Ten years of landscape genetics

Trends in Ecology and Evolution

Volumn 28, Issue 10, 2013, Pages 614-621

  Manel, Stéphanie ^a,b   Holderegger, Rolf ^c,d  

^a Aix Marseille University Marseille   (France)

^b CIRAD   (France)

^c SWISS FEDERAL RESEARCH INSTITUTE WSL   (Switzerland)

^d ETH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

CONSERVATION MANAGEMENT; EVOLUTIONARY THEORY; GENETIC VARIATION; GENETICS; GENOMICS; GLOBAL CHANGE; LANDSCAPE;

ENVIRONMENT; ENVIRONMENTAL PROTECTION; GENE FLOW; GENOMICS; METHODOLOGY; POPULATION GENETICS; REVIEW;

CONSERVATION OF NATURAL RESOURCES; ENVIRONMENT; GENE FLOW; GENETICS, POPULATION; GENOMICS;

EID: 84884354428     PISSN: 01695347     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tree.2013.05.012     Document Type: Review

References (88)

1. Butchart S.H.M., et al. Global biodiversity: indicators of recent declines. Science 2010, 328:1164-1168.
2. Rands M.R.W., et al. Biodiversity conservation: challenges beyond 2010. Science 2010, 329:1298-1303.
3. Kokko H., Lopez-Sepulcre A. From individual dispersal to species ranges: perspectives for a changing world. Science 2006, 313:789-791.
4. Hughes J.B., et al. Population diversity: its extent and extinction. Science 1997, 278:689-692.
5. Hoffmann A., Willi Y. Detecting genetic response to environmental change. Nat. Rev. Genet. 2008, 9:421-432.
6. Norberg J., et al. Eco-evolutionary responses of biodiversity to climate change. Nat. Clim. Change 2012, 2:747-751.
7. Pauls S.U., et al. The impact of global climate change on genetic diversity within populations and species. Mol. Ecol. 2013, 22:925-946.
8. Manel S., et al. Landscape genetics: combining landscape ecology and population genetics. Trends Ecol. Evol. 2003, 18:157-206.
9. Hanotte O., et al. Time to tap Africa's livestock genomes. Science 2010, 328:1640-1641.
10. Schoville S., et al. Adaptive genetic variation on the landscape: methods and cases. Annu. Rev. Ecol. Evol. 2012, 43:23-43.
11. Cushman S.A., et al. Gene flow in complex landscapes: testing multiple hypotheses with causal modeling. Am. Nat. 2006, 168:486-499.
12. McRae B.H., Beier P. Circuit theory predicts gene flow in plant and animal populations. Proc. Natl. Acad. Sci. U.S.A. 2007, 104:19885-19890.
13. Balkenhol N., et al. Statistical approaches in landscape genetics: an evaluation of methods for linking landscape and genetic data. Ecography 2009, 32:818-830.
14. Raufaste N., Rousset F. Are partial Mantel tests adequate?. Evolution 2001, 55:1703-1705.
15. Goldberg C.S., Waits L.P. Using habitat models to determine conservation priorities for pond-breeding amphibians in a privately-owned landscape of northern Idaho, USA. Biol. Conserv. 2009, 142:1096-1104.
16. Van Strien M.J., et al. A new analytical approach to landscape genetic modelling: least-cost transect analysis and linear mixed models. Mol. Ecol. 2012, 21:4010-4023.
17. 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. Resour. 2010, 10:831-844.
18. Anderson C., et al. The importance of spatial and temporal scale in landscape genetics. Mol. Ecol. 2010, 19:3565-3575.
19. Zellmer A.J., Knowles L.L. Disentangling the effects of historic vs. contemporary landscape structure on population genetic divergence. Mol. Ecol. 2009, 18:3593-3602.
20. Landguth E.L., et al. Quantifying the lag time to detect barriers in landscape genetics. Mol. Ecol. 2010, 19:4179-4191.
21. Keller I., Holderegger R. Damselflies use different movement habitats for short- and long-distance dispersal. Insect Conserv. Divers. 2013, 10.1111/icad.12016.
22. Dyer R.J., et al. Pollination graphs: quantifying pollen pool covariance networks and the influence of intervening landscape on genetic connectivity in the North American understory tree Cornus florida L. Landscape Ecol. 2012, 27:239-251.
23. Etherington T.R. Python based GIS tools for landscape genetics: visualising genetic relatedness and measuring landscape connectivity. Methods Ecol. Evol. 2011, 2:52-55.
24. Ewers R.M., et al. Making statistics biologically relevant in fragmented landscapes. Trends Ecol. Evol. 2010, 25:699-704.
25. Hepenstrick D., et al. Genetic discontinuities in roe deer (Capreolus capreolus) coincide with fenced transportation infrastructure. Basic Appl. Ecol. 2012, 13:631-638.
26. Thomassen H.A., et al. Mapping evolutionary process: a multi-taxa approach to conservation prioritization. Evol. Appl. 2011, 4:397-413.
27. Storfer A., et al. Landscape genetics: where are we now?. Mol. Ecol. 2010, 19:3496-3514.
28. Carr M.H., et al. Comparing marine and terrestrial ecosystems: implications for the design of coastal marine reserves. Ecol. Appl. 2003, 13:S90-S107.
29. Galindo H.M., et al. Seascape genetics along a steep cline: using genetic patterns to test predictions of marine larval dispersal. Mol. Ecol. 2010, 19:3692-3707.
30. Selkoe K.A., et al. Seascape genetics and the spatial ecology of marine populations. Fish Fish. 2008, 9:363-377.
31. Selkoe K.A., et al. Taking the chaos out of genetic patchiness: seascape genetics reveals ecological and oceanographic drivers of genetic patterns in three temperate reef species. Mol. Ecol. 2010, 19:3708-3726.
32. Luikart G., et al. The power and promise of population genomics: from genotyping to genome typing. Nat. Rev. Genet. 2003, 4:981-994.
33. Foll M., Gaggiotti O. A genome scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective. Genetics 2008, 180:977-993.
34. Coop G., et al. Using environmental correlations to identify loci underlying local adaptation. Genetics 2010, 185:1411-1423.
35. 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.
36. Manel S., et al. Common factors drive adaptive genetic variation at different spatial scales in Arabis alpina. Mol. Ecol. 2010, 19:3824-3835.
37. Boitard S., et al. Detecting selective sweeps from pooled next-generation sequencing samples. Mol. Evol. Biol. 2012, 29:2177-2186.
38. Segura V., et al. An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations. Nat. Genet. 2012, 44:825-830.
39. Segelbacher G., et al. Applications of landscape genetics in conservation biology: concepts and challenges. Conserv. Genet. 2010, 11:375-385.
40. Holderegger R., et al. Land ahead: using genome scans to identify molecular markers of adaptive relevance. Plant Ecol. Divers. 2008, 1:273-283.
41. Corlatti L., et al. Ability of wildlife overpasses to provide connectivity and prevent genetic isolation. Conserv. Biol. 2009, 23:548-556.
42. Allendorf F.W., et al. Genomics and the future of conservation genetics. Nat. Rev. Genet. 2010, 11:697-709.
43. Bull R.A.S., et al. Why replication is important in landscape genetics: American black bear in the Rocky Mountains. Mol. Ecol. 2011, 20:1092-1107.
44. Amos J.N., et al. Predicting landscape-genetic consequences of habitat loss, fragmentation and mobility for multiple species of woodland birds. PLoS ONE 2012, 7:e30888.
45. Miller M.P., Haig S.M. Identifying shared genetic structure patterns among Pacific Northwest forest taxa: insights from use of visualization tools and computer simulations. PLoS ONE 2010, 5:e30888.
46. Manel S., et al. Broad-scale adaptive genetic variation in alpine plants is driven by temperature and precipitation. Mol. Ecol. 2012, 21:3729-3738.
47. Kelly R.P., Palumbi S.R. Genetic structure among 50 species of the Northeastern Pacific Rocky intertidal community. PLoS ONE 2010, 5:e8594.
48. Johnson C.R., Boerlijst M.C. Selection at the level of the community: the importance of spatial structure. Trends Ecol. Evol. 2002, 17:83-90.
49. Hohenlohe P.A., et al. Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags. PLoS Genet. 2010, 6:e1000862.
50. Ouborg N.J., et al. The rough edges of the conservation genetics paradigm for plants. J. Ecol. 2006, 94:1233-1248.
51. Shao J. Linear-model selection by cross-validation. J. Am. Stat. Assoc. 1993, 88:486-494.
52. Urban D.L., et al. Graph models of habitat mosaics. Ecol. Lett. 2009, 12:260-273.
53. Fortuna M.A., et al. Networks of spatial genetic variation across species. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:19044-19049.
54. Decout S., et al. Integrative approach for landscape-based graph connectivity analysis: a case study with the common frog (Rana temporaria). Landscape Ecol. 2012, 27:267-279.
55. Pimm S.L., Raven P. Biodiversity - extinction by numbers. Nature 2000, 403:843-845.
56. De Kochko A., et al. Advances in Coffea genomics. Adv. Bot. Res. 2010, 53:23-63.
57. Laurance W.F. Averting biodiversity collapse in tropical forest protected areas. Nature 2012, 489:290-294.
58. Laurance W.F. Reflections on the tropical deforestation crisis. Biol. Conserv. 1999, 91:109-117.
59. Perez-Espona S., et al. Landscape genetics of a top neotropical predator. Mol. Ecol. 2012, 21:5969-5985.
60. Angel S., et al. The dimensions of global urban expansion: estimates and projections for all countries, 2000-2050. Prog. Plann. 2011, 75:53-107.
61. Karl S.A., et al. Common misconceptions in molecular ecology: echoes of the modern synthesis. Mol. Ecol. 2012, 21:4171-4189.
62. Niemala J., et al. Urban Ecology: Patterns, Processes, and Applications 2012, Oxford University Press.
63. Unfried T.M., et al. Effects of urbanization on song sparrow (Melospiza melodia) population connectivity. Conserv. Genet. 2013, 14:41-53.
64. Fournier-Level A., et al. A map of local adaptation in Arabidopsis thaliana. Science 2011, 334:86-89.
65. Lasky J., et al. Characterizing genomic variation of Arabidopsis thaliana: the roles of geography and climate. Mol. Ecol. 2012, 21:5512-5529.
66. Poncet B., et al. Tracking genes of ecological relevance using a genome scan: application to Arabis alpina. Mol. Ecol. 2010, 19:2896-2907.
67. Banta J.A., et al. Climate envelope modelling reveals intraspecific relationships among flowering phenology, niche breadth and potential range size in Arabidopsis thaliana. Ecol. Lett. 2012, 15:769-777.
68. Kofler R., et al. PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq). Bioinformatics 2011, 27:3435-3436.
69. Strasburg J.L., et al. What can patterns of differentiation across plant genomes tell us about adaptation and speciation?. Philos. Trans. R. Soc. Lond. B: Biol. Sci. 2012, 367:364-373.
70. Lowe W.H., Allendorf F.W. What can genetics tell us about population connectivity?. Mol. Ecol. 2010, 19:3038-3051.
71. Manel S., et al. Assignment methods: matching biological questions with appropriate techniques. Trends Ecol. Evol. 2005, 20:136-142.
72. Freedman A.H., et al. Genomic signals of diversification along ecological gradients in a tropical lizard. Mol. Ecol. 2010, 19:3773-3788.
73. Andrew R.L., et al. Adaptation with gene flow across the landscape in a dune sunflower. Mol. Ecol. 2012, 21:2078-2091.
74. Andow D.A., Zwahlen C. Assessing environmental risks of transgenic plants. Ecol. Lett. 2006, 9:196-214.
75. Reichman J.R., et al. Establishment of transgenic herbicide-resistant creeping bentgrass (Agrostis stolonifera L.) in nonagronomic habitats. Mol. Ecol. 2006, 15:4243-4255.
76. Nichols J.D. Dispersal 2001, Oxford University Press.
77. Taylor P.D., et al. Connectivity is a vital element of landscape structure. Oikos 1993, 68:571-573.
78. Lindenmayer D., Fisher J. Habitat Fragmentation and Landscape Change: An Ecological and Conservation Synthesis 2006, Island Press.
79. Kool J., et al. Population connectivity: recent advances and new perspectives. Landscape Ecol. 2013, 28:165-185.
80. Wasserman T.N., et al. Simulating the effects of climate change on population connectivity of American marten (Martes americana) in the northern Rocky Mountains, USA. Landscape Ecol. 2012, 27:211-225.
81. Jay F., et al. Forecasting changes in population genetic structure of alpine plants in response to global warming. Mol. Ecol. 2012, 21:2354-2368.
82. Dale M.R., Fortin M. From graphs to spatial graphs. Annu. Rev. Ecol. Evol. 2010, 41:21-38.
83. Hopkins B. Pattern in the plant community. J. Ecol. 1957, 45:451-463.
84. Bodin O., et al. The value of small size: loss of forest patches and ecological thresholds in southern Madagascar. Ecol. Appl. 2006, 16:440-451.
85. Albert E.M., et al. Assessing the robustness of the networks of spatial genetic variation. Ecol. Lett. 2013, 16(Suppl 1):86-93.
86. Carroll C., et al. Use of linkage mapping and centrality analysis across habitat gradients to conserve connectivity of gray wolf populations in Western North America. Conserv. Biol. 2012, 26:78-87.
87. Garroway C.J., et al. Applications of graph theory to landscape genetics. Evol. Appl. 2008, 1:620-630.
88. Dyer R.J., Nason J.D. Population graphs: the graph theoretic shape of genetic structure. Mol. Ecol. 2004, 13:1713-1727.