Partitioning detectability components in populations subject to within-season temporary emigration using binomial mixture models

PLoS ONE

Volumn 10, Issue 3, 2015, Pages

  O'Donnell, Katherine M ^a   Thompson, Frank R ^b   Semlitsch, Raymond D ^a  

^a UNIVERSITY OF MISSOURI   (United States)

^b US Forest Service Northern Research Station   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RAIN;

ARTICLE; BINOMIAL DISTRIBUTION; MATHEMATICAL ANALYSIS; MIGRATION; NONHUMAN; PARTITIONING DETECTABILITY; PLETHODON SERRATUS; POPULATION ABUNDANCE; PREDICTION; PROBABILITY; RELIABILITY; RESOURCE PARTITIONING; ROCK; SALAMANDER; SEASONAL VARIATION; SIMULATION; STRESS; TERRESTRIAL SPECIES; TIME; WOOD; ANIMAL; POPULATION MIGRATION; SEASON; STATISTICAL MODEL; TIME FACTOR; URODELA;

ANIMALIA; PLETHODON SERRATUS; SALAMANDROIDEA;

ANIMAL MIGRATION; ANIMALS; MODELS, STATISTICAL; SEASONS; TIME FACTORS; URODELA;

EID: 84925071132     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0117216     Document Type: Article

References (56)

1. Andrewartha H, Birch L (1954) The distribution and abundance of animals. Chicago, IL: University of Chicago Press.
2. Slobodkin LB (1980) Growth and regulation of animal populations. Dover Publications.
3. Kéry M, Royle JA (2010) Hierarchical modelling and estimation of abundance and population trends in metapopulation designs. J Anim Ecol 79: 453-461. doi: 10.1111/j.1365-2656.2009.01632.x PMID: 19886893
4. Kéry M, Schaub M (2012) Bayesian Population Analysis using WinBUGS: A Hierarchical Perspective. New York: Academic Press.
5. st ed. New York: Academic Press.
6. Royle JA, Kéry M, Gautier R, Schmid H (2007) Hierarchical spatial models of abundance and occurrence from imperfect survey data. Ecol Monogr 77: 465-481.
7. Tyre A, Tenhumberg B, Field S (2003) Improving precision and reducing bias in biological surveys: estimating false-negative error rates. Ecol Appl 13: 1790-1801.
8. Kéry M (2008) Estimating abundance from bird counts: Binomial mixture models uncover complex covariate relationships. Auk 125: 336-345.
9. Kéry M, Schmidt B (2008) Imperfect detection and its consequences for monitoring for conservation. Community Ecol 9: 207-216.
10. Pollock KH, Nichols JD, Simons TR, Farnsworth GL, Bailey LL, et al. (2002) Large scale wildlife monitoring studies: statistical methods for design and analysis. Environmetrics 13: 105-119.
11. Bailey LL, Simons TR, Pollock KH (2004) Estimating detection probability parameters for Plethodon salamanders using the robust capture-recapture design. J Wildl Manage 68: 1-13.
12. Mackenzie DI, Kendall WL (2002) How should detection probability be incorporated into estimates of relative abundance? Ecology 83: 2387-2393.
13. Williams BK, Nichols JD, Conroy MJ (2002) Analysis and Management of Animal Populations: Modeling, Estimation, and Decision Making. San Diego: Academic Press.
14. Halstead BJ, Wylie GD, Coates PS, Valcarcel P, Casazza ML (2012) "Exciting statistics": the rapid development and promising future of hierarchical models for population ecology. Anim Conserv 15: 133-135.
15. Mackenzie DI, Nichols JD, Lachman G (2002) Estimating site occupancy rates when detection probabilities are less than one. Ecology 83: 2248-2255.
16. Royle JA (2004) N-mixture models for estimating population size from spatially replicated counts. Biometrics 60: 108-115. PMID: 15032780
17. Dodd CK Jr., Dorazio RM (2004) Using counts to simultaneously estimate abundance and detection probabilities in a salamander community. Herpetologica 60: 468-478.
18. Peterman WE, Semlitsch RD (2013) Fine-scale habitat associations of a terrestrial salamander: the role of environmental gradients and implications for population dynamics. PLoS One 8: e62184. doi: 10.1371/journal.pone.0062184 PMID: 23671586
19. Martin J, Royle JA, Mackenzie DI, Edwards HH, Kéry M, et al. (2011) Accounting for non-independent detection when estimating abundance of organisms with a Bayesian approach. Methods Ecol Evol 2: 595-601.
20. Kéry M, Dorazio RM, Soldaat L, van Strien A, Zuiderwijk A, et al. (2009) Trend estimation in populations with imperfect detection. J Appl Ecol 46: 1163-1172.
21. Pollock KH, Marsh H, Bailey LL, AlldredgeMW(2004) Separating Components of Detection Probability in Abundance Estimation : An Overview with Diverse Examples. In: Thompson WL, editor. Sampling Rare or Elusive Species: Concepts, Designs, and Techniques for Estimating Population Parameters. Island Press. pp. 43-58.
22. Kendall WL, Nichols JD, Hines JE (1997) Estimating temporary emigration using capture-recapture data with Pollock's robust design. Ecology 78: 563-578.
23. Kendall WL (1999) Robustness of closed capture-recapture methods to violations of the closure assumption. Ecology 80: 2517-2525.
24. Donnelly MA, Guyer C (1994) Mark-recapture. In: Heyer W, Donnelly M, McDiarmid R, Heyer L, Foster MS, editors. Measuring and Monitoring Biological Diversity. Standard Methods for Amphibians. Smithsonian Institution Press. pp. 183-200.
25. Pollock KH, Nichols JD, Brownie C, Hines JE (1990) Statistical inference for capture-recapture experiments. Wildl Monogr 107: 1-97.
26. Jung RE, Droege S, Sauer JR, Landy RB (2000) Evaluation of terrestrial and streamside salamander monitoring techniques at Shenandoah National Park. Environ Monit Assess 63: 65-79.
27. Smith CK, Petranka JW (2000) Monitoring terrestrial salamanders: repeatability and validity of areaconstrained cover object searches. J Herpetol 34: 547-557.
28. Taub F (1961) The distribution of the red-backed salamander, Plethodon c. cinereus, within the soil. Ecology 42: 681-698.
29. Spotila JR (1972) Role of temperature and water in the ecology of lungless salamanders. Ecol Monogr 42: 95-125.
30. Feder ME (1983) Integrating the ecology and physiology of plethodontid salamanders. Herpetologica 39: 291-310.
31. Liebgold EB, Brodie ED, Cabe PR (2011) Female philopatry and male-biased dispersal in a direct-developing salamander, Plethodon cinereus. Mol Ecol 20: 249-257. doi: 10.1111/j.1365-294X.2010. 04946.x PMID: 21134012
32. Kleeberger S, Werner J (1982) Home range and homing behavior of Plethodon cinereus in northern Michigan. Copeia 1982: 409-415.
33. Jaeger RG (1980) Microhabitats of a terrestrial forest salamander. Copeia 1980: 265-268.
34. Grover MC (1998) Influence of cover and moisture on abundances of the terrestrial salamanders Plethodon cinereus and Plethodon glutinosus. J Herpetol 32: 489-497.
35. O 'Donnell KM, Thompson FR III, Semlitsch RD (2014) Predicting variation in microhabitat utilization of terrestrial salamanders. Herpetologica 70: 259-265.
36. Price SJ, Eskew EA, Cecala KK, Browne RA, Dorcas ME (2012) Estimating survival of a streamside salamander: Importance of temporary emigration, capture response, and location. Hydrobiologia 679: 205-215.
37. Davic RD, Welsh HH (2004) On the ecological roles of salamanders. Annu Rev Ecol Evol Syst 35: 405-434.
38. Bailey LL, Simons TR, Pollock KH (2004) Spatial and temporal variation in detection probabilty of Plethodon salamanders using the robust capture-recapture design. J Wildl Manage 68: 14-24.
39. R Core Team (2013) R: A language and environment for statistical computing. Available: http://www.rproject. org/.
40. Plummer M (2003) JAGS: A program for analysis of Bayesian graphical models using Gibbs sampling.
41. Su Y-S, Yajima M (2013) R2jags: A package for running jags from R. Available: http://cran.r-project.org/ package=R2jags.
42. st ed. New York: Cambridge University Press.
43. Petranka JW (1998) Salamanders of the United States and Canada. Washington DC: Smithsonian Institution Press.
44. Herbeck LA, Semlitsch RD (2000) Life history and ecology of the southern redback salamander, Plethodon serratus, in Missouri. J Herpetol 34: 341-347.
45. Kabrick JM, Villwock JL, Dey DC, Keyser TL, Larsen DR (2014) Modeling and mapping oak advance reproduction density using soil and site variables. For Sci 60.
46. Jaeger RG, Inger RF (1994) Quadrat sampling. In: Heyer WR, Donnelly MA, McDiarmid RW, Hayek LC, Foster MS, editors. Measuring and Monitoring Biological Diversity: Standard Methods for Amphibians. Washington DC: Smithsonian Institution Press. pp. 97-102.
47. Gelman A, Jakulin A, Pittau MG, Su Y-S (2008) A weakly informative default prior distribution for logistic and other regression models. Ann Appl Stat 2: 1360-1383.
48. Dodd CK Jr. (2003) Monitoring amphibians in Great Smoky Mountains National Park. U.S. Geological Survey.
49. Mazerolle MJ, Bailey LL, Kendall WL, Royle JA, Converse SJ, et al. (2007) Making great leaps forward: Accounting for detectability in herpetological field studies. J Herpetol 41: 672-689. PMID: 17328165
50. Chandler RB, Royle JA, King D (2011) Inference about density and temporary emigration in unmarked populations. Ecology 92: 1429-1435. PMID: 21870617
51. Dail D, Madsen L (2011) Models for estimating abundance from repeated counts of an open metapopulation. Biometrics 67: 577-587. doi: 10.1111/j.1541-0420.2010.01465.x PMID: 20662829
52. Semlitsch RD, O'Donnell KM, Thompson FR (2014) Abundance, biomass production, nutrient content, and the possible role of terrestrial salamanders in Missouri Ozark forest ecosystems. Can J Zool. Available: http://dx.doi.org/10.1139/cjz-2014-0141.
53. Buderman FE, Liebgold EB (2012) Effect of search method and age class on mark-recapture parameter estimation in a population of red-backed salamanders. Popul Ecol 54: 157-167.
54. Williams AK, Berkson J (2004) Reducing false absences in survey data: Detection probabilities of redbacked salamanders. J Wildl Manage 68: 418-428.
55. McKenny HC, Keeton WS, Donovan TM (2006) Effects of structural complexity enhancement on eastern red-backed salamander (Plethodon cinereus) populations in northern hardwood forests. For Ecol Manage 230: 186-196.
56. Bolker B, Gardner B, Maunder M, Berg C, Brooks M, et al. (2013) Strategies for fitting nonlinear ecological models in R, AD Model Builder, and BUGS. Methods Ecol Evol 4: 501-512.