Biodiversity of man-made open habitats in an underused country: A class of multispecies abundance models for count data

Biodiversity and Conservation

Volumn 21, Issue 6, 2012, Pages 1365-1380

  Yamaura, Yuichi ^a,e   Royle, J Andrew ^b   Shimada, Naoaki ^c   Asanuma, Seigo ^d   Sato, Tamotsu ^a   Taki, Hisatomo ^a   Makino, Shun'ichi ^a  

^a FORESTRY AND FOREST PRODUCTS RESEARCH INSTITUTE   (Japan)

^b PATUXENT WILDLIFE RESEARCH CENTER   (United States)

^c IWATE PREFECTURAL UNIVERSITY   (Japan)

^d Study Club on Regional Environment Planning in Tohoku   (Japan)

^e HOKKAIDO UNIVERSITY   (Japan)

Author keywords

Count data; Functional group; Hierarchical community model; Human disturbance; Plantation forestry; Species richness

Indexed keywords

ABUNDANCE; ANTHROPOGENIC EFFECT; BIODIVERSITY; BIRD; COPPICE; ENVIRONMENTAL DISTURBANCE; FUNCTIONAL GROUP; GRASSLAND; HABITAT MANAGEMENT; HIERARCHICAL SYSTEM; NATURAL RESOURCE; PLANTATION; PROBABILITY; SPECIES RICHNESS;

JAPAN;

APOIDEA; AVES;

EID: 84862782014     PISSN: 09603115     EISSN: 15729710     Source Type: Journal    
DOI: 10.1007/s10531-012-0244-z     Document Type: Article

References (55)

1. Askins RA (2001) Sustaining biological diversity in early successional communities: the challenge of managing unpopular habitats. Wildl Soc Bull 29: 407-412.
2. Asner GP, Rudel TK, Aide TM, DeFries R, Emerson R (2009) A contemporary assessment of change in humid tropical forests. Conserv Biol 23: 1386-1395.
3. Barlow J, Gardner TA, Araujo IS, Avila-Pires TC, Bonaldo AB, Costa JE, Esposito MC, Ferreira LV, Hawes J, Hernandez MIM, Hoogmoed MS, Leite RN, Lo-Man-Hung NF, Malcolm JR, Martins MB, Mestre LAM, Miranda-Santos R, Nunes-Gutjahr AL, Overal WL, Parry L, Peters SL, Ribeiro-Junior MA, da Silva MNF, da Silva Motta C, Peres CA (2007) Quantifying the biodiversity value of tropical primary, secondary, and plantation forests. Proc Natl Acad Sci USA 104: 18555-18560.
4. Beck J, Schwanghart W (2010) Comparing measures of species diversity from incomplete inventories: an update. Methods Ecol Evol 1: 38-44.
5. Betts MG, Hagar JC, Rivers JW, Alexander JD, McGarigal K, McComb BC (2010) Thresholds in forest bird occurrence as a function of the amount of early-seral broadleaf forest at landscape scales. Ecol Appl 20: 2116-2130.
6. Bibby CJ, Aston N, Bellamy PE (1989) Effects of broadleaved trees on birds of upland conifer plantations in north Wales. Biol Conserv 49: 17-29.
7. Bibby CJ, Burgess ND, Hill DA, Mustoe SH (2000) Bird census techniques. Academic Press, San Diego.
8. Buckland ST, Anderson DR, Burnham KP, Laake JL, Borchers DL, Thomas L (2001) Introduction to distance sampling: estimating abundance of biological populations. Oxford University Press, Oxford.
9. Chandler RB, Royle JA, King DI (2011) Inference about density and temporary emigration in unmarked populations. Ecology 92: 1429-1435.
10. Department of Population Dynamics Research (2006) Population projections for Japan: 2001-2050 with long-range population projections: 2051-2100. National Institute of Population and Social Security Research, Tokyo. http://www. ipss. go. jp/pp-newest/e/ppfj02/top. html.
11. Dorazio RM, Royle JA, Söderström B, Glimskär A (2006) Estimating species richness and accumulation by modeling species occurrence and detectability. Ecology 87: 842-854.
12. Ellis EC, Ramankutty N (2008) Putting people in the map: anthropogenic biomes of the world. Front Ecol Environ 6: 439-447.
13. Ellis EC, Goldewijk KK, Siebert S, Lightman D, Ramankutty N (2010) Anthropogenic transformation of the biomes, 1700-2000. Global Ecol Biogeogr 19: 589-606.
14. FAO (2006) Global planted forests thematic study: results and analysis. Forestry Department Food and Agriculture Organization of the United Nations, Rome.
15. FAO (2010) Global forest resources assessment 2010. Food and Agriculture Organization of the United Nations, Rome.
16. Fischer J, Stott J, Law BS (2010) The disproportionate value of scattered trees. Biol Conserv 143: 1564-1567.
17. Forestry Agency (2007) Status of forest resources. Forestry Agency, Ministry of Agriculture, Forestry and Fisheries. http://www. rinya. maff. go. jp/j/keikaku/genkyou/index. html.
18. Franklin JF, Maeda T, Ohsumi Y, Matsui M, Yagi H, Hawk GM (1979) Subalpine coniferous forests of central Honshu, Japan. Ecol Monogr 49: 311-334.
19. Fretwell SD, Lucas HLJ (1969) On territorial behavior and other factors influencing habitat distribution in birds. Acta Biotheor 19: 16-36.
20. Gardner B, Royle JA, Wegan MT, Rainbolt RE, Curtis PD (2010) Estimating black bear density using DNA data from hair snares. J Wildl Manag 74: 318-325.
21. Gaston KJ, Fuller RA (2008) Commonness, population depletion and conservation biology. Trends Ecol Evol 23: 14-19.
22. Gelman A, Hill J (2007) Data analysis using regression and multilevel/hierarchical models. Cambridge University Press, Cambridge.
23. Inoue T (2005) Causes of butterfly decline in Japan. Jpn J Entomol (New Ser) 8: 43-64 (in Japanese).
24. JBOSC (2010) Japan biodiversity outlook. Japan Biodiversity Outlook Science Committee (JBOSC), Ministry of the Environment, Tokyo. (in Japanese).
25. Kauppi PE, Ausubel JH, Fang J, Mather AS, Sedjo RA, Waggoner PE (2006) Returning forests analyzed with the forest identity. Proc Natl Acad Sci USA 103: 17574-17579.
26. Kéry M (2010) Introduction to WinBUGS for ecologists: a Bayesian approach to regression, ANOVA, mixed models and related analysis. Academic Press, San Diego.
27. Kéry M, Spillmann JH, Truong C, Holderegger R (2006) How biased are estimates of extinction probability in revisitation studies? J Ecol 94: 980-986.
28. Kéry M, Dorazio RM, Soldaat L, van Strien A, Zuiderwijk A, Royle JA (2009) Trend estimation in populations with imperfect detection. J Appl Ecol 46: 1163-1172.
29. Lawton JH, Bignell DE, Bolton B, Bloemers GF, Eggleton P, Hammond PM, Hodda M (1998) Biodiversity inventories, indicator taxa and effects of habitat modification in tropical forest. Nature 391: 72-75.
30. Lehner B, Liermann CR, Revenga C, Vörösmarty C, Fekete B, Crouzet P, Döll P, Endejan M, Frenken K, Magome J, Nilsson C, Robertson JC, Rödel R, Sindorf N, Wisser D (2011) High-resolution mapping of the world's reservoirs and dams for sustainable river-flow management. Front Ecol Environ 9: 494-502.
31. Lunn D, Spiegelhalter D, Thomas A, Best N (2009) The BUGS project: evolution, critique and future directions. Stat Med 28: 3049-3067.
32. MacKenzie DI, Nichols JD, Royle JA, Pollock KH, Bailey LL, Hines JE (2006) Occupancy estimation and modeling: inferring patterns and dynamics of species occurrence. Academic Press, Amsterdam.
33. Meyfroidt P, Rudel TK, Lambin EF (2010) Forest transitions, trade, and the global displacement of land use. Proc Natl Acad Sci USA 107: 20917-20922.
34. Miyawaki A. 1994. Handbook of Japanese vegetation. Revised New Ed. Shibundo Pub, Tokyo. (in Japanese).
35. Myers N, Mittermeier RA, Mittermeier CG, da Fonseca GAB, Kent J (2000) Biodiversity hotspots for conservation priorities. Nature 403: 853-858.
36. Nagaike T, Hayashi A, Kubo M, Abe M, Arai N (2006) Plant species diversity in a managed forest landscape composed of Larix kaempferi plantations and abandoned coppice forests in central Japan. For Sci 52: 324-332.
37. Okuda S (1997) Wild plants of Japan. Shogakukan, Tokyo. (in Japanese).
38. Ovaskainen O, Soininen J (2011) Making more out of sparse data: hierarchical modeling of species communities. Ecology 92: 289-295.
39. Ralph CJ, Geupel GR, Pyle P, Martin TE, DeSante DF (1993) Handbook of field methods for monitoring landbirds. USDA For Serv Gen Tech Rep PSW-GTR-144.
40. Royle JA, Dorazio RM (2008) Hierarchical modeling and inference in ecology: the analysis of data from populations, metapopulations and communities. Academic Press, Amsterdam.
41. Royle JA, Dorazio RM, Link WA (2007) Analysis of multinomial models with unknown index using data augmentation. J Comput Graph Stat 16: 67-85.
42. Ruiz-Gutiérrez V, Zipkin EF, Dhondt AA (2010) Occupancy dynamics in a tropical bird community: unexpectedly high forest use by birds classified as non-forest species. J Appl Ecol 47: 621-630.
43. Sauer JR, Link WA (2002) Hierarchical modeling of population stability and species group attributes from survey data. Ecology 83: 1743-1751.
44. Schaffers AP, Raemakers IP, Sýkora KV, ter Braak CJF (2008) Arthropod assemblages are best predicted by plant species composition. Ecology 89: 782-794.
45. Scherber C, Eisenhauer N, Weisser WW, Schmid B, Voigt W, Fischer M, Schulze E-D, Roscher C, Weigelt A, Allan E, Beszler H, Bonkowski M, Buchmann N, Buscot F, Clement LW, Ebeling A, Engels C, Halle S, Kertscher I, Klein A-M, Koller R, Konig S, Kowalski E, Kummer V, Kuu A, Lange M, Lauterbach D, Middelhoff C, Migunova VD, Milcu A, Muller R, Partsch S, Petermann JS, Renker C, Rottstock T, Sabais A, Scheu S, Schumacher J, Temperton VM, Tscharntke T (2010) Bottom-up effects of plant diversity on multitrophic interactions in a biodiversity experiment. Nature 468: 553-556.
46. Schieck J (1997) Biased detection of bird vocalizations affects comparisons of bird abundance among forested habitats. Condor 99: 179-190.
47. Steffan-Dewenter I, Münzenberg U, Bürger C, Thies C, Tscharntke T (2002) Scale-dependent effects of landscape context on three pollinator guilds. Ecology 83: 1421-1432.
48. Sturtz S, Ligges U, Gelman A (2010) R2OpenBUGS: a package for running OpenBUGS from R. http://openbugs. info/w/UserContributedCode.
49. Swanson ME, Franklin JF, Beschta RL, Crisafulli CM, DellaSala DA, Hutto RL, Lindenmayer DB, Swanson FJ (2011) The forgotten stage of forest succession: early-successional ecosystems on forest sites. Front Ecol Environ 9: 117-125.
50. Tscharntke T, Gathmann A, Steffan-Dewenter I (1998) Bioindication using trap-nesting bees and wasps and their natural enemies: community structure and interactions. J Appl Ecol 35: 708-719.
51. Violle C, Navas M-L, Vile D, Kazakou E, Fortunel C, Hummel I, Garnier E (2007) Let the concept of trait be functional! Oikos 116: 882-892.
52. Winfree R, Griswold T, Kremen C (2007) Effect of human disturbance on bee communities in a forested ecosystem. Conserv Biol 21: 213-223.
53. Yamagawa H, Ito S, Nakao T (2010) Restoration of semi-natural forest after clearcutting of conifer plantations in Japan. Landsc Ecol Eng 6: 109-117.
54. Yamaura Y, Amano T, Koizumi T, Mitsuda Y, Taki H, Okabe K (2009) Does land-use change affect biodiversity dynamics at a macroecological scale? A case study of birds over the past 20 years in Japan. Anim Conserv 12: 110-119.
55. Yamaura Y, Royle JA, Kuboi K, Tada T, Ikeno S, Makino S (2011) Modelling community dynamics based on species-level abundance models from detection/nondetection data. J Appl Ecol 48: 67-75.