A new analytical approach to landscape genetic modelling: Least-cost transect analysis and linear mixed models

Molecular Ecology

Volumn 21, Issue 16, 2012, Pages 4010-4023

  Van Strien, Maarten J ^a,b   Keller, Daniela ^a,b   Holderegger, Rolf ^a,b  

^a SWISS FEDERAL RESEARCH INSTITUTE WSL   (Switzerland)

^b ETH ZURICH   (Switzerland)

Author keywords

gene flow; landscape genetics; least cost paths; linear mixed model; migration; resistance surface

Indexed keywords

MICROSATELLITE DNA;

ARTICLE; BIOLOGICAL MODEL; ECOSYSTEM; ENDANGERED SPECIES; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; ODONATA; PHYSIOLOGY; POPULATION GENETICS; POPULATION MIGRATION; STATISTICAL MODEL; SWITZERLAND; THEORETICAL MODEL;

ANIMAL MIGRATION; ECOSYSTEM; ENDANGERED SPECIES; GENETICS, POPULATION; LINEAR MODELS; MICROSATELLITE REPEATS; MODELS, GENETIC; MODELS, THEORETICAL; MOLECULAR SEQUENCE DATA; ODONATA; SWITZERLAND;

COENAGRION MERCURIALE; ZYGOPTERA;

EID: 84864412558     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2012.05687.x     Document Type: Article

References (64)

1. Adriaensen F, Chardon JP, De Blust G, et al. (2003) The application of 'least-cost' modelling as a functional landscape model. Landscape and Urban Planning, 64, 233-247.
2. Anderson CD, Epperson BK, Fortin M-J, et al. (2010) Considering spatial and temporal scale in landscape-genetic studies of gene flow. Molecular Ecology, 19, 3565-3575.
3. Angelone S, Kienast F, Holderegger R, (2011) Where movement happens: scale-dependent landscape effects on genetic differentiation in the European tree frog. Ecography, 34, 714-722.
4. Bates D, Maechler M, Bolker B, (2011) lme4: linear mixed-effects models using S4 classes. R package version 0.999375-999342.
5. Bellamy PE, Rothery P, Hinsley SA, (2003) Synchrony of woodland bird populations: the effect of landscape structure. Ecography, 26, 338-348.
6. Burnham KP, Anderson DR, (2002) Model Selection and Multimodel Inference. A Practical Information-Theoretic Approach. Springer, New York.
7. Clarke KR, Ainsworth M, (1993) A method of linking multivariate community structure to environmental variables. Marine Ecology Progress Series, 92, 205-219.
8. Clarke RT, Rothery P, Raybould AF, (2002) Confidence limits for regression relationships between distance matrices: estimating gene flow with distance. Journal of Agricultural Biological and Environmental Statistics, 7, 361-372.
9. Conover WJ, (1999) Practical Nonparametric Statistics. Wiley, New York.
10. Coulon A, Cosson JF, Angibault JM, et al. (2004) Landscape connectivity influences gene flow in a roe deer population inhabiting a fragmented landscape: an individual-based approach. Molecular Ecology, 13, 2841-2850.
11. Cushman SA, Landguth EL, (2010) Scale dependent inference in landscape genetics. Landscape Ecology, 25, 967-979.
12. Cushman SA, McKelvey KS, Hayden J, Schwartz MK, (2006) Gene flow in complex landscapes: testing multiple hypotheses with causal modeling. American Naturalist, 168, 486-499.
13. Davis ES, Murray TE, Fitzpatrick U, Brown MJF, Paxton RJ, (2010) Landscape effects on extremely fragmented populations of a rare solitary bee, Colletes floralis. Molecular Ecology, 19, 4922-4935.
14. Driezen K, Adriaensen F, Rondinini C, Doncaster CP, Matthysen E, (2007) Evaluating least-cost model predictions with empirical dispersal data: a case-study using radiotracking data of hedgehogs (Erinaceus europaeus). Ecological Modelling, 209, 314-322.
15. 2 statistic for fixed effects in the linear mixed model. Statistics in Medicine, 27, 6137-6157.
16. Emaresi G, Pellet J, Dubey S, Hirzel AH, Fumagalli L, (2011) Landscape genetics of the Alpine newt (Mesotriton alpestris) inferred from a strip-based approach. Conservation Genetics, 12, 41-50.
17. Gigerenzer G, Goldstein DG, (1996) Reasoning the fast and frugal way: models of bounded rationality. International Journal of Psychology, 31, 1315.
18. Gillies CS, Hebblewhite M, Nielsen SE, et al. (2006) Application of random effects to the study of resource selection by animals. Journal of Animal Ecology, 75, 887-898.
19. Gillies CS, Beyer HL, St Clair CC, (2011) Fine-scale movement decisions of tropical forest birds in a fragmented landscape. Ecological Applications, 21, 944-954.
20. Goldberg CS, Waits LP, (2010) Comparative landscape genetics of two pond-breeding amphibian species in a highly modified agricultural landscape. Molecular Ecology, 19, 3650-3663.
21. Gonseth Y, Monnerat C, (2002) Rote Liste der gefährdeten Libellen der Schweiz. BAFU, Bern, Switzerland.
22. Gurka MJ, (2006) Selecting the best linear mixed model under REML. American Statistician, 60, 19-26.
23. Hagerty BE, Nussear KE, Esque TC, Tracy CR, (2011) Making molehills out of mountains: landscape genetics of the Mojave desert tortoise. Landscape Ecology, 26, 267-280.
24. Halekoh U, Højsgaard S, (2011) pbkrtest: parametric bootstrap and Kenward Roger based methods for mixed model comparison. R package version 0.2.0.
25. Hebblewhite M, Merrill E, (2008) Modelling wildlife-human relationships for social species with mixed-effects resource selection models. Journal of Applied Ecology, 45, 834-844.
26. Holderegger R, Wagner HH, (2008) Landscape genetics. BioScience, 58, 199-207.
27. Holland JD, Bert DG, Fahrig L, (2004) Determining the spatial scale of species' response to habitat. BioScience, 54, 227-233.
28. Kenward MG, Roger JH, (1997) Small sample inference for fixed effects from restricted maximum likelihood. Biometrics, 53, 983-997.
29. Legendre P, Fortin MJ, (1989) Spatial pattern and ecological analysis. Vegetatio, 80, 107-138.
30. Legendre P, Fortin MJ, (2010) Comparison of the Mantel test and alternative approaches for detecting complex multivariate relationships in the spatial analysis of genetic data. Molecular Ecology Resources, 10, 831-844.
31. Legendre P, Legendre L, (1998) Numerical Ecology. Elsevier, Amsterdam, The Netherlands.
32. Manel S, Schwartz MK, Luikart G, Taberlet P, (2003) Landscape genetics: combining landscape ecology and population genetics. Trends in Ecology and Evolution, 18, 189-197.
33. McRae BH, (2006) Isolation by resistance. Evolution, 60, 1551-1561.
34. McRae BH, Beier P, (2007) Circuit theory predicts gene flow in plant and animal populations. Proceedings of the National Academy of Sciences of the United States of America, 104, 19885-19890.
35. Meeuwig MH, Guy CS, Kalinowski ST, Fredenberg WA, (2010) Landscape influences on genetic differentiation among bull trout populations in a stream-lake network. Molecular Ecology, 19, 3620-3633.
36. ST and related measures. Molecular Ecology Resources, 11, 5-18.
37. Mysterud A, Ims RA, (1998) Functional responses in habitat use: availability influences relative use in trade-off situations. Ecology, 79, 1435-1441.
38. Orelien JG, Edwards LJ, (2008) Fixed-effect variable selection in linear mixed models using statistics. Computational Statistics & Data Analysis, 52, 1896-1907.
39. Pavlacky DC, Goldizen AW, Prentis PJ, Nicholls JA, Lowe AJ, (2009) A landscape genetics approach for quantifying the relative influence of historic and contemporary habitat heterogeneity on the genetic connectivity of a rainforest bird. Molecular Ecology, 18, 2945-2960.
40. Perez-Espona S, Perez-Barberia FJ, McLeod JE, et al. (2008) Landscape features affect gene flow of Scottish Highland red deer (Cervus elaphus). Molecular Ecology, 17, 981-996.
41. Pinto N, Keitt TH, (2009) Beyond the least-cost path: evaluating corridor redundancy using a graph-theoretic approach. Landscape Ecology, 24, 253-266.
42. Prevedello JA, Vieira MV, (2010) Does the type of matrix matter? A quantitative review of the evidence. Biodiversity and Conservation, 19, 1205-1223.
43. Purse BV, Hopkins GW, Day KJ, Thompson DJ, (2003) Dispersal characteristics and management of a rare damselfly. Journal of Applied Ecology, 40, 716-728.
44. R Development Core Team (2011) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
45. Rayfield B, Fortin MJ, Fall A, (2010) The sensitivity of least-cost habitat graphs to relative cost surface values. Landscape Ecology, 25, 519-532.
46. Ricketts TH, (2001) The matrix matters: effective isolation in fragmented landscapes. American Naturalist, 158, 87-99.
47. Rouquette JR, Thompson DJ, (2005) Habitat associations of the endangered damselfly, Coenagrion mercuriale, in a water meadow ditch system in southern England. Biological Conservation, 123, 225-235.
48. Rouquette JR, Thompson DJ, (2007) Patterns of movement and dispersal in an endangered damselfly and the consequences for its management. Journal of Applied Ecology, 44, 692-701.
49. Rousset F, (2008) GENEPOP'007: a complete re-implementation of the GENEPOP software for Windows and Linux. Molecular Ecology Resources, 8, 103-106.
50. Schwartz MK, Copeland JP, Anderson NJ, et al. (2009) Wolverine gene flow across a narrow climatic niche. Ecology, 90, 3222-3232.
51. Selkoe KA, Watson JR, White C, et al. (2010) Taking the chaos out of genetic patchiness: seascape genetics reveals ecological and oceanographic drivers of genetic patterns in three temperate reef species. Molecular Ecology, 19, 3708-3726.
52. Smouse PE, Long JC, Sokal RR, (1986) Multiple regression and correlation extensions of the Mantel test of matrix correspondence. Systematic Zoology, 35, 627-632.
53. Spear SF, Peterson CR, Matocq MD, Storfer A, (2005) Landscape genetics of the blotched tiger salamander (Ambystoma tigrinum melanostictum). Molecular Ecology, 14, 2553-2564.
54. Spear SF, Balkenhol N, Fortin MJ, McRae BH, Scribner K, (2010) Use of resistance surfaces for landscape genetic studies: considerations for parameterization and analysis. Molecular Ecology, 19, 3576-3591.
55. Srinivasan N, Mukherjee S, (2010) Attribute preference and selection in multi-attribute decision making: implications for unconscious and conscious thought. Consciousness and Cognition, 19, 644-652.
56. Stevens VM, Verkenne C, Vandewoestijne S, Wesselingh RA, Baguette M, (2006) Gene flow and functional connectivity in the natterjack toad. Molecular Ecology, 15, 2333-2344.
57. Storfer A, Murphy MA, Evans JS, et al. (2007) Putting the 'landscape' in landscape genetics. Heredity, 98, 128-142.
58. Storfer A, Murphy MA, Spear SF, Holderegger R, Waits LP, (2010) Landscape genetics: where are we now? Molecular Ecology, 19, 3496-3514.
59. Van Strien MJ, Keller D, Holderegger R, (2012) Data from: a new analytical approach to landscape genetic modeling: least-cost transect analysis and linear mixed models. Dryad Digital Repository, DOI: t.
60. Verbeke G, Molenberghs G, (2000) Linear Mixed Models for Longitudinal Data. Springer, New York.
61. Watts PC, Wu JH, Westgarth C, Thompson DJ, Kemp SJ, (2004) A panel of microsatellite loci for the Southern damselfly, Coenagrion mercuriale (Odonata: Coenagrionidae). Conservation Genetics, 5, 117-119.
62. Weir BS, Cockerham CC, (1984) Estimating F-statistics for the analysis of populations structure. Evolution, 38, 1358-1370.
63. Wu J, (2004) Effects of changing scale on landscape pattern analysis: scaling relations. Landscape Ecology, 19, 125-138.
64. Yang R-C, (2004) A likelihood-based approach to estimating and testing for isolation by distance. Evolution, 58, 1839-1845.