelly, P., Inference of population structure using multilocus genotype data, Genetics, 2000, vol. 155, pp. 945–959.

    PubMed  CAS  Google Scholar 

  71. Guillot, G., Estoup, A., Mortier, F., and Cosson, J.F., A spatial statistical model for landscape genetics, Genetics, 2005, vol. 170, pp. 1261–1280.

    Article  PubMed  CAS  Google Scholar 

  72. Guillot, G., Mortier, F., and Estoup, A., GENELAND: a computer package for landscape genetics, Mol. Ecol. Notes, 2005, vol. 5, pp. 712–715.

    Article  CAS  Google Scholar 

  73. Guillot, G., Santos, F., and Estoup, A., Analyzing georeferenced population genetics data with GENELAND: a new algorithm to deal with null alleles and a friendly graphical user interface, Bioinformatics, 2008, vol. 24, pp. 1406–1407.

    Article  PubMed  CAS  Google Scholar 

  74. Dyer, R.J., Nason, J.D., and Garrick, R.C., Landscape modeling of gene flow: improved power using conditional genetic distance derived from the topology of population networks, Mol. Ecol., 2010, vol. 19, pp. 3746–3759.

    Article  PubMed  Google Scholar 

  75. Landguth, E.L., Cushman, S.A., Schwartz, M.K., et al., Quantifying the lag time to detect barriers in landscape genetics, Mol. Ecol., 2010, vol. 19, pp. 4179–4191.

    Article  Google Scholar 

  76. Jaquiéry, J., Broquet, T., Hirzel, A.H., et al., Inferring landscape effects on dispersal from genetic distances: how far can we go?, Mol. Ecol., 2011, vol. 20, pp. 692–705.

    Article  PubMed  Google Scholar 

  77. Spear, S.R., Balkenhol, N., Fortin, M.-J., et al., Use of resistance surfaces for landscape genetic studies: Considerations for parameterization and analysis, Mol. Ecol., 2010, vol. 19, pp. 3576–3591. doi: 10.1111/j.1365-294X.2010.04657.x

    Article  PubMed  Google Scholar 

  78. Cushman, S.A., McKelvey, K.S., Hayden, J., and Schwartz, M.K., Gene flow in complex landscapes: Testing multiple hypotheses with causal modeling, Am. Nat., 2006, vol. 168, pp. 486–499.

    Article  PubMed  Google Scholar 

  79. Cushman, S.A. and Landguth, E.L., Spurious correlations and inference in landscape genetics, Mol. Ecol., 2010, vol. 19, pp. 3592–3602.

    Article  PubMed  Google Scholar 

  80. Epperson, B.K., McRae, B.H., Scribner, K., et al., Utility of computer simulations in landscape genetics, Mol. Ecol., 2010, vol. 19, pp. 3549–3564.

    Article  PubMed  Google Scholar 

  81. Murphy, M.A., Evans, J.S., Cushman, S.A., and Storfer, A., Representing genetic variation as continuous surfaces: an approach for identifying spatial dependency in landscape genetic studies, Ecography, 2008, vol. 31, pp. 685–697.

    Article  Google Scholar 

  82. Bijlsma, R., Loeschcke, V.N., and Ouborg, N.J., Editorial preface, Conserv. Genet., 2010, vol. 11, p. 347.

    Article  Google Scholar 

  83. Allendorf, F.W., Hohenlohe, P.A., and Luikart, G., Genomics and the future of conservation genetics, Nat. Rev. Genet., 2010, vol. 11, pp. 697–709.

    Article  PubMed  CAS  Google Scholar 

  84. Avise, J.C., Perspective: conservation genetics enters the genomics era, Conserv. Genet., 2010, vol. 11, pp. 665–669. DOI 10.1007/s10592-009-0006-y

    Article  Google Scholar 

  85. Ouborg, N.J., Angeloni, F., and Vergeer, P., An essay on the necessity and feasibility of conservation genomics, Conserv. Genet., 2010, vol. 11, pp. 643–653.

    Article  Google Scholar 

  86. Ouborg, N.J., Pertoldi, C., Loeschcke, V., et al., Conservation genetics in transition to conservation genomics, Trends Genet., 2010, vol. 26, pp. 177–187.

    Article  PubMed  CAS  Google Scholar 

  87. Ouborg, N.J., Vergeer, P., and Mix, C., The rough edges of the conservation genetics paradigm for plants, J. Ecol., 2006, vol. 94, pp. 1233–1248.

    Article  Google Scholar 

  88. Altukhov, Yu.P., Intraspecies genetic diversity: monitoring, conservation, and management, Russ. J. Genet., 1995, vol. 31, no. 10, pp. 1333–1357.

    CAS  Google Scholar 

  89. Lande, R., Genetics and demography in biological conservation, Science, 1988, vol. 241, pp. 1455–1460.

    Article  PubMed  CAS  Google Scholar 

  90. Caughley, G., Directions in conservation biology, J. Anim. Ecol., 1994, vol. 63, pp. 215–244.

    Article  Google Scholar 

  91. Clarke, G.M. and Young, A.G., Introduction: genetics, demography and the conservation of fragmented populations, in Genetics, Demography and Viability of Fragmented Populations, Young, A.G. and Clarke, G.M., Eds., Cambridge: Cambridge University Press, 2000, pp. 1–6.

    Chapter  Google Scholar 

  92. Zablotskii, M.A. and Zablotskaya, M.M., Perspectives of the further works on bison restoration in the Soviet Union, in Pervoe vsesoyuznoe soveshchanie po problemam zookul’tury (First All-Union Conference on the Problems of Zoocultures) (Proc. Conf.), Moscow, 1986, part 2, pp. 29–31.

    Google Scholar 

  93. Frankham, R., Where are we in conservation genetics and where do we need to go?, Conserv. Genet., 2010, vol. 11, pp. 661–663.

    Article  Google Scholar 

  94. Beaumont, M.A. and Balding, D.J., Identifying adaptive genetic divergence among populations from genome scans, Mol. Ecol., 2004, vol. 13, pp. 969–980.

    Article  PubMed  CAS  Google Scholar 

  95. Bakkenes, M., Alkemade, J.R.M., Ihle, F., et al., Assessing effects of forecasted climatic change on the diversity and distribution of European higher plants for 2050, Global Change Biol., 2002, vol. 8, pp. 390–407.

    Article  Google Scholar 

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  1. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia

    E. Ya. Tetushkin

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Original Russian Text © E.Ya. Tetushkin, 2013, published in Genetika, 2013, Vol. 49, No. 10, pp. 1133–1148.

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Tetushkin, E.Y. Landscape and ecological genomics. Russ J Genet 49, 985–998 (2013). https://doi.org/10.1134/S1022795413090111

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