Combining niche modelling and landscape genetics to study local adaptation: A novel approach illustrated using alpine plants

Perspectives in Plant Ecology, Evolution and Systematics

Volumn 17, Issue 6, 2015, Pages 491-499

  Rolland, Jonathan ^a,b   Lavergne, Sébastien ^c   Manel, Stéphanie ^d  

^a UNIVERSITY OF LAUSANNE   (Switzerland)

^b CENTRE DE MATHÉMATIQUES APPLIQUÉES   (France)

^c UNIV GRENOBLE ALPES   (France)

^d UNIV MONTPELLIER   (France)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84952982319     PISSN: 14338319     EISSN: 16180437     Source Type: Journal    
DOI: 10.1016/j.ppees.2015.07.005     Document Type: Note

References (69)

1. Alleaume-Benharira M., Pen I.R., Ronce O. Geographical patterns of adaptation within a species' range, interactions between drift and gene flow. J. Evol. Biol. 2006, 19:203-215.
2. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 1990, 215:403-410.
3. Atkins K.E., Travis J.M.J. Local adaptation and the evolution of species ranges under climate change. J. Theor. Biol. 2010, 266:449-457.
4. Banta J.A., Ehrenreich I.M., Gerard S., Chou L., Wilczek A., Schmitt J., Kover P.X., Purugganan M.D. Climate envelope modelling reveals intraspecific relationships among flowering phenology, niche breadth and potential range size in Arabidopsis thaliana. Ecol. Lett. 2012, 15:769-777.
5. Boucher F.C., Thuiller W., Roquet C., Douzet R., Aubert S., Alvarez N., Lavergne S. Reconstructing the origins of high-alpine niches and cushion life form in the genus Androsace S.L. (Primulaceae). Evolution 2012, 66:1255-1268.
6. Bridle J.R., Vines T.H. Limits to evolution at range margins, when and why does adaptation fail?. Trends Ecol. Evol. 2007, 22:140-147.
7. Bridle J.R., Gavaz S., Kennington W.J. Testing limits to adaptation along altitudinal gradients in rainforest Drosophila. Proc. R. Soc. B 2009, 276:1507-1515.
8. Brawand D., Wagner C.E., Li Y.I., Malinsky M., Keller I., Fan S., et al. The genomic substrate for adaptive radiation in African cichlid fish. Nature 2014, 513:375-381.
9. Cattell R.B. The scree test for the number of factors. Multivar. Behav. Res. 1966, 1:245-276.
10. Colwell R.K., Rangel T.F. Hutchinson's duality: the once and future niche. Proc. Natl. Acad. Sci. U. S. A. 2009, 106:19651-19658.
11. Coop G., Witonsky D., Di Rienzo A., Pritchard J.K. Using environmental correlations to identify loci underlying local adaptation. Genetics 2010, 185:1411-1423.
12. Dolédec S., Chessel D., Gimaret-Carpentier C. Niche separation in community analysis, a new method. Ecology 2000, 81:2914-2927.
13. Dormann C.F., McPherson J.M., Araújo M.B., Bivand R., Bolliger J., Carl G., Davies R.G., Hirzel A., Jetz W., Kissling W.D., Kühn I., Ohlemüller R., Peres-Neto P.R., Reineking B., Schröder B., Schurr F.M., Wilson R. Methods to account for spatial autocorrelation in the analysis of species distributional data: a review. Ecography 2007, 30:609-628.
14. Dray, S., Dufour, A.B., 2009. Ade4: Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences, R package version 1.4-11.
15. Eckert C.G., Samis K.E., Lougheed S.C. Genetic variation across species' geographical ranges: the central-marginal hypothesis and beyond. Mol. Ecol. 2008, 17:1170-1188.
16. Endler J.A. Geographic Variation, Speciation, and Clines 1977, Princeton University Press, Princeton, New Jersey, USA.
17. Endler J.A. Natural Selection in the Wild 1986, Princeton University Press, Princeton, New Jersey, USA.
18. Fournier-Level A., Korte A., Cooper M.D., Nordborg M., Schmitt J., Wilczek A.M. A map of local adaptation in Arabidopsis thaliana. Science 2011, 334:86-89.
19. Frichot E., Schoville S.D., Bouchard G., François O. Testing for associations between loci and environmental gradients using latent factor mixed models. Mol. Biol. Evol. 2013, 30:1687-1699.
20. Fumagalli M., Sironi M., Pozzoli U., Ferrer-Admettla A., Pattini L., Nielsen R. Signatures of environmental genetic adaptation pinpoint pathogens as the main selective pressure through human evolution. PLoS Genet. 2011, 7:e1002355.
21. Gagnaire P.A., Pavey S.A., Normandeau E., Bernatchez L. The genetic architecture of reproductive isolation during speciation -with-gene-flow in lake whitefish species pairs assessed by RAD sequencing. Evolution 2013, 67:2483-2497.
22. Gugerli F., Englisch T., Niklfeld H., Tribsch A., Mirek Z., Ronikier M., Zimmermann N.E., Holderegger R., Taberlet P. Relationships among levels of biodiversity and the relevance of intraspecific diversity in conservation-a project synopsis. Perspect. Plant Ecol. Evol. Syst. 2008, 10:259-281.
23. Guisan A., Thuiller W. Predicting species distribution, offering more than simple habitat models. Ecol. Lett. 2005, 9:993-1009.
24. Guisan A., Petitpierre B., Broennimann O., Daehler C., Kueffer C. Unifying niche shift studies: insights from biological invasions. Trends Ecol. Evol. 2014, 29:260-269.
25. Hampe A., Petit R.P. Conserving biodiversity under climate change, the rear edge matters. Ecol. Lett. 2005, 8:461-467.
26. Hancock A.M., Brachi B., Faure N., Horton M.W., Jarymowycz L.B., Sperone F.G., Toomajian C., Roux F., Bergelson J. Adaptation to climate across the Arabidopsis thaliana genome. Science 2011, 334:83-86.
27. Hendry A.P., Day T., Taylor E.B. Population mixing and the adaptive divergence of quantitative traits in discrete populations, a theoretical framework for empirical tests. Evolution 2001, 55:459-466.
28. Hoekstra H. The secret of a natural blond. Nat. Genet. 2014, 46:660-661.
29. Holderegger R., Herrmann D., Poncet B., Gugerli F., Thuiller W., Taberlet P., Gielly L., Rioux D., Brodbeck S., Aubert S., Manel S. Land ahead: using genome scans to identify molecular markers of adaptive relevance. Plant Ecol. Div. 2008, 1:273-283.
30. Holt R.D. Bringing the Hutchinsonian niche into the 21st century, ecological and evolutionary perspectives. Proc. Natl. Acad. Sci. U. S. A. 2009, 106:19659-19665.
31. Jones M., Forester B., Teufel A., Adams R., Anstett D., Goodrich B., Landguth E., Joost S., Manel S. Integrating landscape genomics and spatially-explicit approaches to detect loci under selection in clinal populations. Evolution 2013, 67:3455-3468.
32. Joost S., Bonin A., Bruford M.W., Després L., Conord C., Erhardt G., Taberlet P. A spatial analysis method (SAM) to detect candidate loci for selection, towards a landscape genomics approach to adaptation. Mol. Ecol. 2007, 18:3955-3969.
33. Joost S., Vuilleumier S., Jensen J.D., Schoville S., Leempoel K., Stucki S., Widmer I., Melodelima C., Rolland J., Manel S. Uncovering the genetic basis of adaptive change, on the intersection of landscape genomics and theoretical population genetics. Mol. Ecol. 2013, 22:3659-3665.
34. Kawecki T.J. Adaptation to marginal habitats. Annu. Rev. Ecol. Evol. Syst. 2008, 39:321-342.
35. Kremer A., Ronce O., Robledo-Arnuncio J.J., Guillaume F., Bohrer G., Nathan R., Bridle J.R., Gomulkiewicz R., Klein E.K., Ritland K., Kuparinen A., Gerber S., Schueler S. Long-distance gene flow and adaptation of forest trees to rapid climate change. Ecol. Lett. 2012, 15:378-392.
36. Lavergne S., Mouquet N., Thuiller W., Ronce O. Biodiversity and climate change, integrating evolutionary and ecological responses of species and communities. Annu. Rev. Ecol. Evol. Syst. 2010, 41:321-350.
37. Leimu R., Fischer M. A meta-analysis of local adaptation in plants. PLoS One 2008, 3:e4010.
38. Liang K.Y., Zeger S.L. Longitudinal data analysis using generalized linear models. Biometrika 1986, 73:13-22.
39. Lowry D.B., Willis J.H. A widespread chromosomal inversion polymorphism contributes to a major life-history transition, local adaptation, and reproductive isolation. PLoS Biol. 2010, 8:e1000500.
40. Manel S., Schwartz M.K., Luikart G., Taberlet P. Landscape genetics, combining landscape ecology and population genetics. Trends Ecol. Evol. 2003, 20:136-142.
41. Manel S., Joost S., Epperson B.K., Holderegger R., Storfer A., Rosenberg, Scribner K.T., Bonin A., Fortin M.J. Perspectives on the use of landscape genetics to detect genetic adaptive variation in the field. Mol. Ecol. 2010, 19:3760-3772.
42. Manel S., Poncet B.N., Legendre P., Gugerli F., Holderegger R. Common factors drive adaptive genetic variation at different scale in Arabis alpina. Mol. Ecol. 2010, 19:2896-2907.
43. Manel S., Gugerli F., Thuiller W., Alvarez N., Legendre P., Holderegger R., Gielly L., Taberlet P. Broad-scale adaptive genetic variation in alpine plants is driven by temperature and precipitation. Mol. Ecol. 2012, 21:3729-3738.
44. Manel S., Holderegger R. Ten years of landscape genetics. Trends Ecol. Evol. 2013, 28:614-621.
45. Meirmans P.G., Goudet J., Gaggiotti O.E. Ecology and life history affect different aspects of the population structure of 27 high-alpine plants. Mol. Ecol. 2011, 20:3144-3155. IntraBioDiv Consortium.
46. Meirmans P.G., Goudet J., Gaggiotti O.E. Data from: Ecology and life history affect different aspects of the population structure of 27 high-alpine plants. Dryad Digital Repos. 2011, IntraBioDiv Consortium, http://datadryad.org/resource/doi:10.5061/dryad.f3rk4.
47. Mumby P.J., Elliott I.A., Eakin C.M., Skirving W., Paris C.B., Edwards H.J., Enríquez S., Iglesias-Prieto R., Cherubin L.M., Stevens J.R. Reserve design for uncertain responses of coral reefs to climate change. Ecol. Lett. 2011, 14:132-140.
48. Narum S.R., Campbell N.R., Meyer K.A., Miller M.R., Hardy R.W. Thermal adaptation and acclimation of ectotherms from differing aquatic climates. Mol. Ecol. 2013, 22:3090-3097.
49. Nosil P., Funk D.J., Ortiz-Barrientos D. Divergent selection and heterogeneous genomic divergence. Mol. Ecol. 2009, 18:375-402.
50. Parmesan C. Ecological and evolutionary responses to recent climate change. Annu. Rev. Ecol. Evol. Syst. 2006, 37:637-669.
51. Pauls S.U., Nowak C., Bálint M., Pfenninger M. The impact of global climate change on genetic diversity within populations and species. Mol. Ecol. 2013, 22:925-946.
52. Peterson A.T., Soberón J., Pearson R.G., Anderson R.P., Martínez-Meyer E., Nakamura M., Araújo M.B. Ecological Niches and Geographic Distributions 2011, Princeton University Press, Princeton, New Jersey, USA.
53. Poncet B.N., Herrmann D., Gugerli F., Taberlet P., Holderegger R., Gielly L., Rioux D., Thuiller W., Aubert S., Manel S. Tracking genes of ecological relevance using a genome scan in two independent regional population samples of Arabis alpina. Mol. Ecol. 2010, 19:2896-2907.
54. Qi J., Liu X., Shen D., Miao H., Xie B., Li X., et al. A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity. Nat. Genet. 2013, 12:1510-1515.
55. Razgour O., Juste J., Ibáñez C., Kiefer A., Rebelo H., Puechmaille S.J., Arlettaz R., Burke T., Dawson D.A., Beaumont M., Jones G. The shaping of genetic variation in edge-of-range populations under past and future climate change. Ecol. Lett. 2013, 16:1258-1266.
56. Rogers S.M., Bernatchez L. FAST-TRACK, integrating QTL mapping and genome scans towards the characterization of candidate loci under parallel selection in the lake whitefish (Coregonus clupeaformis). Mol. Ecol. 2005, 14:351-361.
57. Savolainen O., Lascoux M., Merilä J. Ecological genomics of local adaptation. Nat. Rev. Genet. 2013, 14:807-820.
58. Schoville S.D., Bonin A., François O., Lobreaux S., Melodelima C., Manel S. Adaptive genetic variation on the landscape, methods and cases. Annu. Rev. Ecol. Evol. Syst. 2012, 43:23-43.
59. Seeb J.E., Carvalho G., Hauser L., Naish K., Roberts S., Seeb L.W. Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms. Mol. Ecol. Res. 2011, 11:1-8.
60. Sexton J.P., McIntyre P.J., Angert A.L., Rice K.J. Evolution and ecology of species range limits. Annu. Rev. Ecol. Evol. Syst. 2009, 40:415-436.
61. Sexton J.P., Strauss S.Y., Rice K.J. Gene flow increases fitness at the warm edge of a species' range. Proc. Natl. Acad. Sci. U. S. A. 2011, 108:11704-11709.
62. Stapley J., Reger J., Feulner P.G.D., Smadja C., Galindo J., Ekblom R., Bennison C., Ball A.D., Beckerman A.P., Slate J. Adaptation genomics, the next generation. Trends Ecol. Evol. 2010, 25:705-712.
63. Stinchcombe J.R., Hoekstra H.E. Combining population genomics and quantitative genetics, combined approaches for finding the genes underlying ecologically important traits. Heredity 2008, 100:158-170.
64. Storz J.F. Using genome scans of DNA polymorphism to infer adaptive population divergence. Mol. Ecol. 2005, 14:671-688.
65. Storz J.F., Wheat C.W. Integrating evolutionary and functional approaches to infer adaptation at specific loci. Evolution 2010, 64:2489-2509.
66. Taberlet P., et al. Genetic diversity in widespread species is not congruent with species richness in alpine plant communities. Ecol. Lett. 2012, 15:1439-1448.
67. Thuiller W., Lavorel S., Midgley G., Lavergne S., Rebelo T. Relating plant traits and species distributions along bioclimatic gradients for 88 Leucadendron species in the Cape Floristic Region. Ecology 2004, 85:1688-1699.
68. Tiffin P., Ross-Ibarra J. Advances and limits of using population genetics to understand local adaptation. Trends Ecol. Evol. 2014, 29:673-680.
69. Zimmermann N.E., Kienast F. Predictive mapping of alpine grasslands in Switzerland, species versus community approach. J. Veg. Sci. 1999, 10:469-482.