Habitat selection predicts genetic relatedness in an alpine ungulate

Ecology

Volumn 93, Issue 6, 2012, Pages 1317-1329

  Shafer, Aaron B A ^a   Northrup, Joseph M ^a,b   White, Kevin S ^c   Boyce, Mark S ^a   Côté, Steeve D ^d   Coltman, David W ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

^b Department of Ecosystem Science and Sustainability   (United States)

^c ALASKA DEPARTMENT OF FISH AND GAME   (United States)

^d CENTRE D ÉTUDES NORDIQUES   (Canada)

Author keywords

Expert opinion; Global positioning system; Habitat selection; Landscape genetics; Least cost path; Mountain goats; Oreamnos americanus; Resistance surfaces; Resource selection function; Southeastern Alaska; USA

Indexed keywords

ALPINE ENVIRONMENT; BIOTELEMETRY; EVOLUTIONARY BIOLOGY; GENE FLOW; GENETIC DIFFERENTIATION; GENETIC MARKER; GOAT; GPS; HABITAT SELECTION; HETEROGENEITY; MOVEMENT; RELATEDNESS; SATELLITE DATA;

ANIMAL; ARTICLE; BOVIDS; DEMOGRAPHY; ECOSYSTEM; ENVIRONMENTAL MONITORING; FEMALE; GENETICS; MALE; UNITED STATES;

ALASKA; ANIMALS; DEMOGRAPHY; ECOSYSTEM; ENVIRONMENTAL MONITORING; FEMALE; MALE; RUMINANTS;

ALASKA; UNITED STATES;

EID: 84862271591     PISSN: 00129658     EISSN: None     Source Type: Journal    
DOI: 10.1890/11-0815.1     Document Type: Article

References (82)

1. Aarts, G., M. MacKenzie, B. McConnell, M. Fedak, and J. Matthiopoulos. 2008. Estimating space-use and habitat preference from wildlife telemetry data. Ecography 31:140-160. (Pubitemid 351280981)
2. Adams, L. G., M. A. Masteller, and J. A. Bailey. 1982. Movements and home range of mountain goats, Sheep Mountain-Gladstone Ridge, Colorado. Biennial Symposium of the Northern Wild Sheep and Goat Council 3:391-405.
3. Aldridge, C. L., S. E. Nielsen, H. L. Beyer, M. S. Boyce, J. W. Connelly, S. T. Knick, and M. A. Schroeder. 2008. Rangewide patterns of greater sage-grouse persistence. Diversity and Distributions 14:983-994.
4. Anderson, C. D., B. K. Epperson, M.-J. Fortin, R. Holderegger, P. M. A. James, M. Rosenberg, K. T. Scribner, and S. Spear. 2010. Considering spatial and temporal scale in landscape-genetic studies of gene flow. Molecular Ecology 19:3565-3575.
5. Beier, P., D. R. Majka, and W. D. Spencer. 2008. Forks in the road: Choices and procedures for designing wildland linkages. Conservation Biology 22:836-851.
6. Boyce, M. S., P. R. Vernier, S. E. Nielsen, and F. K. A. Schmiegelow. 2002. Evaluating resource selection functions. Ecological Modelling 157:281-300. (Pubitemid 35255420)
7. Burnham, K. P., and D. R. Anderson. 2002. Model selection and multimodel inference. A practical information-theoretic approach. Second edition. Springer Verlag, Berlin, Germany.
8. Cagnacci, F., L. Boitani, R. A. Powell, and M. S. Boyce. 2010. Animal ecology meets GPS-based radiotelemetry: A perfect storm of opportunities and challenges. Philosophical Transactions of the Royal Society B 1550:2157-2162.
9. Cain, J. W., III, P. R. Krausman, S. S. Rosenstock, and J. C. Turner. 2006. Mechanisms of thermoregulation and water balance in desert ungulates. Wildlife Society Bulletin 34:570-581. (Pubitemid 44784488)
10. Chetkiewicz, C. B., and M. S. Boyce. 2009. Use of resource selection functions to identify conservation corridors. Journal of Applied Ecology 46:1036-1047.
11. Choy, S. L., R. O'Leary, and K. Mengersen. 2009. Elicitation by design in ecology: Using expert opinion to inform priors for Bayesian statistical models. Ecology 90:265-277.
12. Conradt, L., T. H. Clutton-Brock, and F. E. Guinness. 2000. Sex differences in weather sensitivity can cause habitat segregation: Red deer as an example. Animal Behaviour 59:1049-1060. (Pubitemid 30656579)
13. Coulon, A., G. Guillot, J.-F. Cosson, J. M. A. Angibault, S. Aulagnier. B. Cargnelutti, M. Galan, and A. J. M. Hewison. 2006. Genetic structure is influenced by landscape features: Empirical evidence from a roe deer population. Molecular Ecology 15:1669-1679.
14. Coulon, A., N. Morellet, M. Goulard, B. Cargnelutti, J. M. Angibault, and A. J. M. Hewison. 2008. Inferring the effects of landscape structure on roe deer (Capreolus capreolus) movements using a step selection function. Landscape Ecology 23:603-614.
15. Cushman, S. A., and J. S. Lewis. 2010. Movement behavior explains genetic differentiation in American black bears. Landscape Ecology 25:1613-1625.
16. Cushman, S. A., M. K. Schwartz, J. Hayden, and K. McKelvey. 2006. Gene flow in complex landscapes: Testing multiple hypotheses with causal modeling. American Naturalist 168:486-499. (Pubitemid 44582855)
17. D'eon, R. G., and D. Delparte. 2005. Effects of radio-collar position and orientation on GPS radio-collar performance, and the implications of PDOP in data screening. Journal of Applied Ecology 42:383-388. (Pubitemid 40641092)
18. Epperson, B. K., and T. Q. Li. 1997. Gene dispersal and spatial genetic structure. Evolution 51:672-681. (Pubitemid 27324460)
19. Epps, C. W., P. J. Palsbøll, J. D. Wehausen, G. K. Roderick, R. R. Ramey II, and D. R. McCullough. 2005. Highways block gene flow and cause a rapid decline in genetic diversity of desert bighorn sheep. Ecology Letters 8:1029-1038. (Pubitemid 41345833)
20. Epps, C. W., J. D. Wehausen, V. C. Bleich, S. G. Torres, and J. S. Brashares. 2007. Optimizing dispersal and corridor models using landscape genetics. Journal of Applied Ecology 44:714-724. (Pubitemid 47024870)
21. ESRI. 2006. ArcMap 9.2. Environmental Systems Research Institute, Redlands, California, USA.
22. Festa-Bianchet, M., and S. D. Côté . 2008. Mountain goats: Ecology, behavior, and conservation of an alpine ungulate. Island Press, Washington, D.C., USA.
23. Fieberg, J., J. Matthiopoulos, M. Hebblewhite, M. S. Boyce, and J. L. Frair. 2010. Correlation and studies of habitat selection: Problem, red herring or opportunity. Philosophical Transactions of the Royal Society B 365:2233-2244.
24. Fortin, D., H. L. Beyer, M. S. Boyce, D. W. Smith, T. Duchesne, and J. S. Mao. 2005. Wolves influence elk movements: Behavior shapes a trophic cascade in Yellowstone National Park. Ecology 86:1320-1330. (Pubitemid 40641206)
25. Fox, J. L., C. A. Smith, and J. W. Schoen. 1989. Relation between mountain goats and their habitat in southeastern Alaska. USDA Forest Service, Pacific Northwest Research Station General Technical Report PNW-GTR-246.
26. Gonzales, E. K., and S. E. Gergel. 2007. Testing assumptions of cost surface analysis-A tool for invasive species management. Landscape Ecology 22:1155-1168. (Pubitemid 47301387)
27. Goslee, S. C., and D. L. Urban. 2007. The ecodist package for dissimilarity-based analysis of ecological data. Journal of Statistical Software 22:1-19.
28. Guthry, F. S., L. A. Brenna, M. J. Peterson, and J. J. Lusk. 2005. Information theory in wildlife science: Critique and viewpoint. Journal of Wildlife Management 69:457-465. (Pubitemid 41129897)
29. Hamel, S., and S. D. Côté . 2007. Habitat use patterns in relation to escape terrain: Are alpine ungulate females trading-off better foraging sites for safety? Canadian Journal of Zoology 85:933-943. (Pubitemid 350273449)
30. Hardy, O. J., and X. Vekemans. 2002. SPAGeDi: A versatile computer program to analyze spatial genetic structure at the individual or population levels. Molecular Ecology Notes 2:618.
31. Hastie, T., R. Tibshirani, and J. Friedman. 2009. The elements of statistical learning: Data mining, inference, and prediction. Second edition. Springer, New York, New York, USA.
32. Hebblewhite, M., and D. T. Haydon. 2010. Distinguishing technology from biology: A critical review of GPS telemetry data in ecology. Philosophical Transactions of the Royal Society B 1550:2303-2312.
33. Hosmer, D. W., and S. Lemeshow. 2000. Applied logistic regression. Second edition. John Wiley, New York, New York, USA.
34. Johnson, C. J., S. E. Nielsen, E. H. Merrill, T. L. McDonald, and M. S. Boyce. 2006. Resource selection functions based on use-availability data: Theoretical motivation and evaluation methods. Journal of Wildlife Management 70:347-357. (Pubitemid 43736900)
35. King, P. S. 1987. Macro- and microgeographic structure of a spatially subdivided beetle species in nature. Evolution 41:401-416.
36. Leblond, M., C. Dussault, and J. P. Ouellet. 2010. What drives fine-scale movements of large herbivores? A case study using moose. Ecography 33:1102-1112.
37. Legendre, P., and M.-J. Fortin. 1989. Spatial pattern and ecological analysis. Vegetatio 80:107-138. (Pubitemid 20418491)
38. Legendre, P., F. Lapointe, and P. Casgrain. 1994. Modeling brain evolution from behavior: A permutational regression approach. Evolution 48:1487-1499.
39. Legendre, P., and M. Troussellier. 1988. Aquatic heterotrophic bacteria: Modeling in the presence of spatial autocorrelation. Limnology and Oceanography 33:1055-1067.
40. Lele, S. R., and J. L. Keim. 2006. Weighted distributions and estimation of resource selection probability functions. Ecology 87:3021-3028. (Pubitemid 44969253)
41. Lewis, J. S., J. L. Rachlow, E. O. Garton, and L. A. Vierling. 2007. Effects of habitat on GPS collar performance: Using data screening to reduce location error. Journal of Applied Ecology 44:663-671. (Pubitemid 46791171)
42. Loe, L. E., R. J. Irvine, C. Bonenfant, A. Stien, R. Langvatn, S. D. Albon, A. Mysterud, and N. C. Stenseth. 2006. Testing five hypotheses of sexual segregation in an arctic ungulate. Journal of Animal Ecology 75:585-496.
43. Lynch, M., and L. Ritland. 1999. Estimation of pairwise relatedness with molecular markers. Genetics 152:1753-1766. (Pubitemid 29370352)
44. Mainguy, J., and S. D. Côté . 2008. Age- and state-dependent reproductive effort in male mountain goats, Oreamnos americanus. Behavioral Ecology and Sociobiology 62:935-943.
45. Mainguy, J., S. D. Côté, and D. W. Coltman. 2009. Multilocus heterozygosity, parental relatedness and individual fitness components in a wild mountain goat, Oreamnos americanus population. Molecular Ecology 18:2297-2306.
46. Mainguy, J., A. S. Llewellyn, K. Worley, S. D. Côté, and D. W. Coltman. 2005. Characterization of 29 polymorphic artiodactyl microsatellite markers for the mountain goat (Oreamnos americanus). Molecular Ecology Notes 5:809-811. (Pubitemid 43277975)
47. Manel, S., M. K. Schwartz, G. Luikart, and P. Taberlet. 2003. Landscape genetics: Combining landscape ecology and population genetics. Trends in Ecology and Evolution 18:189-197. (Pubitemid 36345738)
48. Manly, B. F. J., L. L. McDonald, D. L. Thomas, T. L. McDonald, and W. P. Erickson. 2002. Resource selection by animals: Statistical design and analysis for field studies. Second edition. Kluwer Academic Publishers, Dordrecht, The Netherlands.
49. Mantel, N. 1967. The detection of disease clustering and a generalized regression approach. Cancer Research 27:209-220.
50. Massé, A., and S. D. Côté . 2009. Habitat selection of a large herbivore at high density and without predation: Trade-off between forage and cover? Journal of Mammalogy 90:961-970.
51. McCrae, B. H. 2006. Isolation by resistance. Evolution 60:1551-1561.
52. McCrae, B. H., and V. B. Shah. 2009. Circuitscape user guide. University of California, Santa Barbara, California, USA. http://www.circuitscape.org [Accessed October, 2011]
53. McCune, B., and D. Keon. 2002. Equations for potential annual direct incident radiation and heat load. Journal of Vegetation Science 13:603-606. (Pubitemid 35259016)
54. Murray, J. V., A. W. Goldizen, R. A. O'Leary, C. A. McAlpine, H. P. Possingham, and S. L. Choy. 2009. How useful is expert opinion for predicting the distribution of a species within and beyond the region of expertise? A case study using brush-tailed rock-wallabies Petrogale penicillata. Journal of Applied Ecology 46:842-851.
55. Nielsen, S. E., G. B. Stenhouse, and M. S. Boyce. 2006. A habitat-based framework for grizzly bear conservation in Alberta. Biological Conservation 130:217-229.
56. Ortego, J., G. Yannic, A. B. A. Shafer, J. Mainguy, M. Festa- Bianchet, D. W. Coltman, and S. D. Côté . 2011. Temporal dynamics of genetic variability in a mountain goat (Oreamnos americanus) population. Molecular Ecology 20:1601-1611.
57. Palsbøll, P. J., M. Berube, and F. W. Allendorf. 2007. Identification of management units using population genetic data. Trends in Ecology and Evolution 22:11-16. (Pubitemid 44959169)
58. Pavlacky, D. C. J., A. W. Goldizen, P. J. Prentis, J. A. Nicholls, and A. J. Lowe. 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.
59. Peduzzi, P. N., J. Concato, E. Kemper, T. R. Holford, and A. R. Feinstein. 1996. A simulation study of the number of events per variable in logistic regression analysis. Journal of Clinical Epidemiology 49:1373-1379. (Pubitemid 27028925)
60. Poissant, J., A. B. A. Shafer, C. S. Davis, J. Mainguy, J. T. Hogg, S. D. Côté, and D. W. Coltman. 2009. Genome-wide cross-amplification of domestic sheep microsatellites in bighorn sheep and mountain goats. Molecular Ecology Resources 9:1121-1126.
61. Poole, K. G., and D. C. Heard. 2003. Seasonal habitat use and movements of mountain goats, Oreamnos americanus, in eastcentral British Columbia. Canadian Field-Naturalist 117:565-576. (Pubitemid 39351193)
62. Pritchard, J. K., M. Stephens, and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959. (Pubitemid 30397141)
63. Queller, D. C., and K. F. Goodnight. 1989. Estimating relatedness using genetic markers. Evolution 43:258-275.
64. R Development Core Team. 2009. R2.9.2. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.r-project.org/
65. Rice, C. G. 2008. Seasonal altitudinal movements of mountain goats. Journal of Wildlife Management 72:1706-1716.
66. Rice, W. R. 1989. Analyzing tables of statistical tests. Evolution 43:223-225.
67. Roever, C., M. S. Boyce, and G. B. Stenhouse. 2010. Grizzly bear movements relative to roads: Application of step selection functions. Ecography 33:1113-1122.
68. Rousset, F. 2008. GENEPOP'007: A complete re-implementation of the GENEPOP software for Windows and Linux. Molecular Ecology Resources 8:103-106. (Pubitemid 350231212)
69. Schick, R. S., S. R. Loarie, F. Colchero, B. D. Best, A. Boustany, D. A. Conde, P. N. Halpin, L. N. Joppa, C. M. McLellan, and J. S. Clark. 2008. Understanding movement data and movement processes: Current and emerging directions. Ecology Letters 11:1338-1350.
70. Schwartz, M. K., G. Luikart, and R. S. Waples. 2007. Genetic monitoring as a promising tool for conservation and management. Trends in Ecology and Evolution 22:25-33. (Pubitemid 44959168)
71. Shafer, A. B. A., S. D. Côté, and D. W. Coltman. 2011a. Hot spots of genetic diversity descended from multiple Pleistocene refugia in an alpine ungulate. Evolution 65:125-138.
72. Shafer, A. B. A., J. Poissant, S. D. Côté, and D. W. Coltman. 2011b. Does reduced heterozygosity influence dispersal? A test using spatially structured populations in an alpine ungulate. Biology Letters 7:433-435.
73. Shirk, A. J., D. O. Wallin, S. A. Cushman, C. G. Rice, and K. I. Warheit. 2010. Inferring landscape effects gene flow: A new model selection framework. Molecular Ecology 19:3603-3619.
74. Smith, B. L. 1977. Influence of snow conditions on winter distribution, habitat use, and group size of mountain goats. Pages 174-189 in W. Samuel and W. G. Macgregor, editors. Proceedings of the First International Mountain Goat Symposium. Kalispell, Montana, USA. British Columbia Ministry of Recreation and Conservation, British Columbia, Canada.
75. Sork, V. L., and L. Waits. 2010. Contributions of landscape genetics-approaches, insights, and future potential. Molecular Ecology 19:3489-3495.
76. Spear, S. F., N. Balkenhol, M.-J. Fortin, B. H. McRae, and K. Scribner. 2010. Use of resistance surfaces for landscape genetic studies: Considerations for parameterization and analysis. Molecular Ecology 19:3576-3591.
77. Taylor, S., W. Wall, and Y. Kulis. 2006. Habitat selection by mountain goats in south coastal British Columbia. Biennial Symposium of the Northern Wild Sheep and Goat Council 15:141-157.
78. Tongass National Forest. 2010. Southeast Alaska GIS Library. http://seakgis.alaska.edu/data/CoverType.zip
79. Van De Casteele, T., P. Galbusera, and E. Matthysen. 2001. A comparison of microsatellite-based pairwise relatedness estimators. Molecular Ecology 10:1539-1549. (Pubitemid 32526126)
80. Wang, Y.-H., K.-C. Yang, C. L. Bridgman, and L.-K. Lin. 2008. Habitat suitability modeling to correlate gene flow with landscape connectivity. Landscape Ecology 23:989-1000.
81. Wasserman, T. N., S. A. Cushman, M. K. Schwartz, and D. O. Wallin. 2010. Spatial scaling and multi-model inference in landscape genetics: Martes americana in northern Idaho. Landscape Ecology 25:1601-1612.
82. White, K. S. 2006. Seasonal and sex-specific variation in terrain use and movement patterns of mountain goats in southeastern Alaska. Biennial Symposium of the Northern Wild Sheep and Goat Council 15:183-193.