Assessing biodiversity with sound: Do acoustic diversity indices reflect phylogenetic and functional diversities of bird communities?

Ecological Indicators

Volumn 25, Issue , 2013, Pages 279-287

  Gasc, A ^a   Sueur, J ^a   Jiguet, F ^a   Devictor, V ^b   Grandcolas, P ^a   Burrow, C ^a   Depraetere, M ^a   Pavoine, S ^a,c  

^a MUSÉUM NATIONAL D'HISTOIRE NATURELLE   (France)

^b UNIV MONTPELLIER   (France)

^c UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Acoustic diversity; Biodiversity assessment; Biodiversity indices; Bird community

Indexed keywords

ACOUSTIC DATA; ACOUSTIC DISTANCE; ANIMAL COMMUNITIES; AS SPECIES; BIODIVERSITY INDEXES; BIRD COMMUNITIES; BODY MASS; BRANCH LENGTH; BREEDING BIRD SURVEY; COMMUNITY STRUCTURES; CORRELATION ANALYSIS; DESCRIPTORS; DISTANCE MATRICES; DIVERSITY INDEX; ECOLOGICAL PROCESS; FUNCTIONAL DATAS; FUNCTIONAL DIVERSITY; NULL MODEL; PHYLOGENETIC DIVERSITY; SPATIAL AND TEMPORAL VARIATION; SPECIES ASSEMBLAGE; SPECIES RICHNESS; SPECTRAL COMPONENTS;

BIODIVERSITY; BIRDS; ECOLOGY;

BIOACOUSTICS;

ACOUSTIC DATA; BIODIVERSITY; BIOINDICATOR; BIRD; BREEDING POPULATION; CONSERVATION MANAGEMENT; LITERATURE REVIEW; PHYLOGENETICS; SPATIAL VARIATION; SPECIES RICHNESS; TAXONOMY; TEMPORAL VARIATION;

ANIMALIA; AVES;

EID: 84868492371     PISSN: 1470160X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ecolind.2012.10.009     Document Type: Article

References (94)

1. M.A. Acevedo, C.J. Corrada-Bravo, H. Corrada-Bravo, L.J. Villanueva-Rivera, and T.M. Aide Automated classification of bird and amphibian calls using machine learning: a comparison of methods Ecol. Informatics 4 2009 206 214
2. R.V. Alatalo, C. Glynn, and A. Lundberg Singing rate and female attraction in the pied flycatcher - an experiment Anim. Behav. 39 1990 601 603
3. D.T. Blumstein, D.J. Mennill, P. Clemins, L. Girod, K. Yao, G. Patricelli, J.L. Deppe, A.H. Krakauer, C. Clark, K.A. Cortopassi, S.F. Hanser, B. McCowan, A.M. Ali, and A.N.G. Kirschel Acoustic monitoring in terrestrial environments using microphone arrays: applications, technological considerations and prospectus J. Appl. Ecol. 48 2011 758 767
4. G. Boncoraglio, and N. Saino Habitat structure and the evolution of bird song: a meta-analysis of the evidence for the acoustic adaptation hypothesis Funct. Ecol. 21 2007 134 142 (Pubitemid 46095647)
5. A. Bossu, and F. Charron Le chant des oiseaux 1998 Sang de la terre Paris
6. A. Bossu, and F. Charron Guide des chants d'oiseaux d'Europe occidentale: description et comparaison des chants et des cris 2004 Delachaux et Niestlé Neuchâtel, Switzerland
7. T.S. Brandes, P. Naskrecki, and H.K. Figueroa Using image processing to detect and classify narrow-band cricket and frog calls J. Acoust. Soc. Am. 120 2006 2950 2957 (Pubitemid 44631728)
8. D.R. Brooks, and D.A. McLennan Phylogeny, Ecology, and Behavior: A Research Program in Comparative Biology 1991 University of Chicago Press Chicago
9. G.C. Cardoso, and T.D. Price Community convergence in bird song Evol. Ecol. 24 2010 447 461
10. C.K. Catchpole, and P.J.B. Slater Bird Song: Biological Themes and Variations 1995 Cambridge University Press Cambridge, UK
11. J. Cavender-Bares, D.D. Ackerly, D.A. Baum, and F.A. Bazzaz Phylogenetic overdispersion in Floridian oak communities Am. Nat. 163 2004 823 843 (Pubitemid 38852137)
12. A. Chao, C.H. Chiu, and L. Jost Phylogenetic diversity measures based on Hill numbers Philos. Trans. R. Soc. B: Biol. Sci. 365 2010 3599 3609
13. J. Chave, G. Chust, and C. Thébaud The importance of phylogenetic structure in biodiversity studies D. Storch, P. Marquet, J. Brown, Scaling Biodiversity 2007 Cambridge University Press Cambridge, UK 151 167
14. A.A. Chek, J.P. Bogart, and S.C. Lougheed Mating signal partitioning in multi-species assemblages: a null model test using frogs Ecol. Lett. 6 2003 235 247 (Pubitemid 36453459)
15. W.K. Cornwell, D.W. Schwilk, and D.D. Ackerly A trait-based test for habitat filtering: convex hull volume Ecology 87 2006 1465 1471 (Pubitemid 44066096)
16. S. Cramp, K.E.L. Simmons, D.W. Snow, and C.M. Perrins The Birds of the Western Palearctic; Interactive 2004 BirdGuides Sheffield, UK
17. F. Dalerum, E.Z. Cameron, K. Kunkel, and M.J. Somers Diversity and depletions in continental carnivore guilds: implications for prioritizing global carnivore conservation Biol. Lett. 5 2009 35 38
18. C.E. Davies, D. Moss, and M. O'Hill EUNIS Habitat Classification Revised 2004 2004 Report to the European Topic Centre on Nature Protection and Biodiversity European Environment Agency, Paris
19. Davis, K.E.; 2008. Reweaving the tapestry: a supertree of birds. PhD Thesis. University of Glasgow. http://linnaeus.zoology.gla.ac.uk/∼rpage/ birdsupertree/index.php.
20. D.K. Dawson, and M.G. Efford Bird population density estimated from acoustic signals J. Appl. Ecol. 46 2009 1201 1209
21. M. Depraetere, S. Pavoine, F. Jiguet, A. Gasc, S. Duvail, and J. Sueur Monitoring animal diversity using acoustic indices: implementation in a temperate woodland Ecol. Indic. 13 2012 46 54
22. F. Deroussen Oiseaux des jardins de France 2001 Nashvert Production Charenton, France
23. F. Deroussen, and F. Jiguet La sonothèque du Muséum: Oiseaux de France, les passereaux 2006 Nashvert production, Charenton France
24. F. Deroussen Sound Library of the National Museum of natural History of Paris 2011 National Museum of Natural History Paris http://museumedia.mnhn.fr/ content/sons
25. V. Devictor, D. Mouillot, C. Meynard, F. Jiguet, W. Thuiller, and N. Mouquet Spatial mismatch and congruence between taxonomic, phylogenetic and functional diversity: the need for integrative conservation strategies in a changing world Ecol. Lett. 13 2010 1030 1040
26. J.L. Dickinson, B. Zuckerberg, and D.N. Bonter Citizen science as an ecological research tool: challenges and benefits Annu. Rev. Ecol. Evol. Syst. 41 2010 149 172
27. S. Diwakar, and R. Balakrishnan Vertical stratification in an acoustically communicating ensiferan assemblage of a tropical evergreen forest in southern India J. Trop. Ecol. 23 2007 479 486 (Pubitemid 47026199)
28. S. Dray, and A.B. Dufour The ade4 package: implementing the duality diagram for ecologists J. Stat. Softw. 22 2007 1 20
29. B.C. Emerson, and R.G. Gillespie Phylogenetic analysis of community assembly and structure over space and time Trends Ecol. Evol. 23 2008 619 630
30. P. Escoufier Le traitement des variables vectorielles Biometrics 29 1973 751 760
31. D.P. Faith Conservation evaluation and phylogenetic diversity Biol. Conserv. 61 1992 1 10
32. A. Farina, N. Pieretti, and L. Piccioli The soundscape methodology for long-term bird monitoring: a mediterranean Europe case-study Ecol. Informatics 6 2011 354 363
33. N.H. Fletcher A simple frequency-scaling rule for animal communication J. Acoust. Soc. Am. 115 2004 2334 2338 (Pubitemid 38542149)
34. T.G. Forrest Using insect sounds to estimate and monitor their populations Fla. Entomol. 71 1988 416 426
35. J.C. Gower A general coefficient of similarity and some of its properties Biometrics 27 1971 857 871
36. P.W. Greig-smith Song rates and parental care by individual male stonechats (Saxicola torquata) Anim. Behav. 30 1982 245 252
37. P. Grandcolas The origin of biological diversity in a tropical cockroach lineage - a phylogenetic analysis of habitat choice and biome occupancy Acta Oecol. 14 1993 259 270 (Pubitemid 24414010)
38. P. Grandcolas Phylogenetic analysis and the study of community structure Oikos 82 1998 397 400 (Pubitemid 28336126)
39. N.C. Han, S.V. Muniandy, and J. Dayou Acoustic classification of Australian anurans based on hybrid spectral-entropy approach Appl. Acoust. 72 2011 639 645
40. O.J. Hardy Testing the spatial phylogenetic structure of local communities: statistical performances of different null models and test statistics on a locally neutral community J. Ecol. 96 2008 914 926
41. O. Hardy, and S. Pavoine Assessing phylogenetic signal with measurement error: a comparison of Mantel tests, Blomberg et al.'s K and phylogenetic distograms Evolution 66 2012 2614 2621
42. R.J. Holdaway, and A.D. Sparrow Assembly rules operating along a primary riverbed-grassland successional sequence J. Ecol. 94 2006 1092 1102 (Pubitemid 44510999)
43. F. Husson, J. Josse, S. Le, and J. Mazet FactoMineR: Multivariate Exploratory Data Analysis and Data Mining with R. R Package Version 1.16 2011
44. N.J.B. Isaac, S.T. Turvey, B. Collen, C. Waterman, and J.E.M. Baillie Mammals on the EDGE: conservation priorities based on threat and phylogeny PLoS One 2 2007 e296
45. P. Jaccard Étude comparative de la distribution florale dans une portion des Alpes et des Jura Bulletin de la Société Vaudoise des Sciences Naturelles, 37 1901 547 579
46. F. Jiguet, V. Devictor, R. Julliard, and D. Couvet French citizens monitoring ordinary birds provide tools for conservation and ecological sciences Acta Oecol. 44 2012 58 66
47. J. Josse, J. Pages, and F. Husson Testing the significance of the RV coefficient Comput. Stat. Data Anal. 53 2008 82 91
48. L. Jost Partitioning diversity into independent alpha and beta components Ecology 88 2007 2427 2439 (Pubitemid 351345099)
49. R. Julliard, J. Clavel, V. Devictor, F. Jiguet, and D. Couvet Spatial segregation of specialists and generalists in bird communities Ecol. Lett. 9 2006 1237 1244 (Pubitemid 44571665)
50. F. Kazi-aoual, S. Hitier, R. Sabatier, and J.D. Lebreton Refined approximations to permutation tests for multivariate inference Comput. Stat. Data Anal. 20 1995 643 656
51. S. Kullback, and R.A. Leibler On information and sufficiency Ann. Math. Stat. 22 1951 79 86
52. E. Lebrija-Trejos, E.A. Perez-Garcia, J.A. Meave, F. Bongers, and L. Poorter Functional traits and environmental filtering drive community assembly in a species-rich tropical system Ecology 91 2010 386 398
53. F. Legendre, T. Robillard, L. Desutter-Grandcolas, M.F. Whiting, and P. Grandcolas Phylogenetic analysis of non-stereotyped behavioural sequences with a successive event-pairing method Biol. J. Linn. Soc. 94 2008 853 867
54. P. Legendre, and L. Legendre Numerical Ecology 2nd ed. 1998 Amsterdam Elsevier
55. J.J. Luczkovich, D.A. Mann, and R.A. Rountree Passive acoustic as a tool in fisheries Science Trans. Am. Fish. Soc. 137 2008 533 541 (Pubitemid 351668748)
56. N. Mantel The detection of disease clustering and a generalized regression approach Cancer Res. 27 1967 209 220
57. A. Magurran Measuring Biological Diversity 2004 Blackwell Oxford
58. R.W. Mankin, J. Brandhorst-Hubbard, K.L. Flanders, M. Zhang, R.L. Crocker, S.L. Lapointe, C.W. McCoy, J.R. Fisher, and D.K. Weaver Eavesdropping on insects hidden in soil and interior structures of plants J. Econ. Entomol. 93 2000 1173 1182
59. J.P. Martin, S.M. Doucet, R.C. Knox, and D.J. Mennill Body size correlates negatively with the frequency of distress calls and songs of Neotropical birds J. Field Ornithol. 82 2011 259 268
60. C.F.J. Meyer, L.M.S. Aguiar, L.F. Aguirre, J. Baumgarten, F.M. Clarke, J.F. Cosson, S.E. Villegas, J. Fahr, D. Faria, N. Furey, M. Henry, R. Hodgkison, R.K.B. Jenkins, K.G. Jung, T. Kingston, T.H. Kunz, M.C. MacSwiney, I. Moya, B.D. Patterson, J.M. Pons, P.A. Racey, K. Rex, E.M. Sampaio, S. Solari, K.E. Stoner, C.C. Voigt, D. von Staden, C.D. Weise, and E.K.V. Kalko Accounting for detectability improves estimates of species richness in tropical bat surveys J. Appl. Ecol. 48 2011 777 787
61. M.K. Obrist, R. Boesch, and P.F. Fluckiger Variability in echolocation call design of 26 Swiss bat species: consequences, limits and options for automated field identification with a synergetic pattern recognition approach Mammalia 68 2004 307 322 (Pubitemid 40068373)
62. M.K. Obrist, G. Pavan, J. Sueur, K. Riede, D. Llusia, and R. Marquez Bioacoustics approaches in biodiversity inventories Abc Taxa 8 2010 68 99
63. J. Oksanen, F.G. Blanchet, R. Kindt, P. Legendre, P.R. Minchin, R.B. O'Hara, G.L. Simpson, P. Solymos, M. Henry, H. Stevens, and H. Wagner Vegan: Community Ecology Package. R Package Version 2. 0-0 2011
64. G.P. Patil, and C. Taillie Diversity as a concept and its measurement J. Am. Stat. Assoc. 77 1982 548 561
65. S. Pavoine, A.B. Dufour, and D. Chessel From dissimilarities among species to dissimilarities among communities: a double principal coordinate analysis J. Theor. Biol. 228 2004 523 537 (Pubitemid 38726073)
66. S. Pavoine, S. Ollier, and A.B. Dufour Is the originality of a species measurable? Ecol. Lett. 8 2005 579 586 (Pubitemid 40802024)
67. S. Pavoine, S. Ollier, and D. Pontier Measuring, diversity from dissimilarities with Rao's quadratic entropy: are any dissimilarities suitable? Theor. Popul. Biol. 67 2005 231 239 (Pubitemid 40678711)
68. S. Pavoine, J. Vallet, A.B. Dufour, S. Gachet, and H. Daniel On the challenge of treating various types of variables: application for improving the measurement of functional diversity Oikos 118 2009 391 402
69. S. Pavoine, and M.B. Bonsall Measuring biodiversity to explain community assembly: a unified approach Biol. Rev. 86 2011 792 812
70. O.L. Petchey, K.L. Evans, I.S. Fishburn, and K.J. Gaston Low functional diversity and no redundancy in British avian assemblages J. Anim. Ecol. 76 2007 977 985 (Pubitemid 47262779)
71. O.L. Petchey, and K.J. Gaston Functional diversity (FD), species richness and community composition Ecol. Lett. 5 2002 402 411 (Pubitemid 34523107)
72. O.L. Petchey, E. O'Gorman, and D.F.B. Flynn A functional guide to functional diversity measures S. Naeem, D.E. Bunker, A. Hector, M. Loreau, C. Perrings, Biodiversity and Human Impacts 2009 Oxford University Press Oxford 49 60
73. N. Pieretti, A. Farina, and D. Morri A new methodology to infer the singing activity of an avian community: the Acoustic Complexity Index (ACI) Ecol. Indic. 11 2011 868 873
74. B.C. Pijanowski, A. Farina, S.H. Gage, S.L. Dumyahn, and B.L. Krause What is soundscape ecology? An introduction and overview of an emerging new science Landscape Ecol. 26 2011 1213 1232
75. V.D. Pillar, L.D. Duarte, E.E. Sosinski, and F. Joner Discriminating trait-convergence and trait-divergence assembly patterns in ecological community gradients J. Veg. Sci. 20 2009 334 348
76. K.A. Pollard, D.T. Blumstein, and S.C. Griffin Pre-screening acoustic and other natural signatures for use in noninvasive individual identification J. Appl. Ecol. 47 2010 1103 1109
77. R Development Core Team R A Language and Environment for Statistical Computing 2010 R Foundation for Statistical Computing Vienna, Austria 3-900051-07-0 http://www.R-project.org/
78. S.T. Rachev Probability Metrics and Stability of Stochastic Models 1991 John Wiley & Sons New York
79. C.R. Rao Rao's axiomization of diversity measures Encyclopedia Stat. Sci. 7 1986 614 617
80. K. Riede Monitoring Biodiversity: analysis of Amazonian Rainforest Sounds Ambio 22 1993 546 548
81. K. Riede Bioacoustic monitoring of insect communities in a Bornean rainforest canopy N.E. Stork, J.A. Adis, R.K. Didham, Canopy Arthropods 1997 Chapman & Hall London 442 452
82. P. Robert, and Y. Escoufier A unifying tools for linear multivariate statistical methods J. R. Stat. Soc. 25 1976 257 265
83. T. Robillard, and L. Desutter-Grandcolas Evolution of calling songs as multicomponent signals in crickets (Orthoptera: Grylloidea: Eneopterinae) Behaviour 148 2011 627 672
84. Roché, J.C.; 1990. Oiseaux d'Europe, Sitelle. Mens.
85. H. Slabbekoorn Singing in the wild: the ecology of birdsong P. Marler, H. Slabbekoorn, Nature's Music: The Science of Birdsong 2004 Academic Press/Elsevier New York 178 207
86. M.D. Skowronski, and J.G. Harris Acoustic detection and classification of microchiroptera using machine learning: lessons learned from automatic speech recognition J. Acoust. Soc. Am. 119 2006 1817 1833 (Pubitemid 43326045)
87. J.A. Slingsby, and G.A. Verboom Phylogenetic relatedness limits co-occurrence at fine spatial scales: evidence from the schoenoid sedges (Cyperaceae: Schoeneae) of the Cape Floristic Region, South Africa Am. Nat. 168 2006 14 27 (Pubitemid 44100594)
88. J. Sueur, T. Aubin, and C. Simonis Seewave, a free modular tool for sound analysis and synthesis Bioacoustics 18 2008 213 226
89. J. Sueur, S. Pavoine, O. Hamerlynck, and S. Duvail Rapid acoustic survey for biodiversity appraisal PLoS One 3 2008 e4065
90. W. Thuiller, S. Lavergne, C. Roquet, I. Boulangeat, B. Lafourcade, and M.B. Araujo Consequences of climate change on the tree of life in Europe Nature 470 2011 531 534
91. R.I. Vane-Wright, C.J. Humphries, and P.H. Williams What to protect? Systematics and the agony of choice Biol. Conserv. 55 1991 235 254
92. D. Wallschläger Correlation of song frequency and body weight in passerines birds Experientia 36 1980 412 (Pubitemid 10081642)
93. C.O. Webb, D.D. Ackerly, M.A. McPeek, and M.J. Donoghue Phylogenies and community ecology Annu. Rev. Ecol. Syst. 33 2002 475 505 (Pubitemid 36035149)
94. H.R. Wiley, and D.G. Richards Physical constraints on acoustic communication in the atmosphere: implications for the evolution of animal vocalizations Behav. Ecol. Sociobiol. 3 1978 69 94