Estimating abundance of Sitka black-tailed deer using DNA from fecal pellets

Journal of Wildlife Management

Volumn 75, Issue 1, 2011, Pages 232-242

  Brinkman, Todd J ^a   Person, David K ^b   Chapin III, F Stuart ^a   Smith, Winston ^c   Hundertmark, Kris J ^a  

^a UNIVERSITY OF ALASKA FAIRBANKS   (United States)

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

^c PACIFIC NORTHWEST RESEARCH STATION   (United States)

Author keywords

abundance; Alaska; density; DNA; fecal pellets; forest; logging; mark recapture; Odocoileus hemionus sitkensis; Sitka black tailed deer

Indexed keywords

ABUNDANCE; BIOLOGICAL INVASION; DEER; FECAL PELLET; GENETIC MARKER; MARK-RECAPTURE METHOD; POPULATION DECLINE; POPULATION DENSITY; SAMPLING; SPATIOTEMPORAL ANALYSIS; WILDLIFE MANAGEMENT;

ALASKA; ALEXANDER ARCHIPELAGO; PRINCE OF WALES ISLAND [ALEXANDER ARCHIPELAGO]; UNITED STATES;

CERVIDAE; ODOCOILEUS HEMIONUS COLUMBIANUS; ODOCOILEUS HEMIONUS SITKENSIS; UNGULATA;

EID: 79951905743     PISSN: 0022541X     EISSN: None     Source Type: Journal    
DOI: 10.1002/jwmg.22     Document Type: Article

References (80)

1. Alaback, P. B., 1982. Dynamics of understory biomass in Sitka spruce-western hemlock forests of southeast Alaska. Ecology 63: 1932-1948. (Pubitemid 13286700)
2. Alaska Climate Research Center, 2009. International Arctic Research Center, University of Alaska Fairbanks, Fairbanks, Alaska. Accessed 1 Jun 2009.
3. Anderson, D. R., and, K. P. Burnham., 2002. Avoiding pitfalls when using information-theoretic methods. Journal of Wildlife Management 66: 912-918. (Pubitemid 34915247)
4. Ball, M. C., R. Pither, M. Manseau, J. Clark, S. D. Petersen, S. Kingston, N. Morrill, and, P. Wilson., 2007. Characterization of target nuclear DNA from faeces reduces technical issues associated with the assumptions of low-quality and quantity template. Conservation Genetics 8: 577-586. (Pubitemid 46682956)
5. Belant, J. L., T. W. Seamans, and, D. Paetkau., 2007. Genetic tagging free-ranging white-tailed deer using hair snares. Ohio Journal of Science 107: 50-56. (Pubitemid 350238750)
6. Bellemain, E., J. E. Swenson, D. Tallmon, S. Brunberg, and, P. Taberlet., 2005. Estimating population size of elusive animals with DNA from hunter-collected feces: four methods for brown bears. Conservation Biology 19: 150-161. (Pubitemid 40274149)
7. Beyer, H. L., 2007. Hawth's analysis tools for ArcGIS (version 3.27). Accessed on 3 Apr 2009.
8. Boulanger, J., B.N. McLellan, J.G. Woods, M.F. Proctor, and, C. Strobeck., 2004. Sampling design and bias in DNA-based capture-mark-recapture population and density estimates of grizzly bears. Journal of Wildlife Management 68: 457-469. (Pubitemid 39033501)
9. Brinkman, T. J., 2009. Resilience of a deer hunting system in Southeast Alaska: integrating social, ecological, and genetic dimensions. Dissertation. University of Alaska Fairbanks, USA.
10. Brinkman, T. J., D. K. Person, M. K. Schwartz, K. L. Pilgrim, K. E. Colson, and, K. Hundertmark., 2010. Individual identification of Sitka black-tailed deer using DNA from fecal pellets. Conservation Genetics Resources 2: 115-118.
11. Brinkman, T. J., M. K. Schwartz, D. K. Person, K. Pilgrim, and, K. J. Hundertmark., 2009a. Effects of time and rainfall on PCR success using DNA extracted from deer fecal pellets. Conservation Genetics 11: 1547-1552.
12. Brinkman, T. J., F. S. Chapin, III, G. Kofinas, and, D. K. Person., 2009b. Linking hunter knowledge with forest change to understand changing deer harvest opportunities in intensively logged landscapes. Ecology and Society 14 (1): 36. http://www.ecologyandsociety.org/vol14/iss1/art36/ Accessed 12 Jan 2010.
13. Buchan, J. C., E. A. Archie, R. C. VanHorn, C. J. Moss, and, S. C. Alberts., 2005. Locus effects and sources of error in noninvasive genotyping. Molecular Ecology Notes 5: 680-683. (Pubitemid 41716885)
14. Buckland, S. T., K. P. Burnham, and, N. H. Augustin., 1997. Model selection: an integral part of inference. Biometrics 53: 603-618.
15. Burnham, K. P., and, D. R. Anderson, 2002. Model selection and inference: a practical information theoretic approach. Springer, New York, New York, USA.
16. Campbell, D., G. M. Swanson, and, J. Sales., 2004. Comparing the precision and cost-effectiveness of faecal pellet group count methods. Journal of Applied Ecology 41: 1185-1196. (Pubitemid 40033204)
17. Conroy, M. J., J. P. Runge, R. J. Barker, M. R. Schofield, and, C. J. Fonnesbeck., 2008. Efficient estimation of abundance for patchily distributed populations via two-phase, adaptive sampling. Ecology 89: 3362-3370.
18. Creel, S., G. Spong, J. L. Sands, J. Rotella, J. Zeigle, L. Joe, K. M. Murphy, and, D. Smith., 2003. Population size estimation in Yellowstone wolves with error-prone noninvasive microsatellite genotypes. Molecular Ecology 12: 2003-2009. (Pubitemid 36815033)
19. Deal, R. L., and, W. A. Farr, 1994. Composition and development of conifer regeneration in thinned and unthinned natural stands of western hemlock and Sitka spruce in southeast Alaska. Canadian Journal of Forest Resources 24: 976-984. (Pubitemid 2112900)
20. Efford, M. G., D. K. Dawson, and, C. S. Robbins., 2004. DENSITY: software for analyzing capture-recapture data from passive detector arrays. Animal Biodiversity and Conservation 27: 217-228. (Pubitemid 40958913)
21. Ernest, H. B., M. C. T. Penedo, B. P. May, M. Syvanen, and, W. M. Boyce., 2000. Molecular tracking of mountain lions in Yosemite Valley region in California: genetic analysis using microsatellites and faecal DNA. Molecular Ecology 9: 433-442.
22. Farmer, C. J., D. K. Person, and, R. T. Bowyer., 2006. Risk factors and mortality of black-tailed deer in a managed forest landscape. Journal of Wildlife Management 70: 1403-1415. (Pubitemid 44907108)
23. Fisch, G., 1979. Deer pellet deterioration. Pages 207-218 in, O. C. Wallmo, J. W. Schoen, editors. Sitka black-tailed deer: Proceedings of a conference: 1978 February, 22-24; Juneau, Alaska. Ser. No. R10-48. U.S. Department of Agriculture, Forest Service, Alaska Region, Juneau, Alaska, USA.
24. Forsyth, D. M., R. J. Barker, G. Morriss, and, M. P. Scroggie., 2007. Modeling the relationship between fecal pellet indices and deer density. Journal of Wildlife Management 71: 964-970.
25. Fuller, T. K., 1991. Do pellet count index white-tailed deer numbers and population change ? Journal of Wildlife Management 55: 393-396.
26. Gebremedhin, B., G. F. Ficetola, S. Naderi, H. R. Rezaei, C. Maudet, D. Rioux, G. Luikart, Ø. Flagstad, W. Thuiller, and, P. Taberlet., 2009. Combining genetic and ecological data to assess the conservation status of the endangered Ethopian walia ibex. Animal Conservation 12: 89-100.
27. Hanley, T. A., 1993. Balancing economic development, biological conservation, and human culture: the Sitka black-tailed Odocoileus hemionus sitkensis deer as an ecological indicator. Biological Conservation 66: 61-67. (Pubitemid 24385401)
28. Hanley, T. A., and, J. D. McKendrick, 1983. Seasonal changes in chemical composition and nutritive value of native forages in a spruce-hemlock forest, southeastern Alaska. USDA Forest Service Resource Paper PNW-312, Portland, Oregon, USA.
29. Harestad, A. S., and, F. L. Bunnell., 1987. Persistence of black-tailed deer fecal pellets in coastal habitats. Journal of Wildlife Management 51: 33-37.
30. Hedmark, E., O. Flagstad, P. Segerström, J. Persson, A. Landa, and, H. Ellegren., 2004. DNA-based individual and sex identification from wolverine (Gulo gulo) faeces and urine. Conservation Genetics 5: 405-410. (Pubitemid 38983087)
31. Herbert, D. M., 1979. Wildlife forestry planning in the coastal forests of Vancouver Island. Pages 133-158 in, O. C. Wallmo, J. W. Schoen, editors. Sitka black-tailed deer: Proceedings of a conference: 1978 February, 22-24; Juneau, Alaska. Ser. No. R10-48. U.S. Department of Agriculture, Forest Service, Alaska Region, Juneau, Alaska, USA.
32. Huggins, R. M., 1991. Some practical aspects of a conditional likelihood approach to capture experiments. Biometrics 47: 725-732.
33. Kendall, W. L., and, R. Bjorkland, 2001. Using open robust design models to estimate temporary emigration from capture-recapture data. Biometrics 57: 1113-1122. (Pubitemid 33108103)
34. Kendall, K. C., J. B. Stetz, D. A. Roon, L. P. Waits, J. B. Boulanger, and, D. Paetkau., 2008. Grizzly bear density in Glacier National Park, Montana. Journal of Wildlife Management 72: 1693-1705.
35. Kirchhoff, M. D., and, K. W. Pitcher, 1988. Deer pellet-group surveys in southeast Alaska 1981-1987. Alaska Department of Fish and Game. Project W-22-6, Job 2.9, Objective 1, Juneau, Alaska, USA.
36. Kirchhoff, M. D., 1994. Deer pellet-group surveys in Southeast Alaska. 1994 report. Department of Fish and Game, Wildlife Conservation, Douglas, Alaska, USA.
37. Klein, D. R., 1965. Ecology of deer range in Alaska. Ecological Monographs 35: 259-284.
38. Koster, S. H., and, J. A. Hart, 1988. Methods of estimating ungulate populations in tropical forests. African Journal of Ecology 26: 117-126. (Pubitemid 19321151)
39. Kruse, J., and, R. Frazier, 1988. Community Profile Series, Volume 2: Klawock-Yakutat. Tongass Resource Use Cooperaive Study (TRUCS). Institute of Social and Economic Research, Anchorage, Alaska, USA.
40. Lukacs, P. M., and, K. P. Burnham, 2005. Estimating population size from DNA-based closed capture-recapture data incorporating genotyping error. Journal of Wildlife Management 69: 396-403. (Pubitemid 40600560)
41. Maudet, C., G. Luikart, and, D. Dubray., 2004. Low genotyping error rates in wild ungulate feces sampled in winter. Molecular Ecology Notes 4: 772-775. (Pubitemid 39569235)
42. Mazza, R., 2003. Hunter demand for deer on Prince of Wales Island, Alaska: an analysis of influencing factors. General Technical Report PNW-GTR-581. USDA Forest Service, Pacific Northwest Research Station, Portland, Oregon, USA.
43. McNay, R. S., and, D. D. Doyle, 1987. Winter habitat selection by black-tailed deer on Vancouver Island; a job completion report. B.C. Ministry of forest lands, Research Branch, Victoria, British Columbia, Canada.
44. Miller, C. R., P. Joyce, and, L. P. Waits., 2002. Assessing allelic dropout and genotype reliability using maximum likelihood. Genetics 160: 357-366. (Pubitemid 34118297)
45. Murphy, M. A., K. C. Kendall, A. Robinson, and, L. P. Waits., 2007. The impact of time and field conditions on brown bear (Ursus arctos) faecal DNA amplification. Conservation Genetics 8: 1219-1224. (Pubitemid 47174989)
46. Neff, D. J., 1968. A pellet group count technique for big game trend, census and distribution: a review. Journal of Wildlife Management 32: 597-614.
47. Otis, D. L., K. P. Burnham, G. C. White, and, D. R. Anderson., 1978. Statistical inference from capture data on closed animal populations. Wildlife Monographs 62.
48. Parker, K. L., M. P. Gillingham, T. A. Hanley, and, C. T. Robbins., 1999. Energy and protein balance of free-ranging black-tailed deer in a natural forest environment. Wildlife Monographs 143.
49. Parmenter, R. R., T. L. Yates, D. R. Anderson, K. P. Burnham, J. L. Dunnum, A. B. Franklin, M. T. Friggens, B. C. Lubow, M. Miller, G. S. Olson, C. A. Parmenter, J. Pllard, E. Rexstad, T. M. Shenk, T. R. Stanley, and, G. C. White., 2003. Small-mammal density estimation: a field comparison of grid-based vs. web-based density estimators. Ecological Monographs 73: 1-26. (Pubitemid 36247190)
50. Patterson, B. R., and, V. A. Power, 2002. Contributions of forage competition, harvest, and climate fluctuation to changes in population growth of northern white-tailed deer. Oecologia 130: 62-71. (Pubitemid 36064138)
51. Pauli, J. N., M. B. Hamilton, E. B. Crane, and, S. W. Buskirk., 2008. A single-sampling hair trap for mesocarnivores. Journal of Wildlife Management 72: 1650-1652.
52. Peakall, R., and, P. E. Smouse., 2006. GENALE 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6: 288-295. (Pubitemid 43373825)
53. Pledger, S., 2000. Unified maximum likelihood estimates for closed models using mixtures. Biometrics 56: 434-442. (Pubitemid 30422633)
54. Pojar, J., 1994. Plants of the Pacific northwest: Washington, Oregon, British Columbia, and Alaska. Lone Pine Publishing, Redmond, Washington, USA.
55. Putman, R. J., 1984. Facts from faeces. Mammal Review 14: 79-97.
56. Ratcliffe, P. R., 1987. Red deer population changes and the independent assessment of population size. Symposia of the Zoological Society of London 58: 153-165.
57. Schoen, J. W., M. D. Kirchhoff, and, J. H. Hughes., 1988. Wildlife and old-growth forests in southeastern Alaska. Natural Areas Journal 8: 138-145.
58. Schoen, J. W., and, M. D. Kirchhoff, 1990. Seasonal habitat use by Sitka black-tailed deer on Admiralty Island, Alaska. Journal of Wildlife Management 54: 371-378.
59. Schwartz, M. K., and, S. L. Monfort, 2008. Genetic and endocrine tools for carnivore surveys. Pages 238-262 in, R. A. Long, P. Mackay, W. J. Zielinski, J. C. Ray, editors. Noninvasive survey methods for carnivores. Island Press, Washington, D.C., USA.
60. Seber, G. A. F., 1982. The estimation of animal abundance. Macmillan Publishing Co., Inc, New York, New York, USA.
61. Smart, J. C. R., A. I. Ward, and, P. C. L. White., 2004. Monitoring woodland deer populations in the UK: an imprecise science. Mammal Review 34: 99-114. (Pubitemid 38345711)
62. Smith, I. D., and, R. G. Davies, 1975. A preliminary investigation of the deer and elk range in the Tsitika River watershed, Vancouver Island. British Columbia Fish and Wildlife Branch, Report, Nanaimo, Canada. 71 pp (cited in Herbert 1979).
63. Southeast Alaska GIS Library, 2010. Spatial data at University of Alaska Southeast, Juneau, Alaska, USA. Accessed 1 Jun 2010.
64. Stanley, T. R., and, K. P. Burnham., 1999. A closure test for time-specific capture-recapture data. Environmental and Ecological Statistics 6: 197-209.
65. Taberlet, P., S. Griffin, B. Goosens, S. Questiau, V. Manceau, N. Escaravage, L. P. Waits, and, J. Bouvet., 1996. Reliable genotyping of samples with very low DNA quantities using PCR. Nucleic Acids Research 24: 3189-3194. (Pubitemid 26278559)
66. Ulizio, T. J., J. R. Squires, D. H. Pletscher, M. K. Schwartz, J. J. Claar, and, L. F. Ruggiero., 2006. The efficacy of obtaining genetic-based identifications from putative wolverine snow tracks. Wildlife Society Bulletin 34: 1326-1332. (Pubitemid 46213314)
67. Unit 2 Deer Planning Subcommittee, 2005. Unit 2 Deer Management. Southeast Alaska Subsistence Regional Advisory Council. U.S. Fish and Wildlife Service. Anchorage, Alaska, USA.
68. United States Department of Agriculture, 1997. Tongass National Forest Land and Resource Management Plan. Alaska Region R10-MB-338dd. On file with: USDA Forest Service, Alaska Region, Juneau, Alaska, USA.
69. United States Department of Agriculture, 2007. Tongass land and resource management plan amendment: draft environmental impact statement. US Forest Service, Ketchikan, Alaska, USA.
70. Valière, N., C. Bonenfant, C. Toïgo, G. Luikart, J. Gaillard, and, F. Klein., 2007. Importance of a pilot study for non-invasive genetic sampling: genotyping errors and population size estimation in red deer. Conservation Genetics 8: 69-78. (Pubitemid 46035951)
71. Van Vliet, N., S. Zundel, C. Miquel, P. Taberlet, and, R. Nasi., 2008. Distinguishing dung from blue, red and yellow-backed duikers through noninvasive genetic techniques. African Journal of Ecology 46: 411-417.
72. Waits, L. P., and, D. Paetkau, 2005. Noninvasive genetic sampling of wildlife. Journal of Wildlife Management 69: 1419-1433.
73. Wallmo, O. C., and, J. W. Schoen., 1980. Response of deer to secondary forest succession in southeast Alaska. Forest Science 26: 448-462.
74. Wallmo, O. C., 1981. Mule and black-tailed deer distribution and habitats. Pages 1-25 in, O. C. Wallmo, editor. Mule and black-tailed deer of North America. University of Nebraska Press, Lincoln, USA.
75. White, G. C., and, K. P. Burnham, 1999. Program MARK: survival estimation from populations of marked animals. Bird Study Supplement 46: 120-138.
76. White, G. C., 2008. Closed population estimation models and their extensions in program MARK. Environmental and Ecological Statistics 15: 89-99. (Pubitemid 351233976)
77. White, K. S., G. W. Pendleton, and, E. Hood., 2009. Effects of snow on Sitka black-tailed deer browse availability and nutritional carrying capacity in Southeast Alaska. Journal of Wildlife Management 73: 481-487.
78. Williams, B. W., D. R. Etter, D. W. Linden, K. F. Millenbah, S. R. Winterstein, and, K. T. Scribner., 2009. Noninvasive hair sampling and genetic tagging of co-distributed fishers and American martens. Journal of Wildlife Management 73: 26-34.
79. Wilson, K. R., and, D. J. Anderson, 1985. Evaluation of two density estimators of small mammal population size. Journal of Mammalogy 66: 13-21.
80. Wright, J. A., R. J. Barker, M. R. Schofield, A. C. Frantz, A. E. Byrom, and, D. M. Gleeson., 2009. Incorporating genotype uncertainty into mark-recapture-type models for estimating abundance using DNA samples. Biometrics 65: 833-840.