Forecasting changes in population genetic structure of alpine plants in response to global warming

Molecular Ecology

Volumn 21, Issue 10, 2012, Pages 2354-2368

  Jay, Flora ^a   Manel, Stéphanie ^a,b   Alvarez, Nadir ^c   Durand, Eric Y ^d   Thuiller, Wilfried ^a   Holderegger, Rolf ^e   Taberlet, Pierre ^a   François, Olivier ^a  

^a UNIV GRENOBLE ALPES   (France)

^b Aix Marseille University Marseille   (France)

^c UNIVERSITY OF LAUSANNE   (Switzerland)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e SWISS FEDERAL RESEARCH INSTITUTE WSL   (Switzerland)

Author keywords

Alpine plants; ancestry distribution models; climate change; intra specific variation; landscape genetics

Indexed keywords

ADAPTATION; ALTITUDE; ARTICLE; BIOLOGICAL MODEL; FORECASTING; GENETICS; GENOTYPE; GREENHOUSE EFFECT; METHODOLOGY; PLANT; POPULATION DYNAMICS; POPULATION GENETICS; TEMPERATURE;

ADAPTATION, PHYSIOLOGICAL; ALTITUDE; FORECASTING; GENETICS, POPULATION; GENOTYPE; GLOBAL WARMING; MODELS, GENETIC; PLANTS; POPULATION DYNAMICS; TEMPERATURE;

EID: 84860539395     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2012.05541.x     Document Type: Article

References (82)

1. Aitken SN, Yeaman S, Holliday JA, et al. (2008) Adaptation, migration or extirpation: climate change outcomes for tree populations. Evolutionary Applications, 1, 95-111.
2. Albert C, Yoccoz N, Edwards Jr T, et al. (2010) Sampling in ecology and evolution - bridging the gap between theory and practice. Ecography, 33, 1028-1037.
3. Alvarez N, Thiel-Egenter C, Tribsch A, et al. (2009) History or ecology? Substrate type as a major driver of spatial genetic structure in alpine plants. Ecology Letters, 12, 632-640.
4. Austerlitz F, Mariette S, Machon N, et al. (2000) Effects of colonization processes on genetic diversity: differences between annual plants and tree species. Genetics, 154, 1309-1321. (Pubitemid 30140715)
5. Balkenhol N, Waits LP, Dezzani RJ, (2009) Statistical approaches in landscape genetics: an evaluation of methods for linking landscape and genetic data. Ecography, 32, 818-830.
6. Benjamini Y, Hochberg Y, (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society Series B (Methodological), 57, 289-300.
7. Besag J, (1975) Statistical analysis of non-lattice data. The Statistician, 24, 179-195.
8. Bierne N, Welch J, Loire E, et al. (2011) The coupling hypothesis: why genome scans may fail to map local adaptation genes. Molecular Ecology, 20, 2044-2072.
9. Bonin A, Ehrich D, Manel S, (2007) Statistical analysis of AFLP data: a toolbox for molecular ecologists and evolutionists. Molecular Ecology, 16, 3737-3758. (Pubitemid 47397323)
10. Buggs RJA, (2007) Empirical study of hybrid zone movement. Heredity, 99, 301-312. (Pubitemid 47295860)
11. Chen C, Durand E, Forbes F, François O, (2007) Bayesian clustering algorithms ascertaining spatial population structure: a new computer program and a comparison study. Molecular Ecology Notes, 7, 747-756. (Pubitemid 47329398)
12. Chevin L-M, Lande R, Mace GM, (2010) Adaptation, plasticity, and extinction in a changing environment: towards a predictive theory. PLoS Biology, 8, e1000357.
13. Coop G, Witonsky D, Di Rienzo A, Pritchard JK, (2010) Using environmental correlations to identify loci underlying local adaptation. Genetics, 185, 1411-1423.
14. Currat M, Ray N, Excoffier L, (2004) SPLATCHE: a program to simulate genetic diversity taking into account environmental heterogeneity. Molecular Ecology Notes, 4, 139-142. (Pubitemid 38261336)
15. Currat M, Ruedi M, Petit RJ, Excoffier L, (2008) The hidden side of invasions: massive introgression by local genes. Evolution, 62, 1908-1920. (Pubitemid 352033252)
16. Davis MB, Shaw RG, (2001) Range shifts and adaptive responses to quaternary climate change. Science, 292, 673-679. (Pubitemid 32385531)
17. Davis MB, Shaw RG, Etterson JR, (2005) Evolutionary responses to changing climate. Ecology, 86, 1704-1714. (Pubitemid 40938771)
18. Doi H, Takahashi M, Katano I, (2010) Genetic diversity increases regional variation in phenological dates in response to climate change. Global Change Biology, 16, 373-379.
19. Dukes JS, Mooney HA, (1999) Does global change increase the success of biological invaders? Trends in Ecology and Evolution, 14, 135-139. (Pubitemid 29135462)
20. Duminil J, Fineschi S, Hampe A, et al. (2007) Can population genetic structure be predicted from life-history traits? The American Naturalist, 169, 662-672. (Pubitemid 46656062)
21. Durand E, Jay F, Gaggiotti OE, François O, (2009) Spatial inference of admixture proportions and secondary contact zones. Molecular Biology and Evolution, 26, 1963-1973.
22. Engler R, Randin CF, Thuiller W, et al. (2011) 21st century climate change threatens mountain flora unequally across Europe. Global Change Biology, 17, 2330-2341.
23. Foll M, Gaggiotti OE, (2006) Identifying the environmental factors that determine the genetic structure of populations. Genetics, 174, 875-891. (Pubitemid 44656475)
24. François O, Durand E, (2010) Spatially explicit Bayesian clustering models in population genetics. Molecular Ecology Resources, 10, 773-784.
25. François O, Blum MGB, Jakobsson M, Rosenberg NA, (2008) Demographic history of European populations of Arabidopsis thaliana. PLoS Genetics, 4, e1000075.
26. Gallien L, Münkemüller T, Albert CH, et al. (2010) Predicting potential distributions of invasive species: where to go from here? Diversity and Distributions, 16, 331-342.
27. Gienapp P, Teplitsky C, Alho JS, et al. (2008) Climate change and evolution: disentangling environmental and genetic responses. Molecular Ecology, 17, 167-178. (Pubitemid 350292455)
28. Grabherr G, Gottfried M, Pauli H, (1994) Climate effects on mountain plants. Nature, 369, 448.
29. Gugerli F, Englisch T, Niklfeld H, et al. (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.
30. Guisan A, Thuiller W, (2005) Predicting species distribution: offering more than simple habitat models. Ecology Letters, 8, 993-1009. (Pubitemid 41247275)
31. Guisan A, Zimmermann NE, (2000) Predictive habitat distribution models in ecology. Ecological Modelling, 135, 147-186. (Pubitemid 32102782)
32. Haldane JBS, (1948) The theory of a cline. Journal of Genetics, 48, 277-284.
33. Hampe A, Petit RJ, (2005) Conserving biodiversity under climate change: the rear edge matters. Ecology Letters, 8, 461-467. (Pubitemid 40641134)
34. Hedrick PW, Ginevan ME, Ewing EP, (1976) Genetic polymorphism in heterogeneous environments. Annual Review of Ecology and Systematics, 7, 1-32.
35. Higgins SI, Richardson DM, (1999) Predicting plant migration rates in a changing world: the role of long-distance dispersal. American Naturalist, 153, 464-475. (Pubitemid 29285412)
36. Holderegger R, Wagner HH, (2008) Landscape genetics. BioScience, 58, 199-207. (Pubitemid 351481619)
37. IPCC (2007) Climate Change 2007 - The Physical Science Basis. Cambridge University Press, Cambridge, UK.
38. Jay F, (2011) POPS: Prediction of Population Structure. Program Documentation, University Joseph Fourier Grenoble.
39. Jay F, François O, Blum MGB, (2011) Predictions of Native American population structure using linguistic covariates in a hidden regression framework. PLoS One, 6, e16227.
40. 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. Molecular Ecology, 16, 3955-3969. (Pubitemid 47397327)
41. Jump AS, Peñuelas J, (2005) Running to stand still: adaptation and the response of plants to rapid climate change. Ecology Letters, 8, 1010-1020. (Pubitemid 41247276)
42. Jump AS, Marchant R, Peñuelas J, (2009a) Environmental change and the option value of genetic diversity. Trends in Plant Sciences, 14, 51-58.
43. Jump AS, Mátyás C, Peñuelas J, (2009b) The altitude-for-latitude disparity in the range retractions of woody species. Trends in Ecology and Evolution, 24, 694-701.
44. Kunstler G, Thuiller W, Curt T, et al. (2007) Fagus sylvatica L. recruitment across a fragmented Mediterranean Landscape, importance of long distance effective dispersal, abiotic conditions and biotic interactions. Diversity and Distributions, 13, 799-807. (Pubitemid 47622032)
45. Leimu R, Fischer M, (2008) A meta-analysis of local adaptation in plants. PLoS One, 3, e4010.
46. Lichstein JW, Simons TR, Shriner SA, et al., (2002) Spatial autocorrelation and autoregressive models in ecology. Ecological Monographs, 72, 445-463. (Pubitemid 36219454)
47. Malcolm JR, Markham A, Neilson RP, Garaci M, (2002) Estimated migration rates under scenarios of global climate change. Journal of Biogeography, 29, 835-849. (Pubitemid 34869594)
48. Manel S, Joost S, Epperson BK, et al. (2010a) Perspectives on the use of landscape genetics to detect genetic adaptive variation in the field. Molecular Ecology, 19, 3760-3772.
49. Manel S, Poncet BN, Legendre P, et al. (2010b) Common factors drive adaptive genetic variation at different spatial scales in Arabis alpina. Molecular Ecology, 19, 3824-3835.
50. Nathan R, (2006) Long-distance dispersal of plants. Science, 313, 786-788. (Pubitemid 44223337)
51. Nosil P, Funk DJ, Ortiz-Barrientos D, (2009) Divergent selection and heterogeneous genomic divergence. Molecular Ecology, 18, 375-402.
52. Parmesan C, Yohe G, (2003) A globally coherent fingerprint of climate change impacts across natural systems. Nature, 421, 37-42. (Pubitemid 36077078)
53. Pereira HM, Leadley PW, Proenca V, et al. (2010) Scenarios for global biodiversity in the 21st century. Science, 330, 1496-1501.
54. Petit RJ, (2004) Biological invasions at the gene level. Diversity and Distributions, 10, 159-165. (Pubitemid 38592379)
55. Poncet BN, Herrmann D, Gugerli F, et al. (2010) Tracking genes of ecological relevance using a genome scan in two independent regional population samples of Arabis alpina. Molecular Ecology, 19, 2896-2907.
56. Pritchard JK, Stephens M, Donnelly P, (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-59. (Pubitemid 30397141)
57. R Development Core Team (2010). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0,.
58. Richardson B, Rehfeldt G, Kim M, (2009) Congruent climate-related genecological responses from molecular markers and quantitative traits for western white pine (pinus monticola). International Journal of Plant Sciences, 170, 1120-1131.
59. Saitou N, Nei M, (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4, 406-425.
60. Salamin N, Würst R, Lavergne S, et al. (2010) Assessing rapid evolution in a changing environment. Trends in Ecology and Evolution, 25, 692-698.
61. Scherrer D, Körner C, (2011) Topogaphically controlled thermal-habitat differentiation buffers alpine plant diversity against climate warming. Journal of Biogeography, 38, 406-416.
62. Schönswetter P, Stehlik I, Holderegger R, Tribsch A, (2005) Molecular evidence for glacial refugia of mountain plants in the European Alps. Molecular Ecology, 14, 3547-3555.
63. Slatkin M, (1973) Gene flow and selection in a cline. Genetics, 75, 733-756.
64. Sork VL, Davis FW, Wang H, et al. (2010) Gene movement and genetic association with regional climate gradients in California valley oak (Quercus lobata Née). Molecular Ecology, 19, 3806-3823.
65. Stanton ML, Galen C, (1997) Life on the edge: adaptation versus environmentally mediated gene flow in the snow buttercup, Ranunculus adoneus. American Naturalist, 150, 143-178. (Pubitemid 27433814)
66. Stinson KA, (2004) Natural selection favors rapid reproductive phenology in Potentilla pulcherrima (Rosaceae) at opposite ends of a subalpine snowmelt gradient. American Journal of Botany, 91, 531-539. (Pubitemid 39217839)
67. Storfer A, Murphy MA, Evans JS, et al. (2007) Putting the "landscape" in landscape genetics. Heredity, 98, 128-142.
68. Tackenberg O, Stöcklin J, (2008) Wind dispersal of alpine plant species: a comparison with lowland species. Journal of Vegetation Science, 19, 109-118. (Pubitemid 351448467)
69. Theurillat J-P, Guisan A, (2001) Potential impact of climatic change on vegetation in the European Alps: a review. Climate Change, 50, 77-109. (Pubitemid 32665125)
70. Thibert-Plante X, Hendry AP, (2010) When can ecological speciation be detected with neutral loci? Molecular Ecology, 19, 2301-2314.
71. Thiel-Egenter C, Gugerli F, Alvarez N, et al. (2009) Effects of species traits on the genetic diversity of high-mountain plants: a multi-species study across the Alps and the Carpathians. Global Ecology and Biogeography, 18, 78-87.
72. Thiel-Egenter C, Alvarez N, Holderegger R, et al. (2011) Break zones in the distributions of alleles and species in alpine plants. Journal of Biogeography, 38, 772-782.
73. Thomassen HA, Cheviron ZA, Freedman AH, et al. (2010) Spatial modelling and landscape-level approaches for visualizing intra-specific variation. Molecular Ecology, 17, 3532-3548.
74. Thornton PE, Running SW, White MA, (1997) Generating surfaces of daily meteorological variables over large regions of complex terrain. Journal of Hydrology, 190, 214-251.
75. Thuiller W, Lavorel S, Araújo MB, et al. (2005) Climate change threats to plant diversity in Europe. Proceedings of the National Academy of Sciences USA, 102, 8245-8250. (Pubitemid 40800074)
76. Thuiller W, Albert C, Araújo MB, et al. (2008) Predicting global change impacts on plant species' distributions: future challenges. Perspectives in Plant Ecology, Evolution and Systematics, 9, 137-152. (Pubitemid 351192351)
77. Turesson G, (1925) The plant species in relation to habitat and climate. Hereditas, 6, 147-236.
78. Verhoeven KJF, Macel M, Wolfe LM, et al. (2011) Population admixture, plant invasions and the balance between local adaptation and inbreeding depression. Proceedings of the Royal Society B-Biological Sciences, 278, 2-8.
79. Walther G-R, (2003) Plants in a warmer world. Perspectives in Plant Ecology, Evolution and Systematics, 6, 169-185. (Pubitemid 38329467)
80. Walther G-R, Post E, Convey P, et al. (2002) Ecological responses to recent climate change. Nature, 416, 389-395. (Pubitemid 34272866)
81. Walther G-R, Roques A, Hulme PE, et al. (2009) Alien species in a warmer world: risks and opportunities. Trends in Ecology and Evolution, 24, 686-693.
82. Wang RH, Farrona S, Vincent C, et al. (2009) PEP1 regulates perennial flowering in Arabis alpina. Nature, 459, 423-427.