Climate change, genetic markers and species distribution modelling

Journal of Biogeography

Volumn 42, Issue 9, 2015, Pages 1577-1585

  Gotelli, Nicholas J ^a   Stanton Geddes, John ^a  

^a UNIVERSITY OF VERMONT   (United States)

Author keywords

Climate change; Genetic clusters; Genetic markers; MaxEnt; MaxLike; Species distribution modelling; Species range shifts

Indexed keywords

EID: 84938744725     PISSN: 03050270     EISSN: 13652699     Source Type: Journal    
DOI: 10.1111/jbi.12562     Document Type: Note

References (90)

1. Araújo, M.B. & Luoto, M. (2007) The importance of biotic interactions for modelling species distributions under climate change. Global Ecology and Biogeography, 16, 743-753.
2. Atkins, K.E. & Travis, J.M.J. (2010) Local adaptation and the evolution of species' ranges under climate change. Journal of Theoretical Biology, 266, 449-457.
3. Bahn, V. & McGill, B.J. (2007) Can niche-based distribution models outperform spatial interpolation? Global Ecology and Biogeography, 16, 733-742.
4. Beaumont, L.J., Hughes, L. & Poulsen, M. (2005) Predicting species distributions: use of climatic parameters in BIOCLIM and its impact on predictions of species' current and future distributions. Ecological Modelling, 186, 250-269.
5. Blois, J.L., Zarnetske, P.L., Fitzpatrick, M.C. & Finnegan, S. (2013) Climate change and the past, present & future of biotic interactions. Science, 341, 499-504.
6. Bonin, A.E.D. & Manel, S. (2007) Statistical analysis of amplified fragment length polymorphism data: a toolbox for molecular ecologists and evolutionists. Molecular Ecology, 16, 3737-3758.
7. Broman, K.W., Murray, J.C., Sheffield, V.C., White, R.L. & Weber, J.L. (1998) Comprehensive human genetic maps: individual and sex-specific variation in recombination. American Journal of Human Genetics, 63, 861-869.
8. Burrows, M.T., Schoeman, D.S., Buckley, L.B., Moore, P., Poloczanska, E.S., Brander, K.M., Brown, C., Bruno, J.F., Duarte, C.M., Halpern, B.S., Holding, J., Kappel, C.V., Kiessling, W., O'Connor, M.I., Pandolfi, J.M., Parmesan, C., Schwing, F.B., Sydeman, W.J. & Richardson, A.J. (2011) The pace of shifting climate in marine and terrestrial ecosystems. Science, 334, 652-655.
9. Burrows, M.T., Schoeman, D.S., Richardson, A.J. et al. (2014) Geographical limits to species-range shifts are suggested by climate velocity. Nature, 507, 492.
10. Collins, W.D., Bitz, C.M., Blackmon, M.L., Bonan, G.B., Bretherton, C.S., Carton, J.A., Chang, P., Doney, S.C., Hack, J.J., Henderson, T.B., Kiehl, J.T., Large, W.G., McKenna, D.S., Santer, B.D. & Smith, R.D. (2006) The community climate system model version 3 (CCSM3). Journal of Climate, 19, 2122-2143.
11. Coop, G. & Ralph, P. (2012) Patterns of neutral diversity under general models of selective sweeps. Genetics, 192, 205-240.
12. Coop, G., Pickrell, J.K., Novembre, J., Kudaravalli, S., Li, J., Absher, D., Myers, R.M., Cavalli-Sforza, L.L., Feldman, M.W. & Pritchard, J.K. (2009) The role of geography in human adaptation. PLoS Genetics, 5, e1000500.
13. 2 and climate change: results from six dynamic global vegetation models. Global Change Biology, 7, 357-373.
14. D'Amen, M., Zimmermann, N.E. & Pearman, P.B. (2013) Conservation of phylogeographic lineages under climate change. Global Ecology and Biogeography, 22, 93-104.
15. Diggle, P.J. & Ribeiro, P.J. (2007) Model-based geostatistics. Springer-Verlag, New York.
16. Dyer, R.J. (2013) gstudio: analyses and functions related to the spatial analysis of genetic marker data. Available at: https://github.com/dyerlab/ (last accessed 18 June 2015).
17. Dyer, R.J. & Nason, J.D. (2004) Population graphs: the graph theoretic shape of genetic structure. Molecular Ecology, 13, 1713-1727.
18. Dyer, R.J., Nason, J.D. & Garrick, R.C. (2010) Landscape modelling of gene flow: improved power using conditional genetic distance derived from the topology of population networks. Molecular Ecology, 19, 3746-3759.
19. Elith, J. & Leathwick, J.R. (2009) Species distribution models: ecological explanation and prediction across space and time. Annual Review of Ecology, Evolution, and Systematics, 40, 677-697.
20. Elith, J., Phillips, S.J., Hastie, T., Dudík, M., Chee, Y.E. & Yates, C.J. (2011) A statistical explanation of MaxEnt for ecologists. Diversity and Distributions, 17, 43-57.
21. Elshire, R.J., Glaubitz, J.C., Sun, Q., Poland, J.A., Kawamoto, K., Buckler, E.S. & Mitchell, S.E. (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE, 6, e19379-e19379.
22. Etterson, J.R. (2004) Evolutionary potential of Chamaecrista fasciculata in relation to climate change. I. Clinal patterns of selection along an environmental gradient in the great plains. Evolution, 58, 1446-1458.
23. Fenster, C.B., Vekemans, X. & Hardy, O.J. (2003) Quantifying gene flow from spatial genetic structure data in a metapopulation of Chamaecrista fasciculata (Leguminosae). Evolution, 57, 995-1007.
24. Fithian, W. & Hastie, T. (2013) Finite-sample equivalence in statistical models for presence-only data. The Annals of Applied Statistics, 7, 1917-1939.
25. Fitzpatrick, M.C. & Keller, S.R. (2015) Ecological genomics meets community-level modeling of biodiversity: mapping the genomic landscape of current and future environmental adaptation. Ecology Letters, 18, 1-16.
26. Fitzpatrick, M.C., Gotelli, N.J. & Ellison, A.M. (2013) MaxEnt versus MaxLike: empirical comparisons with ant species distributions. Ecosphere, 4, Article 55.
27. Gao, H., Bryc, K. & Bustamante, C. (2011) On identifying the optimal number of population clusters via the deviance information criterion. PLoS ONE, 6, e21014.
28. Gaston, K.J. (2009) Geographic range limits: achieving synthesis. Proceedings of the Royal Society B: Biological Sciences, 276, 1395-1406.
29. Gilbert, K.J., Andrew, R.L., Bock, D.G., Franklin, M.T., Kane, N.C., Moore, J.-S., Moyers, B.T., Renaut, S., Rennison, D.J., Veen, T. & Vines, T.H. (2012) Recommendations for utilizing and reporting population genetic analyses: the reproducibility of genetic clustering using the program structure. Molecular Ecology, 21, 4925-4930.
30. Gonzalez, S.C., Soto-Centeno, J.A. & Reed, D.L. (2011) Population distribution models: species distributions are better modeled using biologically relevant data partitions. BMC Ecology, 11, 20.
31. Goodchild, M.E. (2003) Geographic information science and systems for environmental management. Annual Review of Environment and Resources, 28, 493-519.
32. Gotelli, N.J. & Ellison, A.M. (2012) A primer of ecological statistics, 2nd edn. Sinauer Associates, Sunderland, MA.
33. Gotelli, N.J., Anderson, M.J., Arita, H.T. et al. (2009) Patterns and causes of species richness: a general simulation model for macroecology. Ecology Letters, 12, 873-886.
34. Gugerli, F., Englisch, T., Niklfeld, H., Tribsch, A., Mirek, Z., Ronikier, M., Zimmermann, N.E., Holderegger, R. & Taberlet, P. (2008) Relationships among levels of biodiversity and the relevance of intraspecific diversity in conservation - a project synopsis. Perspectives in Plant Ecology, Evolution and Systematics, 10, 259-281.
35. Guillot, G., Renaud, S., Ledevin, R., Michaux, J. & Claude, J. (2012) A unifying model for the analysis of phenotypic, genetic and geographic data. Systematic Biology, 61, 897-911.
36. Hampe, A. & Petit, R.J. (2005) Conserving biodiversity under climate change: the rear edge matters. Ecology Letters, 8, 461-467.
37. Hampe, A., El Masri, L. & Petit, R.J. (2010) Origin of spatial genetic structure in an expanding oak population. Molecular Ecology, 19, 459-471.
38. Hancock, A.M., Brachi, B., Faure, N., Horton, M.W., Jarymowycz, L.B., Sperone, F.G., Toomajian, C., Roux, F. & Bergelson, J. (2011) Adaptation to climate across the Arabidopsis thaliana genome. Science, 334, 83-86.
39. Hansen, J., Kharecha, P., Sato, M., Masson-Delmotte, V., Ackerman, F., Beerling, D.J., Hearty, P.J., Hoegh-Guldberg, O., Hsu, S.L., Parmesan, C., Rockstrom, J., Rohling, E.J., Sachs, J., Smith, P., Steffen, K., Van Susteren, L., von Schuckmann, K. & Zachos, J.C. (2013) Assessing "dangerous climate change": required reduction of carbon emissions to protect young people, future generations and nature. PLoS ONE, 8, e81648.
40. Hanski, I. & Ovaskainen, O. (2000) The metapopulation capacity of a fragmented landscape. Nature, 404, 755-758.
41. Hargreaves, A.L., Samis, K.E. & Eckert, C.G. (2014) Are species' range limits simply niche limits writ large? A review of transplant experiments beyond the range. The American Naturalist, 183, 157-173.
42. Hastie, T. & Fithian, W. (2013) Inference from presence-only data; the ongoing controversy. Ecography, 36, 864-867.
43. Hereford, J. (2009) A quantitative survey of local adaptation and fitness trade-offs. The American Naturalist, 173, 579-588.
44. Hernandez, P.A., Graham, C.H., Master, L.L. & Albert, D.L. (2006) The effect of sample size and species characteristics on performance of different species distribution modeling methods. Ecography, 29, 773-785.
45. James, F.C. (1971) Ordinations of habitat relationships among breeding birds. The Wilson Bulletin, 83, 215-236.
46. Jay, F., Manel, S., Alvarez, N., Durand, E.Y., Thuiller, W., Holderegger, R., Taberlet, P. & François, O. (2012) Forecasting changes in population genetic structure of alpine plants in response to global warming. Molecular Ecology, 21, 2354-2368.
47. Joost, S., Bonin, A., Bruford, M.W., Despres, L., Connord, C., Erhardt, G. & Taberlet, P. (2007) A spatial analysis method (SAM) to detect candidate loci for selection: towards a landscape genomics approach to adaptation. Molecular Ecology, 16, 3955-3969.
48. Keller, S.R. & Taylor, D.R. (2010) Genomic admixture increases fitness during a biological invasion. Journal of Evolutionary Biology, 23, 1720-1731.
49. Leimu, R. & Fischer, M. (2008) A meta-analysis of local adaptation in plants. PLoS ONE, 3, e4010.
50. Linhart, Y.B. & Grant, M.C. (1996) Evolutionary significance of local genetic differentiation in plants. Annual Review of Ecology and Systematics, 27, 237-277.
51. Loarie, S.R., Duffy, P.B., Hamilton, H., Asner, G.P., Field, C.B. & Ackerly, D.D. (2009) The velocity of climate change. Nature, 462, 1052-1055.
52. Mardis, E.R. (2011) A decade's perspective on DNA sequencing technology. Nature, 470, 198-203.
53. Marsico, T.D. & Hellmann, J.J. (2009) Dispersal limitation inferred from an experimental translocation of Lomatium (Apiaceae) species outside their geographic ranges. Oikos, 118, 1783-1792.
54. McCullagh, P. & Nelder, J.A. (1989) Generalized linear models, 2nd edn. Chapman & Hall, London.
55. McGarigal, K., Cushman, S. & Stafford, S. (2000) Multivariate statistics for wildlife and ecology research. Springer-Verlag, New York.
56. Merow, C. & Silander, J.A. (2014) A comparison of Maxlike and Maxent for modelling species distributions. Methods in Ecology and Evolution, 5, 215-225.
57. Merow, C., Smith, M.J. & Silander, J.A. (2013) A practical guide to MaxEnt for modeling species' distributions: what it does, and why inputs and settings matter. Ecography, 36, 1058-1069.
58. Miller, J.A. (2014) Virtual species distribution models: using simulated data to evaluate aspects of model performance. Progress in Physical Geography, 38, 117-128.
59. Neteler, M., Bowman, M.H., Landa, M. & Metz, M. (2012) GRASS GIS: a multi-purpose open source GIS. Environmental Modelling & Software, 31, 124-130.
60. Newbold, T., Reader, T., El-Gabbas, A., Berg, W., Shohdi, W.M., Zalat, S., El Din, S.B. & Gilbert, F. (2010) Testing the accuracy of species distribution models using species records from a new field survey. Oikos, 119, 1326-1334.
61. Olesen, J.E. & Bindi, M. (2002) Consequences of climate change for European agricultural productivity, land use and policy. European Journal of Agronomy, 16, 239-262.
62. Pagel, J. & Schurr, F.M. (2012) Forecasting species ranges by statistical estimation of ecological niches and spatial population dynamics. Global Ecology and Biogeography, 21, 293-304.
63. Parmesan, C. (2006) Ecological and evolutionary responses to recent climate change. Annual Review of Ecology, Evolution, and Systematics, 37, 637-669.
64. Pearce, J. & Ferrier, S. (2000) Evaluating the predictive performance of habitat models developed using logistic regression. Ecological Modelling, 133, 225-245.
65. Pearman, P.B., D'Amen, M., Graham, C.H., Thuiller, W. & Zimmermann, N.E. (2010) Within-taxon niche structure: niche conservatism, divergence and predicted effects of climate change. Ecography, 33, 990-1003.
66. Peterson, A.T., Soberón, J., Pearson, R.G., Anderson, R.P., Martínez-Meyer, M.N. & Araújo, M.B. (2011) Ecological niches and geographic distributions. Princeton University Press, Princeton, NJ.
67. Peterson, B.K., Weber, J.N., Kay, E.H., Fisher, H.S. & Hoekstra, H.E. (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE, 7, e37135.
68. Phillips, S.J. & Dudík, M. (2008) Modeling of species distributions with Maxent: new extensions and a comprehensive evaluation. Ecography, 31, 161-175.
69. Phillips, S.J., Anderson, R.P. & Schapire, R.E. (2006) Maximum entropy modeling of species geographic distributions. Ecological Modelling, 190, 231-259.
70. Pritchard, J.K., Stephens, M. & Donnelly, P. (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-959.
71. Pujol, B. & Pannell, J.R. (2008) Reduced responses to selection after species range expansion. Science, 321, 96.
72. R Core Team (2013) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
73. Radosavljevic, A. & Anderson, R.P. (2014) Making better Maxent models of species distributions: complexity, overfitting and evaluation. Journal of Biogeography, 41, 629-643.
74. Reusch, T.B.H. & Wood, T.E. (2007) Molecular ecology of global change. Molecular Ecology, 16, 3973-3992.
75. Royle, J.A. & Dorazio, R.M. (2008) Hierarchical modeling and inference in ecology: the analysis of data from populations, metapopulations and communities. Elsevier, London.
76. Royle, J.A., Chandler, R.B., Yackulic, C. & Nichols, J.D. (2012) Likelihood analysis of species occurrence probability from presence-only data for modelling species distributions. Methods in Ecology and Evolution, 3, 545-554.
77. Santure, A.W., De Cauwer, I., Robinson, M.R., Poissant, J., Sheldon, B.C. & Slate, J. (2013) Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population. Molecular Ecology, 22, 3949-3962.
78. Scott, J.M., Heglund, P.J. & Morrison, M.I. (2002) Predicting species occurrences: issues of accuracy and scale. Island Press, Washington, DC.
79. Shaw, R.G. & Etterson, J.R. (2012) Rapid climate change and the rate of adaptation: insight from experimental quantitative genetics. New Phytologist, 195, 752-765.
80. Sork, V.L., Davis, F.W., Westfall, R., Flint, A., Ikegami, M., Wang, H. & Grivet, D. (2010) Gene movement and genetic association with regional climate gradients in California valley oak (Quercus lobata Née) in the face of climate change. Molecular Ecology, 19, 3806-3823.
81. Stanton-Geddes, J., Tiffin, P. & Shaw, R.G. (2012) Role of climate and competitors in limiting fitness across range edges of an annual plant. Ecology, 93, 1604-1613.
82. Svenning, J.C. & Sandel, B. (2013) Disequilibrium vegetation dynamics under future climate change. American Journal of Botany, 100, 1266-1286.
83. Thuiller, W., Munkemuller, T., Lavergne, S., Mouillot, D., Mouquet, N., Schiffers, K. & Gravel, D. (2013) A road map for integrating eco-evolutionary processes into biodiversity models. Ecology Letters, 16, 94-105.
84. Urban, M., Tewksbury, J. & Sheldon, K. (2012) On a collision course: competition and dispersal differences create no-analogue communities and cause extinctions during climate change. Proceedings of the Royal Society B: Biological Sciences, 279, 2072-2080.
85. Vignal, A., Milan, D., SanCristobal, M. & Eggen, A. (2002) A review on SNP and other types of molecular markers and their use in animal genetics. Genetics Selection Evolution, 34, 275-305.
86. Waters, J.M., Fraser, C.I. & Hewitt, G.M. (2013) Founder takes all: density-dependent processes structure biodiversity. Trends in Ecology and Evolution, 28, 78-85.
87. Weatherhead, P.J. & Forbes, M.R.L. (1992) Natal philopatry in passerine birds: genetic or ecological influences. Behavioral Ecology, 5, 426-433.
88. Williams, J.W., Blois, J.L., Gill, J.L., Gonzalez, L.M., Grimm, E.C., Jackson, S.T., Ordonez, A., Shuman, B. & Veloz, S.D. (2013) Model systems for a no-analog future: species associations and climates during the last deglaciation. Annals of the New York Academy of Sciences, 1297, 29-43.
89. Yackulic, C.B., Chandler, R., Zipkin, E.F., Royle, J.A., Nichols, J.D., Grant, E.H.C. & Veran, S. (2013) Presence-only modelling using MAXENT: when can we trust the inferences? Methods in Ecology and Evolution, 4, 236-243.
90. Zuur, A., Ieno, E.N., Walker, N., Savaliev, A.A. & Smith, G.M. (2009) Mixed effects models and extensions in ecology with R. Springer-Verlag, New York.