Ecological genomics and process modeling of local adaptation to climate

Current Opinion in Plant Biology

Volumn 18, Issue 1, 2014, Pages 66-72

  Weinig, Cynthia ^a   Ewers, Brent E ^a   Welch, Stephen M ^b  

^a UNIVERSITY OF WYOMING   (United States)

^b KANSAS STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTATION; CLIMATE; ECOLOGY; GENETICS; GENOMICS; PROCEDURES; QUANTITATIVE TRAIT; THEORETICAL MODEL;

ADAPTATION, PHYSIOLOGICAL; CLIMATE; ECOLOGY; GENOMICS; MODELS, THEORETICAL; QUANTITATIVE TRAIT, HERITABLE;

EID: 84896035994     PISSN: 13695266     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pbi.2014.02.007     Document Type: Review

References (77)

1. Hereford J. A quantitative survey of local adaptation and fitness trade-offs. Am Nat 2009, 173:579-588.
2. Leimu R., Fischer M. A meta-analysis of local adaptation in plants. PLoS One 2008, 3.
3. Turesson G. The plant species and variety as ecological units. Hereditas 1922, 3:100-113.
4. Turesson G. The plant species in relation to habitat and climate. Hereditas 1925, 6:147-236.
5. Clausen J., Keck D.D., Hiesey W.M. Regional differentiation in plant species. Am Nat 1941, 75:231-250.
6. 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.
7. 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.
8. Ågren J., Schemske D.W. Reciprocal transplants demonstrate strong adaptive differentiation of the model organism Arabidopsis thaliana in its native range. New Phytol 2012, 194:1112-1122.
9. 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.
10. Lasky J.R., Des Marais D.L., McKay J.K., Richards J.H., Juenger T.E., Keitt T.H. Characterizing genomic variation of Arabidopsis thaliana: the roles of geography and climate. Mol Ecol 2012, 21:5512-5529.
11. Stearns F.W., Fenster C.B. Evidence for parallel adaptation to climate across the natural range of Arabidopsis thaliana. Ecol Evol 2013, 3:2241-2250.
12. Mitchell-Olds T., Schmitt J. Genetic mechanisms and evolutionary significance of natural variation in Arabidopsis. Nature 2006, 441:947-952.
13. Kawecki T.J., Ebert D. Conceptual issues in local adaptation. Ecol Lett 2004, 7:1225-1241.
14. Weinig C., Dorn L.A., Kane N.C., German Z.M., Halldorsdottir S.S., Ungerer M.C., Toyonaga Y., Mackay T.F.C., Purugganan M.D., Schmitt J. Heterogeneous selection at specific loci in natural environments in Arabidopsis thaliana. Genetics 2003, 165:321-329.
15. Huang X., Schmitt J., Dorn L., Griffith C., Effgen S., Takao S., Koornneef M., Donohue K. The earliest stages of adaptation in an experimental plant population: strong selection on QTLS for seed dormancy. Mol Ecol 2010, 19:1335-1351.
16. Mackay T.F.C. Quantitative trait loci in Drosophila. Nat Rev Genet 2001, 2:11-20.
17. 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. 10.1371/journal.pbio.1000500.
18. Leinonen P.H., Remington D.L., LeppÄLÄ J., Savolainen O. Genetic basis of local adaptation and flowering time variation in Arabidopsis lyrata. Mol Ecol 2013, 22:709-723.
19. Anderson J.T., Lee C.-R., Rushworth C.A., Colautti R.I., Mitchell-Olds T. Genetic trade-offs and conditional neutrality contribute to local adaptation. Mol Ecol 2013, 22:699-708.
20. Ågren J., Oakley C.G., McKay J.K., Lovell J.T., Schemske D.W. Genetic mapping of adaptation reveals fitness tradeoffs in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2013, 10.1073/pnas.1316773110.
21. Anderson J.T., Willis J.H., Mitchell-Olds T. Evolutionary genetics of plant adaptation. Trends Genet 2011, 27:258-266.
22. Leinonen P.H., Remington D.L., Savolainen O. Local adaptation, phenotypic differentiation, and hybrid fitness in diverged natural populations of Arabidopsis lyrata. Evolution 2011, 65:90-107.
23. Vergeer P., Kunin W.E. Life history variation in Arabidopsis lyrata across its range: effects of climate, population size and herbivory. Oikos 2011, 120:979-990.
24. Hoffmann M.H. Biogeography of Arabidopsis thaliana (L.) Heynh. (Brassicaceae). J. Biogeogr. 2002, 29:125-134.
25. Hoffmann M.H. Evolution of the realized climatic niche in the genus: Arabidopsis (Brassicaceae). Evolution 2005, 59:1425-1436.
26. Zhen Y., Ungerer M.C. Clinal variation in freezing tolerance among natural accessions of Arabidopsis thaliana. New Phytol 2008, 177:419-427.
27. Zuther E., Schulz E., Childs L.H., Hincha D.K. Clinal variation in the non-acclimated and cold-acclimated freezing tolerance of Arabidopsis thaliana accessions. Plant Cell Environ 2012, 35:1860-1878.
28. Richards C.L., Rosas U., Banta J., Bhambhra N., Purugganan M.D. Genome-wide patterns of Arabidopsis gene expression in nature. PLoS Genet 2012, 8.
29. Aranzana M.J., Kim S., Zhao K., Bakker E., Horton M., et al. Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genet 2005, 1. 10.1371/journal.pgen.0010060.
30. Cao J., Schneeberger K., Ossowski S., Gunther T., Bender S., Fitz J., Koenig D., Lanz C., Stegle O., Lippert C., et al. Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet 2011, 43:956-963.
31. Eckert A.J., Bower A.D., GonzÁLez-MartÍNez S.C., Wegrzyn J.L., Coop G., Neale D.B. Back to nature: ecological genomics of loblolly pine (Pinus taeda, Pinaceae). Mol Ecol 2010, 19:3789-3805.
32. Holliday J.A., Ritland K., Aitken S.N. Widespread, ecologically relevant genetic markers developed from association mapping of climate-related traits in Sitka spruce (Picea sitchensis). New Phytol 2010, 188:501-514.
33. Stinchcombe J.R., Weinig C., Ungerer M., Olsen K.M., Mays C., Halldorsdottir S.S., Purugganan M.D., Schmitt J. A latitudinal cline in flowering time in Arabidopsis thaliana modulated by the flowering time gene FRIGIDA. Proc Natl Acad Sci U S A 2004, 101:4712-4717.
34. Samis K.E., Murren C.J., Bossdorf O., Donohue K., Fenster C.B., Malmberg R.L., Purugganan M.D., Stinchcombe J.R. Longitudinal trends in climate drive flowering time clines in North American Arabidopsis thaliana. Ecol Evol 2012, 2:1162-1180.
35. Brachi B., Villoutreix R., Faure N., Hautekèete N., Piquot Y., Pauwels M., Roby D., Cuguen J., Bergelson J., Roux F. Investigation of the geographical scale of adaptive phenological variation and its underlying genetics in Arabidopsis thaliana. Mol Ecol 2013, 22:4222-4240.
36. Fournier-Level A., Wilczek A.M., Cooper M.D., Roe J.L., Anderson J., Eaton D., Moyers B.T., Petipas R.H., Schaeffer R.N., Pieper B., et al. Paths to selection on life history loci in different natural environments across the native range of Arabidopsis thaliana. Mol Ecol 2013, 22:3552-3566.
37. Montesinos-Navarro A., Wig J., Xavier Pico F., Tonsor S.J. Arabidopsis thaliana populations show clinal variation in a climatic gradient associated with altitude. New Phytol 2011, 189:282-294.
38. Wolfe M.D., Tonsor S.J. Adaptation to spring heat and drought in northeastern Spanish Arabidopsis thaliana. New Phytol 2013.
39. Ahuja I., de Vos R.C.H., Bones A.M., Hall R.D. Plant molecular stress responses face climate change. Trends Plant Sci 2010, 15:664-674.
40. Nicotra A.B., Atkin O.K., Bonser S.P., Davidson A.M., Finnegan E.J., Mathesius U., Poot P., Purugganan M.D., Richards C.L., Valladares F., et al. Plant phenotypic plasticity in a changing climate. Trends Plant Sci 2010, 15:684-692.
41. Earley E.J., Ingland B., Winkler J., Tonsor S.J. Inflorescences contribute more than rosettes to lifetime carbon gain in Arabidopsis thaliana (Brassicaceae). Am J Bot 2009, 96:786-792.
42. Hultine K.R., Burtch K.G., Ehleringer J.R. Gender specific patterns of carbon uptake and water use in a dominant riparian tree species exposed to a warming climate. Glob Change Biol 2013, 19:3390-3405.
43. Sevanto S., McDowell N.G., Dickman L.T., Pangle R., Pockman W.T. How do trees die? A test of the hydraulic failure and carbon starvation hypotheses. Plant Cell Environ 2013.
44. Cochard H. Xylem embolism and drought-induced stomatal closure in maize. Planta 2002, 215:466-471.
45. Tixier A., Cochard H., Badel E., Dusotoit-Coucaud A., Jansen S., Herbette S. Arabidopsis thaliana as a model species for xylem hydraulics: does size matter?. J Exp Bot 2013, 64:2295-2305.
46. Davis M.B., Shaw R.G. Range shifts and adaptive responses to quaternary climate change. Science 2001, 292:673-679.
47. MEMBERS C. Climatic changes of the last 18,000 years: observations and model simulations. Science 1988, 241:1043-1052.
48. Fornara F., de Montaigu A., Coupland G. SnapShot: control of flowering in Arabidopsis. Cell 2010, 141:024.
49. Wilczek A.M., Roe J.L., Knapp M.C., Cooper M.D., Lopez-Gallego C., Martin L.J., Muir C.D., Sim S., Walker A., Anderson J., et al. Effects of genetic perturbation on seasonal life history plasticity. Science 2009, 323:930-934.
50. Chew Y.H., Wilczek A.M., Williams M., Welch S.M., Schmitt J., Halliday K.J. An augmented Arabidopsis phenology model reveals seasonal temperature control of flowering time. New Phytol 2012, 194:654-665.
51. Wilczek A.M., Burghardt L.T., Cobb A.R., Cooper M.D., Welch S.M., Schmitt J. Genetic and physiological bases for phenological responses to current and predicted climates. Phil Trans R Soc B: Biol Sci 2010, 365:3129-3147.
52. Kuwahara H., Soyer O.S. Bistability in feedback circuits as a byproduct of evolution of evolvability. Mol Syst Biol 2012, 8:98.
53. Kwon Y.K., Cho K.H. Analysis of feedback loops and robustness in network evolution based on Boolean models. BMC Bioinformatics 2007, 8:430.
54. Leclerc R.D. Survival of the sparsest: robust gene networks are parsimonious. Mol Syst Biol 2008, 4:5.
55. Etterson J.R., Shaw R.G. Constraint to adaptive evolution in response to global warming. Science 2001, 294:151-154.
56. Lovell J.T., Juenger T.E., Michaels S.D., Lasky J.R., Platt A., Richards J.H., Yu X., Easlon H.M., Sen S., McKay J.K. Pleiotropy of FRIGIDA enhances the potential for multivariate adaptation. Proc R Soc B: Biol Sci 2013, 280:20131043.
57. Masle J., Gilmore S.R., Farquhar G.D. The ERECTA gene regulates plant transpiration efficiency in Arabidopsis. Nature 2005, 436:866-870.
58. Brock M.T., Stinchcombe J.R., Weinig C. Indirect effects of FRIGIDA: floral trait (co)variances are altered by seasonally variable abiotic factors associated with flowering time. J Evol Biol 2009, 22:1826-1838.
59. Brock M.T., Kover P.X., Weinig C. Natural variation in GA1 associates with floral morphology in Arabidopsis thaliana. New Phytol 2012, 195:58-70.
60. Evolutionary Quantitative Genetics 1997, Chapman and Hall, New York, NY. D.A. Roff (Ed.).
61. Hall M.C., Lowry D.B., Willis J.H. Is local adaptation in Mimulus guttatus caused by trade-offs at individual loci?. Mol Ecol 2010, 19:2739-2753.
62. Mariac C., Jehin L., SaÏDou A.-A., Thuillet A.-C., Couderc M., Sire P., JugdÉ.H., Adam H., BezanÇOn G., Pham J-L., et al. Genetic basis of pearl millet adaptation along an environmental gradient investigated by a combination of genome scan and association mapping. Mol Ecol 2011, 20:80-91.
63. Keller S.R., Levsen N., Olson M.S., Tiffin P. Local adaptation in the flowering-time gene network of Balsam Poplar, Populus balsamifera L. Mol Biol Evol 2012, 29:3143-3152.
64. Parchman T.L., Gompert Z., Mudge J., Schilkey F.D., Benkman C.W., Buerkle C.A. Genome-wide association genetics of an adaptive trait in lodgepole pine. Mol Ecol 2012, 21:2991-3005.
65. McMahon S.M., Harrison S.P., Armbruster W.S., Bartlein P.J., Beale C.M., Edwards M.E., Kattge J., Midgley G., Morin X., Prentice I.C. Improving assessment and modelling of climate change impacts on global terrestrial biodiversity. Trends Ecol Evol 2011, 26:249-259.
66. Guisan A., Thuiller W. Predicting species distribution: offering more than simple habitat models. Ecol Lett 2005, 8:993-1009.
67. Dawson T.P., Jackson S.T., House J.I., Prentice I.C., Mace G.M. Beyond predictions: biodiversity conservation in a changing climate. Science 2011, 332:53-58.
68. Schurr F.M., Pagel J., Cabral J.S., Groeneveld J., Bykova O., O'Hara R.B., Hartig F., Kissling W.D., Linder H.P., Midgley G.F., et al. How to understand species' niches and range dynamics: a demographic research agenda for biogeography. J Biogeogr 2012, 39:2146-2162.
69. 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.
70. Rosenzweig C., Elliott J., Deryng D., Ruane A.C., Müller C., Arneth A., Boote K.J., Folberth C., Glotter M., Khabarov N., et al. Assessing agricultural risks of climate change in the 21st century in a global gridded crop model intercomparison. Proc Natl Acad Sci U S A 2013.
71. Yin X., Struik P.C. The role of QTL-based physiological modelling in crop improvement. Proceedings of the Conference on Systems Approaches to Crop Improvement 2011, N. Halford, M. Semenov (Eds.).
72. Mitchell-Olds T. Selection on QTL and complex traits in complex environments. Ecol Lett 2013, 22:3247-3429.
73. Hammer G., Cooper M., Tardieu F., Welch S., Walsh B., van Eeuwijk F., Chapman S., Podlich D. Models for navigating biological complexity in breeding improved crop plants. Trends Plant Sci 2006, 11:587-593.
74. Morin X., Thuiller W. Comparing niche- and process-based models to reduce prediction uncertainty in species range shifts under climate change. Ecology 2009, 90:1301-1313.
75. Urban M.C., Tewksbury J.J., Sheldon K.S. On a collision course: competition and dispersal differences create no-analogue communities and cause extinctions during climate change. Proc Biol Sci 2012, 279:2072-2080.
76. Fennell M., Murphy J.E., Gallagher T., Osborne B. Simulating the effects of climate change on the distribution of an invasive plant, using a high resolution, local scale, mechanistic approach: challenges and insights. Glob Change Biol 2013, 19:1262-1274.
77. McDowell N.G., Fisher R.A., Xu C., Domec J.C., Holtta T., Mackay D.S., Sperry J.S., Boutz A., Dickman L., Gehres N., et al. Evaluating theories of drought-induced vegetation mortality using a multimodel-experiment framework. New Phytol 2013, 200:304-321.