Landscape genetics of plants

Trends in Plant Science

Volumn 15, Issue 12, 2010, Pages 675-683

  Holderegger, Rolf ^a,b   Buehler, Dominique ^a,b   Gugerli, Felix ^a   Manel, Stéphanie ^c,d  

^a SWISS FEDERAL RESEARCH INSTITUTE WSL   (Switzerland)

^b ETH ZURICH   (Switzerland)

^c Aix Marseille University Marseille   (France)

^d UNIVERSITÉ JOSEPH FOURIER   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ECOLOGY; ECOSYSTEM; GENE FLOW; GENETIC VARIABILITY; GENETICS; PLANT; PLANT PHYSIOLOGY; REVIEW;

ECOLOGY; ECOSYSTEM; GENE FLOW; GENETIC VARIATION; PLANT PHYSIOLOGICAL PHENOMENA; PLANTS;

ANIMALIA;

EID: 78649635469     PISSN: 13601385     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tplants.2010.09.002     Document Type: Review

References (102)

1. Manel S., et al. Landscape genetics: combining landscape ecology and population genetics. Trends Ecol. Evol. 2003, 18:189-197.
2. Reusch T.B.H., Wood T.E. Molecular ecology of global change. Mol. Ecol. 2007, 16:3973-3992.
3. Ouburg N.J., et al. An essay on the necessity and feasibility of conservation genomics. Conserv. Genet. 2010, 11:643-653.
4. Holderegger R., Wagner H.H. A brief guide to landscape genetics. Landsc. Ecol. 2006, 21:793-796.
5. Storfer A., et al. Putting the "landscape" in landscape genetics. Heredity 2006, 98:128-142.
6. Holderegger R., Wagner H.H. Landscape genetics. BioScience 2008, 58:199-207.
7. Storfer A., et al. Landscape genetics: where are we now?. Mol. Ecol. 2010, 19:3496-3514.
8. Lowry D.B. Landscape evolutionary genomics. Biol. Lett. 2010, 6:502-504.
9. Holderegger R., et al. Land ahead: using genome scans to identify molecular markers of adaptive relevance. Plant Ecol. Div. 2008, 1:273-283.
10. Manel S., et al. Perspectives on the use of landscape genetics to detect adaptive genetic variation in the field. Mol. Ecol. 2010, 19:3760-3772.
11. Segelbacher G., et al. Landscape genetics: concepts and challenges in a conservation context. Conserv. Genet. 2010, 11:375-385.
12. Holderegger R., Di Giulio M. The genetic effects of roads: a review of empirical evidence. Basic Appl. Ecol. 2010, 11:522-531.
13. Manel S., et al. Common factors drive genetic variation of adaptive relevance on different spatial scales in Arabis alpina. Mol. Ecol. 2010, 19:3824-3835.
14. Joost S., et al. A spatial analysis method (SAM) to detect candidate loci for selection: towards a landscape genomics approach to adaptation. Mol. Ecol. 2007, 16:3955-3969.
15. ST ≠ 1/(4Nm+1). Heredity 1999, 82:117-125.
16. Lowe A.J., et al. Ecological Genetics. Design, Analysis and Application 2004, Blackwell.
17. Adriaensen F., et al. The application of "least-cost" modeling as a functional landscape model. Landsc. Urban Plan. 2003, 64:233-247.
18. Baguette M., Van Dyck H. Landscape connectivity and animal behaviour: functional grain as a key determinant for dispersal. Landsc. Ecol. 2007, 22:117-1129.
19. Smouse P.E., et al. Multiple regression and correlation extensions of the Mantel tests of matrix correspondence. Syst. Zool. 1986, 35:627-632.
20. Wright S. Isolation by distance. Genetics 1943, 28:114-138.
21. Cushman S.A., et al. Gene flow in complex landscapes: testing multiple hypotheses with causal modeling. Am. Nat. 2006, 168:486-499.
22. Raufaste N., Rousset F. Are partial Mantel tests adequate?. Evolution 2001, 55:1703-1705.
23. Balkenhol N., et al. Statistical approaches in landscape genetics: an evaluation of methods for linking landscape and genetic data. Ecography 2009, 32:818-830.
24. Legendre P., Fortin M.-J. Comparison of the Mantel test and alternative approaches for detecting complex multivariate relationships in the spatial analysis of genetic data. Mol. Ecol. Res. 2010, 10:831-844.
25. McRae B.H. Isolation by resistance. Evolution 2006, 60:1551-1561.
26. Trénel P., et al. Landscape genetics, historical isolation and cross-Andean gene flow in the wax palm, Ceroxylon echinulatum (Arecaceae). Mol. Ecol. 2008, 17:3528-3540.
27. Fievet V., et al. Spatial analysis of nuclear and cytoplasmic DNA diversity in wild sea beet (Beta vulgaris ssp. maritima) populations: do marine currents shape genetic structure?. Mol. Ecol. 2007, 16:1847-1864.
28. Kitamoto N., et al. Spatial genetic structure among and within populations of Primula sieboldii growing on separate streams. Mol. Ecol. 2005, 14:149-157.
29. Hirao A.S., Kudo G. Landscape genetics of alpine-snowbed plants: comparisons along geographic and snowmelt gradients. Heredity 2004, 93:290-298.
30. Hirao A.S., Kudo G. The effect of segregation of flowering time on fine-scale spatial genetic structure in an alpine-snowbed herb Primula cuneifolia. Heredity 2008, 100:424-430.
31. Legendre P., et al. Modeling brain evolution from behaviour: a permutational regression approach. Evolution 1994, 48:1487-1499.
32. Cade B.S., Richards J.D. User Manual BLOSSOM Statistical Software 2005, US Geological Survey.
33. Johnson J.B., et al. Model selection in ecology and evolution. Trends Ecol. Evol. 2004, 19:101-108.
34. Parisod C., Christin P.-A. Genome-wide association to fine-scale ecological heterogeneity within a continuous population of Biscutella laevigata (Brassicaceae). New Phytol. 2008, 178:436-447.
35. Helm A., et al. Human influence lowers plant genetic diversity in communities with extinction debt. J. Ecol. 2009, 97:1329-1336.
36. Manel S., et al. Assignment methods: matching biological questions with appropriate techniques. Trends Ecol. Evol. 2005, 20:136-142.
37. Pritchard J.K., et al. Inference of population structure using multilocus genotype data. Genetics 2000, 155:945-959.
38. Corander J., et al. Enhanced Bayesian modeling in BAPS software for learning genetic structures of populations. BMC Bioinformatics 2008, 9:539.
39. François O., et al. Bayesian clustering using hidden Markov random fields in spatial population genetics. Genetics 2006, 174:805-816.
40. Guillot G., et al. GENELAND: a computer package for landscape genetics. Mol. Ecol. Notes 2005, 5:712-715.
41. Dupanloup I., et al. A simulated annealing approach to define the genetic structure of populations. Mol. Ecol. 2002, 11:2571-2581.
42. Gaudeul M., Till-Bottraud I. Genetic structure of the endangered perennial plant Eryngium alpinum (Apiaceae) in an alpine valley. Biol. J. Linn. Soc. 2008, 93:667-677.
43. Born C., et al. Small-scale spatial genetic structure in the Central African rainforest tree species Aucomea klaineana: a stepwise approach to infer the impact of limited gene dispersal, population history and habitat fragmentation. Mol. Ecol. 2008, 17:2041-2050.
44. Kang M., et al. Understanding population structure and historical demography in a conservation context: population genetics of an endangered fern. Divers. Distrib. 2008, 14:799-807.
45. Manni F., et al. Geographic patterns of (genetic, morphologic, linguistic) variation: how barriers can be detected by using Monmonier's algorithm. Hum. Biol. 2004, 76:173-190.
46. Miller M.P. ALLELES IN SPACE (AIS): computer software for the joint analysis of interindividual spatial and genetic information. J. Hered. 2005, 96:722-724.
47. Manel S., et al. A new individual-based spatial approach for identifying genetic discontinuities in natural populations. Mol. Ecol. 2007, 16:2031-2043.
48. Soares T.N., et al. Landscape conservation genetics of Dipetryx alata (" baru" tree: Fabaceae) from Cerrado region of Central Brazil. Genetica 2008, 132:9-19.
49. Torres E., et al. Analysis of within-population spatial genetic structure in Antirrhinum microphyllum (Scrophulariaceae). Am. J. Bot. 2003, 90:1688-1695.
50. Fortin M.-J., Dale M.R.T. Spatial Analysis. A Guide for Ecologists 2005, Cambridge University Press.
51. Fortin M.-J., et al. Species' geographic ranges and distribution limits: pattern analysis and statistical issues. Oikos 2005, 108:7-17.
52. St. Louis V., et al. Spatial association between forest heterogeneity and breeding territory boundaries of two forest songbirds. Landsc. Ecol. 2004, 19:591-601.
53. Avise J.C. Molecular Markers, Natural History and Evolution 1994, Chapman and Hall.
54. Coulon A., et al. Genetic structure is influenced by landscape features: empirical evidence from a roe deer population. Mol. Ecol. 2006, 15:1669-1679.
55. Kuehn R., et al. Genetic effect of transportation infrastructure on roe deer populations (Capreolus capreolus). J. Hered. 2007, 98:13-22.
56. Balkenhol N., et al. Identifying future research needs in landscape genetics: where to from here?. Landsc. Ecol. 2009, 24:455-463.
57. Anderson C.D., et al. Considering spatial and temporal scale in landscape-genetic studies of gene flow. Mol. Ecol. 2010, 19:3565-3575.
58. Jones A.G., et al. A practical guide to methods of parentage analysis. Mol. Ecol. Res. 2010, 10:6-30.
59. Sork V.L., Smouse P.E. Genetic analysis of landscape connectivity in tree populations. Landsc. Ecol. 2006, 21:821-836.
60. Marshall T.C., et al. Statistical confidence for likelihood-based paternity inference in natural populations. Mol. Ecol. 1998, 7:639-655.
61. Walling C.A., et al. Comparing parentage inference software: reanalysis of a red deer pedigree. Mol. Ecol. 2010, 19:1914-1928.
62. Godoy J.A., Jordano P. Seed dispersal by animals: exact identification of source trees with endocarp DNA microsatellites. Mol. Ecol. 2001, 10:2275-2283.
63. Kamm U., et al. Frequent long-distance gene flow in a rare temperate forest tree (Sorbus domestica) on the landscape scale. Heredity 2009, 103:476-482.
64. White G.M., et al. Increased pollen flow counteracts fragmentation in a tropical dry forest: an example from Swietenia humilis Zuccarini. Proc. Natl. Acad. Sci. U. S. A. 2002, 99:2038-2042.
65. Bacles C.F.E., Ennos R.A. Paternity analysis of pollen-mediated gene flow for Fraxinus excelsior L. in a chronically fragmented landscape. Heredity 2008, 101:368-380.
66. Hoebee S.E., et al. Mating patterns and contemporary gene flow by pollen in a large continuous and a small isolated population of the scattered forest tree Sorbus torminalis. Heredity 2007, 99:47-55.
67. Kamm U., et al. Open areas in a landscape enhance pollen-mediated gene flow of a tree species: evidence from northern Switzerland. Landsc. Ecol. 2010, 25:903-911.
68. Piry S., et al. GENECLASS2: a software for genetic assignment and first-generation migrant detection. J. Hered. 2004, 95:536-539.
69. Wilson G.A., Rannala B. Bayesian inference of recent migration rates using multilocus genotypes. Genetics 2003, 163:1177-1191.
70. He T., et al. Long-distance dispersal of seeds in the fire-tolerant shrub Banksia attenuata. Ecography 2009, 32:571-580.
71. Raffl C., et al. Patterns in genetic diversity of Trifolium pallescens populations do not reflect chronosequence on alpine glacier forelands. Heredity 2008, 100:526-532.
72. Mitsiu Y., et al. Multiple spatial scale patterns of genetic diversity in riparian populations of Ainslianaea faurieana (Asteraceae) on Yakushima Island, Japan. Am. J. Bot. 2010, 97:101-110.
73. Faubet P., Gaggiotti O.E. A new Bayesian method to identify the environmental factors that influence recent migration. Genetics 2008, 178:1491-1504.
74. Honnay O., et al. Low impact of present and historical landscape configuration on the genetics of fragmented Anthyllis vulneraria populations. Biol. Conserv. 2006, 127:411-419.
75. Schmidt T., et al. Effects of landscape structure on genetic diversity of Geum urbanum L. populations in agricultural landscapes. Flora 2008, 204:549-559.
76. Vandepitte K., et al. Landscape genetics of the self-compatible forest herb Geum urbanum: effects of habitat age, fragmentation and local environment. Mol. Ecol. 2007, 16:4171-4179.
77. Merilä J., Crnokrak P. Comparison of genetic differentiation at marker loci and quantitative traits. J. Evol. Biol. 2001, 14:892-903.
78. Reed D.H., Frankham R. How closely correlated are molecular and quantitative measures of genetic variation? A meta-analysis. Evolution 2001, 55:1095-1103.
79. Leimu R., et al. How general are positive relationships between plant population size, fitness and genetic variation?. J. Ecol. 2006, 94:942-952.
80. Hoffmann A.A., Willi Y. Detecting genetic responses to environmental change. Nat. Rev. Genet. 2008, 9:421-432.
81. Storz J.F. Using genome scans of DNA polymorphism to infer adaptive population divergence. Mol. Ecol. 2005, 14:671-688.
82. Stinchcombe J.R., Hoekstra H.E. Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits. Heredity 2008, 100:158-170.
83. Beaumont M.A., Balding D.J. Identifying adaptive genetic divergence among populations from genome scans. Mol. Ecol. 2004, 13:969-980.
84. Savolainen V., et al. Sympatric speciation in palms on an oceanic island. Nature 2006, 441:210-213.
85. Bonin A., et al. Population adaptive index: a new method to help measure intraspecific genetic diversity and prioritize populations for conservation. Conserv. Biol. 2007, 21:697-708.
86. Meudt H.M., Clarke A.C. Almost forgotten or latest practice? AFLP applications, analyses and advances. Trends Plant Sci. 2007, 12:106-117.
87. Joost S., et al. Spatial analysis method (SAM): a software tool combining molecular and environmental data to identify candidate loci for selection. Mol. Ecol. Res. 2008, 8:957-960.
88. Todesco M., et al. Natural allelic variation underlying a major fitness trade-off in Arabidopsis thaliana. Nature 2010, 465:632-636.
89. Excoffier L., et al. Detecting loci under selection in a hierarchically structured population. Heredity 2009, 103:285-298.
90. Guillot G., et al. Statistical methods in spatial genetics. Mol. Ecol. 2009, 18:4734-4756.
91. Fortuna M.A., et al. Networks of spatial genetic variation across species. Proc. Natl. Acad. Sci. U. S. A. 2009, 106:19044-19049.
92. Poncet B.N., et al. Tracking genes of ecological relevance using a genome scan in two independent regional population samples of Arabis alpina. Mol. Ecol. 2010, 19:2896-2907.
93. Alvarez N., et al. History or ecology? Substrate type as a major driver of spatial genetic structure in alpine plants. Ecol. Lett. 2009, 12:632-640.
94. Nordborg M., Weigel D. Next-generation genetics in plants. Nature 2008, 456:720-723.
95. Besenbacher S., et al. A fast algorithm for genome-wide haplotype pattern mining. BMC Bioinformatics 2009, 10:S74.
96. Schmidt P.S., et al. Ecological genetics in the North Atlantic: environmental gradients and adaptation at specific loci. Ecology 2008, 89:S91-S107.
97. ST approaches reveal single nucleotide polymorphisms under selection in goat breeds of North-East Mediterranean. BMC Genetics 2009, 10:7.
98. Parisod C., Joost S. Divergent selection in trailing- versus leading-edge populations of Biscutella laevigata. Ann. Bot. 2010, 105:655-660.
99. Jump A.S., et al. Natural selection and climate change: temperature-linked spatial and temporal trends in gene frequency in Fagus sylvatica. Mol. Ecol. 2006, 15:3469-3480.
100. Bradbury P.J., et al. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 2007, 23:2633-2635.
101. Borcard D., Legendre P. All-scale spatial analysis of ecological data by means of principal coordinates of neighbour matrices. Ecol. Model. 2002, 153:51-68.
102. R Development Core Team (2007) R: a Language and Environment for Statistical Computing. http://www.r-project.org/.