Efficient Species-Level Monitoring at the Landscape Scale

Conservation Biology

Volumn 26, Issue 3, 2012, Pages 432-441

  Noon, Barry R ^a   Bailey, Larissa L ^a   Sisk, Thomas D ^b   Mckelvey, Kevin S ^c  

^a Veterinary Dentistry and Oral Surgery   (United States)

^b NORTHERN ARIZONA UNIVERSITY   (United States)

^c ROCKY MOUNTAIN RESEARCH STATION   (United States)

Author keywords

Abundance; Detectability; Occupancy; Range

Indexed keywords

ABUNDANCE; CONSERVATION GENETICS; DEMOGRAPHIC SURVEY; DEMOGRAPHIC TREND; DETECTION METHOD; ECOSYSTEM FUNCTION; ENVIRONMENTAL CHANGE; MONITORING; PERSISTENCE; PROBABILITY; RANGE EXPANSION;

BIOLOGICAL MODEL; BIOTA; ECONOMICS; ECOSYSTEM; ENVIRONMENTAL PROTECTION; METHODOLOGY; POPULATION DENSITY; REVIEW; SPECIES DIFFERENCE; SPECIES EXTINCTION;

BIOTA; CONSERVATION OF NATURAL RESOURCES; ECOSYSTEM; EXTINCTION, BIOLOGICAL; MODELS, BIOLOGICAL; POPULATION DENSITY; SPECIES SPECIFICITY;

ANIMALIA;

EID: 84861145563     PISSN: 08888892     EISSN: 15231739     Source Type: Journal    
DOI: 10.1111/j.1523-1739.2012.01855.x     Document Type: Review

References (84)

1. Andelman, S. J., and W. F. Fagan 2000. Umbrellas and flagships: efficient conservation surrogates or expensive mistakes? Proceeding of the National Academy of Sciences (USA) 97:5954-5959.
2. Azuma, D. L., J. A. Baldwin, and B. R. Noon 1990. Estimating the occupancy of spotted owl habitat areas by sampling and adjusting for bias. General technical report PSW-124. U.S. Department of Agriculture, Berkeley, California
3. Bart, J., and S. P. Klosiewski 1989. Use of presence-absence to measure change in avian density. Journal of Wildlife Management 53:847-852.
4. Borregaard, M. K., and C. Rahbek 2010. Causality of the relationship between geographic distribution and species abundance. The Quarterly Review of Biology 85:3-25.
5. Brown, J. H. 1984. On the relationship between abundance and distribution of species. The American Naturalist 124:255-279.
6. Buckley, H. L., and R. P. Freckleton 2010. Understanding the role of species dynamics in abundance-occupancy relationships. Journal of Ecology 98:645-658.
7. Caro, T. M. 2010. Conservation by proxy: indicator, umbrella, keystone, flagship, and other surrogate species. Island Press, Washington, D.C.
8. Cottingham, K. L., B. L. Brown, and J. T. Lennon 2001. Biodiversity may regulate the temporal variability of ecological systems. Ecology Letters 4:72-85.
9. Cushman, S. A., K. S. McKelvey, B. R. Noon, and K. McGarigal 2010. Use of abundance of one species as a surrogate for abundance of others. Conservation Biology 24:830-840.
10. den Boer, P. J. 1981. On the survival of populations in a heterogeneous and variable environment. Oecologia 50:39-53.
11. Estes, J. A., et al. 2011. Trophic downgrading of planet Earth. Science 333:301-306.
12. Flather, C. H., and M. Bevers 2002. Patchy reaction-diffusion and population abundance: the relative importance of habitat amount and arrangement. The American Naturalist 159:40-56.
13. Flather, C. H., K. R. Wilson, and S. A. Shriner 2009. Geographic approaches to biodiversity conservation: implications of scale and error to landscape planning. Pages 85-121 in J. J. Millspaugh and F. R. Thompson III, editors. Models for planning wildlife conservation in large landscapes. Academic Press, New York
14. Foley, P. 1994. Predicting extinction times from environmental stochasticity and carrying-capacity. Conservation Biology 8:124-137.
15. Forsman, E. D., et al. 2011. Population demography of Northern Spotted Owls. Studies in Avian Biology 40:1-103.
16. Gaston, K. J. 2003. The structure and dynamics of geographic ranges. Oxford University Press, Oxford, United Kingdom
17. Gaston, K. J., and R. A. Fuller 2009. The sizes of species' geographic ranges. Journal of Applied Ecology 46:1-9.
18. Gaston, K. J., and T. M. Blackburn 2000. Pattern and process in macroecology. Blackwell Science, Oxford, United Kingdom
19. Gaston, K. J., T. M. Blackburn, and R. D. Gregory 1997. Interspecific abundance-range size relationships: range position and phylogeny. Ecography 20:390-399.
20. Gaston, K. J., and T. M. Blackburn, and R. D. Gregory 1999. Intraspecific abundance-occupancy relationships: case studies for six bird species in Britain. Diversity and Distributions 5:197-212.
21. Gaston, K. J., T. M. Blackburn, J. J. D. Greenwood, R. D. Gregory, R. M. Quinn, and J. H. Lawton 2000. Abundance-occupancy relationships. Journal Applied Ecology 37:39-59.
22. Gu, W., and R. K. Swihart 2004. Absent or undetected? Effects of non-detection of species occurrence on wildlife-habitat models. Biological Conservation 116:195-203.
23. Haile J., et al. 2009. Ancient DNA reveals late survival of mammoth and horse in interior Alaska. Proceedings of the National Academy of Sciences (USA) 106:22363-22368.
24. Hanski, I. 1994. A practical model of metapopulation dynamics. Journal of Animal Ecology 63:151-162.
25. Hanski, I., J. Kouki, and A. Halkka 1993. Three explanations for the positive relationship between the distribution and abundance of species. Pages 108-116 in R. E. Ricklefs and D. Schluter, editors. Species diversity in ecological communities: historical and geographic perspectives. University of Chicago Press, Chicago
26. Harris, G., and S. L. Pimm 2008. Range size and extinction risk in forest birds. Conservation Biology 22:163-171.
27. Haufler, J. B., C. A. Mehl, and G. J. Roloff 1996. Using a coarse-filter approach with species assessment for ecosystem management. Wildlife Society Bulletin 24:200-208.
28. Holt, R. D., J. H. Lawton, K. J. Gaston, and T. M. Blackburn 1997. On the relationship between range size and local abundance. Oikos 78:183-190.
29. Hooper, D. U., et al. 2000. Effects of biodiversity on ecosystem functioning: a consensus of current knowledge. Ecological Monographs 75:3-35.
30. Hurlbert, A. H., and W. Jetz 2007. Species richness, hotspots, and the scale dependence of range maps in ecology and conservation. Proceedings of the National Academy of Sciences (USA) 104:140-147.
31. Kendall, W. L., and G. C. White 2009. A cautionary note on substituting spatial subunits for repeated temporal sampling in studies of site occupancy. Journal of Applied Ecology 46:1182-1188.
32. Kocher, T.D., W. K. Thomas, A. Meyer, S. V. Edwards, S. Pääbo, F. X. Villablanca, A. C. Wilson 1989. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proceedings of the National Academy of Sciences 86:6196-6200.
33. Kunin, W. E. 1998. Extrapolating species abundances across spatial scales. Science 281:1513-1515.
34. Lande, R. 1993. Risks of population extinction from demographic and environmental stochasticity and random catastrophes. The American Naturalist 142:911-927.
35. Landres P. B., J. Verner, and J. W. Thomas 1988. Ecological uses of vertebrate indicator species: a critique. Conservation Biology 2:316-328.
36. Lawton, J. H. 1993. Range, population abundance and conservation. Trends in Ecology & Evolution 8:409-413.
37. Leigh, E. G. 1981. The average lifetime of a population in a varying environment. Journal Theoretical Biology 90:213-239.
38. Long, R. A., P. Mackay, W. J. Zielinski, and J. C. Ray 2008. Noninvasive survey techniques for carnivores. Island Press, Washington, D.C.
39. Mace, G. M., N. J. Collier, K. J. Gaston, C. Hilton-Taylor, H. R. Akcakaya, N. Leader-Williams, E. J. Milner-Gulland, and S. N. Stuart 2008. Quantification of extinction risk: ICUN's system for classifying threatened species. Conservation Biology 22:1424-1442.
40. MacKenzie, D. I., and J. D. Nichols 2004. Occupancy as a surrogate for abundance estimation. Animal Biodiversity and Conservation 27:461-467.
41. MacKenzie, D. I., L. L. Bailey, J. E. Hines and J. D. Nichols 2011. An integrated model of habitat and species occurrence dynamics. Methods in Ecology and Evolution 2:612-627.
42. MacKenzie, D. I., J. D. Nichols, J. E. Hines, M. G. Knutson, and A. B. Franklin 2003. Estimating site occupancy, colonization, and local extinction when a species is detected imperfectly. Ecology 84:2200-2207.
43. MacKenzie, D. I., J. D. Nichols, G. B. Lachman, S. Droege, J. A. Royle, and C. A. Langtimm 2002. Estimating site occupancy rates when detection probabilities are less than one. Ecology 83:2248-2255.
44. MacKenzie, D. I., J. D. Nichols, J. A. Royle, K. H. Pollock, L. L. Bailey, and J.E. Hines 2006. Occupancy estimation and modeling: inferring patterns and dynamics of species occurrence. Academic Press, Boston
45. MacKenzie, D. I., J. D. Nichols, M. E. Seamans, and R. J. Gutierrez 2009. Modeling species occurrence dynamics with multiple states and imperfect detection. Ecology 90:823-835.
46. MacKenzie, D. I., J. D. Nichols, N. Sutton, K. Kawanishi, and L. L. Bailey 2005. Improving inferences in population studies of rare species that are detected imperfectly. Ecology 86:1101-1113.
47. Manley, P. N., M. D. Schlesinger, J. K. Roth, and B. Van Horne 2005. A field-based evaluation of a presence-absence protocol for monitoring ecoregional-scale biodiversity. Journal Wildlife Management 69:950-966.
48. Manley, P. N., W. J. Zielinski, M. D. Schlesinger, and S. R. Mori 2004. Evaluation of a multispecies approach to monitoring species at the ecoregional scale. Ecological Applications 14:296-310.
49. Manne, L. L., and S. L. Pimm 2001. Beyond eight forms of rarity: which species are threatened and which will be next? Animal Conservation 4:221-229.
50. Martin, J., S. Chamaillé-Jammes, J. D. Nichols, H. Fritz, J. E. Hines, C. J. Fonnesbeck, D. I. MacKenzie, and L. L. Bailey 2010. Simultaneous modeling of habitat suitability, occupancy, and relative abundance: African elephants in Zimbabwe. Ecological Applications 20:1173-1182.
51. McClintock, B. T., J. D. Nichols, L. L. Bailey, D. I. MacKenzie, W. L. Kendall, and A. B. Franklin 2010. Seeking a second opinion: uncertainty in wildlife disease ecology. Ecology Letters 13:659-674.
52. Miller, D. A., J. D. Nichols, B. T. McClintock, E. H. Campbell Grant, L. L. Bailey, and L. A. Weir 2011. Improving occupancy estimation when two types of observational error occur: non-detection and species misidentification. Ecology 92:1422-1428.
53. Naeem, S., D. E. Bunker, A. Hector, M. Loreau, and C. Perrings, editors. 2009. Biodiversity, ecosystem functioning, and human wellbeing: an ecological and economic perspective. Oxford University Press, New York
54. Nichols, J. D., J. E. Hines, D. I. MacKenzie, M. E. Seamans, and R. J. Gutierrez 2007. Occupancy estimation and modeling with multiple state uncertainty. Ecology 88:1395-1400.
55. Nichols, J. D., L. L. Bailey, A. F. O'Connell Jr., N. W. Talanacy, E. H. C. Grant, A. T. Gilbert, E. M. Annand, T. P. Husband, and J. E. Hines 2008. Multi-scale occupancy estimation and modelling using multiple detection methods. Journal of Applied Ecology 45:1321-1329.
56. Noon, B. R., P. Parenteau, and S. C. Trombulak 2005. Conservation science, biodiversity, and the 2005 U.S. Forest Service regulations. Conservation Biology 19:1359-1361.
57. Noon, B. R., K. S. McKelvey, and B. G. Dickson 2009. Multispecies conservation planning on U.S. Federal lands. Pages 51-84 in J. J. Millspaugh and F. R. Thompson III, editors. Models for planning wildlife conservation in large landscapes. Academic Press, New York
58. Ovaskainen, O., and B. Meerson 2010. Stochastic models of population extinction. Trends in Ecology & Evolution 25:643-652.
59. Palumbi, S. R., K. L. Mcleod, and D. Grunbaum 2008. Ecosystems in action: lessons from marine ecology about recovery, resistance, and reversibility. BioScience 58:33-42.
60. Pegard, A., C. Miquel, A. Valentini, E. Coissac, F. Bouvier, D. Francois, P. Taberlet, E. Engel, and F. Pompanon 2009. Universal DNA-based methods for assessing the diet of grazing livestock and wildlife from feces. Journal of Agricultural and Food Chemistry 57:5700-5706.
61. Pollock, J. F. 2006. Detecting population declines over large areas with presence-absence, time to encounter, and count survey methods. Conservation Biology 20:882-892.
62. Pollock, K. H., J. D. Nichols, T. R. Simons, G. L. Farnsworth, L. L. Bailey, and J. R. Sauer 2002. Large scale wildlife monitoring studies: statistical methods for design and analysis. Envirometrics 13:105-109.
63. Ratnasingham, S., and P. D. N. Hebert 2007. BOLD: the barcode of life data system (accessed April 13, 2012). Molecular Ecology Notes 7:355-364.
64. Royle, J. A. 2004. N-mixture models for estimating population size from spatially replicated counts. Biometrics 60:108-115.
65. Royle, J. A., and J. D. Nichols 2003. Estimating abundance from repeated presence absence data or point counts. Ecology 84:777-790.
66. Royle, J. A., J. D. Nichols, and M. Kéry 2005. Modelling occurrence and abundance of species when detection is imperfect. Oikos 110:353-359.
67. Royle, J. A., and R. M. Dorazio 2008. Hierarchical modeling and inference in ecology. Academic Press, New York
68. Sauer, J. R., J. E. Fallon, and R. Johnson 2003. Use of the North American Breeding Bird Survey data to estimate population change for bird conservation regions. Journal of Wildlife Management 67:372-389.
69. Schlossberg S., and D. L. King 2009. Modeling animal habitats based on cover types: a critical review. Environmental Management 43:609-618.
70. Schwartz, M. K., G. Luikart, and R. S. Waples 2006. Genetic monitoring as a promising tool for conservation and management. Trends in Ecology & Evolution 22:25-33.
71. Simberloff, D. 1998. Flagships, umbrellas, and keystones: is single-species management passe in the landscape era? Biological Conservation 83:247-257.
72. Traill, L. W., C. J. A. Bradshaw, and B. W. Brook 2007. Minimum viable population size: a meta-analysis of 30 years of published estimates. Biological Conservation 139:159-166.
73. Tingley, M. W., and S. R. Beissinger 2009. Detecting range shifts from historical species occurrences: new perspectives on old data. Trends in Ecology & Evolution 24:625-633.
74. Venier, L. A., and L. Fahrig 1998. Intra-specific abundance-distribution relationships. Oikos 82:483-490.
75. Vojta, C. D. 2005. Old dog, new tricks: innovations with presence/absence information. Journal of Wildlife Management 69:845-848.
76. Waits, L. P. 2004. Using noninvasive genetic sampling to detect and estimate abundance of rare wildlife species. Pages 211-228 in W. L. Thompson, editor. Sampling rare and elusive species. Island Press, Washington, D.C.
77. Walker, B. 1992. Biodiversity and ecological redundancy. Conservation Biology 6:18-23.
78. White, G. C., and K. P. Burnham 1999. Program MARK: survival estimation from populations of marked animals. Bird Study 46:S120-S138.
79. Wiens, J. A. 1989. Spatial scaling in ecology. Functional Ecology 3:385-397.
80. Wiens, J. A., G. D. Hayward, R. S. Holthausen, and M. J. Wisdom 2008. Using surrogate species and groups for conservation and management. BioScience 58:241-252.
81. Wilson, P. D. 2008. The pervasive influence of sampling and methodological artefacts on a macroecological pattern: the abundance-occupancy relationship. Global Ecology and Biogeography 17:457-464.
82. Wilson, P. D. 2011. The consequences of using different measures of mean abundance to characterize the abundance-occupancy relationship. Global Ecology and Biogeography 20:193-202.
83. Zipkin, E. F., J. A. Royle, D. K. Dawson, and S. Bates 2010. Multispecies occurrence models to evaluate the effects of conservation and management actions. Biological Conservation 143:479-484.
84. Zuckerberg, B., W. F. Porter, and K. Corwin 2009. The consistency and stability of abundance-occupancy relationships in large-scale population dynamics. Journal of Animal Ecology 78:172-181.