Abstract
Qualitative and quantitative assessments of bird song repertoires are important in studies related to song learning, sexual selection and cultural evolution. Despite methods for automatic analysis, it is still necessary to engage in manual cutting, segmenting and clustering of bird song elements in many cases. Here, we describe a program, the Ficedula Toolbox, which has been made available for free to the bird song research community and has recently come into extensive use. The main advantages of this package are the opportunity to conduct all processing steps in one framework and the option of carrying out computer-aided manual clustering. Output files are ready for further analyses, such as estimation of repertoire size, sequential analysis and repertoire overlap calculation. With this program, findings based on empirical data from the Collared Flycatcher (Ficedula albicollis) song show high inter-observer similarity, and thus, reproducible results. The toolbox may be especially applicable to the analysis of song in species with moderately high repertoires.
Zusammenfassung
“Ficedula”—eine open-source MATLAB toolbox für Schnitt, Segmentierung und computerunterstütztes Clustering von Vogelgesang
Die qualitative und quantitative Bewertung von Gesangsrepertoires von Vögeln ist wesentlich in Studien im Zusammenhang mit Themen wie Gesangslernen, sexuelle Selektion und kulturelle Evolution. Trotz automatischer Analysemöglichkeiten ist es in vielen Fällen immer noch nötig, die Gesänge manuell zu Schneiden, zu Segmentierung und zu Clustern. Hier beschreiben wir das Programm „Ficedula Toolbox“, welches für Vogelgesangsforscher frei verfügbar gemacht wurde und das neuerdings in größerem Umfang genutzt wird. Die größten Vorteile dieses Paketes sind zum einen die Möglichkeit, alle Verarbeitungsschritte in einem System vorzunehmen und zum anderen die Option der Durchführung von computerunterstütztem manuellen Clustern. Die Ausgabedateien sind bereit für weitere Auswertungen, wie beispielsweise die Bestimmung des Repertoireumfangs, sequentielle Analysen und die Berechnung von Repertoireüberlappungen. Mit Hilfe dieses Programms zeigen die Ergebnisse, basierend auf empirischen Daten zum Halsbandschnäpper-Gesang (Ficedula albicollis) eine große Ähnlichkeit zwischen den Beobachtern und daher reproduzierbare Resultate. Die Nutzung dieser Toolbox könnte insbesondere für Arten mit einem moderat hohen Gesangsrepertoire von Vorteil sein.
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References
Boogert NJ, Giraldeau L-AA, Lefebvre L (2008) Song complexity correlates with learning ability in Zebra Finch males. Anim Behav 76:1735–1741. https://doi.org/10.1016/j.anbehav.2008.08.009
Briefer E, Aubin T, Lehongre K, Rybak F (2008) How to identify dear enemies: the group signature in the complex song of the Skylark Alauda arvensis. J Exp Biol 211:317–326. https://doi.org/10.1242/jeb.013359
Briefer E, Osiejuk TS, Rybak F, Aubin T (2010) Are bird song complexity and song sharing shaped by habitat structure? An information theory and statistical approach. J Theor Biol 262:151–164. https://doi.org/10.1016/j.jtbi.2009.09.020
Brumm H, Zollinger SA, Niemelä PT, Sprau P (2017) Measurement artefacts lead to false positives in the study of birdsong in noise. Methods Ecol Evol 8:1617–1625. https://doi.org/10.1111/2041-210X.12766
Catchpole CK, Slater PJB (2008) Bird song: biological themes and variations, vol 2nd. Cambridge University Press, Cambridge
Cohen J (1960) A coefficient of agreement for nominal scales. Educ Psychol Meas 20:37–46
Daou A, Johnson F, Wu W, Bertram R (2012) A computational tool for automated large-scale analysis and measurement of bird-song syntax. J Neurosci Methods 210:147–160. https://doi.org/10.1016/j.jneumeth.2012.07.020
Derégnaucourt S, Mitra PP, Fehér O et al (2005) How sleep affects the developmental learning of bird song. Nature 433:710–716. https://doi.org/10.1038/nature03275
Fayet AL, Tobias JA, Hintzen RE, Seddon N (2014) Immigration and dispersal are key determinants of cultural diversity in a songbird population. Behav Ecol 25:744–753. https://doi.org/10.1093/beheco/aru047
Freeberg TM, Lucas JR (2012) Information theoretical approaches to chick-a-dee calls of Carolina Chickadees (Poecile carolinensis). J Comp Psychol 126:68–81. https://doi.org/10.1037/a0024906
Garamszegi LZ, Török J, Hegyi G et al (2007) Age-dependent expression of song in the Collared Flycatcher, Ficedula albicollis. Ethology 113:246–256. https://doi.org/10.1111/j.1439-0310.2007.01337.x
Garamszegi LZ, Zsebők S, Török J et al (2012) The relationship between syllable repertoire similarity and pairing success in a passerine bird species with complex song. J Theor Biol 295:68–76. https://doi.org/10.1016/j.jtbi.2011.11.011
Gil D, Gahr M (2002) The honesty of bird song: multiple constraints for multiple traits. Trends Ecol Evol 17:133–141. https://doi.org/10.1016/S0169-5347(02)02410-2
Godard R (1991) Long-term memory of individual neighbours in a migratory songbird. Nature 350:228–229. https://doi.org/10.1038/350228a0
Katz J, Hafner SD, Donovan T (2016) Tools for automated acoustic monitoring within the R package monitoR. Bioacoustics 25(2):197–210. https://doi.org/10.1080/09524622.2016.1138415
Hailman JP, Ficken JP, Ficken RW (1985) The “chick-a-dee” calls of Parus atricapillus: a recombinant system of animal communication compared with written English. Semiotica 56:191–224
Hesler N, Mundry R, Sacher T et al (2012) Song repertoire size correlates with measures of body size in Eurasian blackbirds. Behaviour 149:645–665. https://doi.org/10.1163/156853912X649920
Kershenbaum A, Freeberg TM, Gammon DE (2015) Estimating vocal repertoire size is like collecting coupons: a theoretical framework with heterogeneity in signal abundance. J Theor Biol 373:1–11. https://doi.org/10.1016/j.jtbi.2015.03.009
Kiefer S, Scharff C, Hultsch H, Kipper S (2014) Learn it now, sing it later? Field and laboratory studies on song repertoire acquisition and song use in nightingales. Naturwissenschaften 101(11):955–963. https://doi.org/10.1007/s00114-014-1236-5
Lachlan RF, Verzijden MN, Bernard CS et al (2013) The progressive loss of syntactical structure in bird song along an island colonization chain. Curr Biol 23:1896–1901. https://doi.org/10.1016/j.cub.2013.07.057
Lachlan RF, van Heijningen CAA, Ter Haar SM, ten Cate C (2016) Zebra Finch song phonology and syntactical structure across populations and continents—a computational comparison. Front Psychol 7:980. https://doi.org/10.3389/FPSYG.2016.00980
Landis JR, Koch GG (1977) The measurement of observer agreement for categorical data. Biometrics 33:159–174
Linossier J, Zsebők S, Baudry E et al (2016) Acoustic but no genetic divergence in migratory and sedentary populations of Blackcaps. Biol J Linn Soc, Sylvia atricapilla. https://doi.org/10.1111/bij.12799
Nelson DA, Hallberg KI, Soha JA (2004) Cultural evolution of Puget Sound White-crowned Sparrow song dialects. Ethology 110:879–908
O’Loghlen AL, Rothstein SI (2012) Delayed vocal ontogeny in songbirds: a laboratory study validates a model for delayed development derived from field studies. J Ethol 30:369–378. https://doi.org/10.1007/s10164-012-0334-0
Sueur J, Aubin T, Simonis C (2008) Seewave: a free modular tool for sound analysis and synthesis. Bioacoustics 18:213–226
Tchernichovski O, Nottebohm F, Ho C et al (2000) A procedure for an automated measurement of song similarity. Anim Behav 59:1167–1176. https://doi.org/10.1006/anbe.1999.1416
Temeles EJ (1994) The role of neighbours in territorial systems: when are they “dear enemies”? Anim Behav 47:339–350
Thompson NS, LeDoux K, Moody K (1994) A system for describing bird song units. Bioacoustics 5:267–279
Vaskuti É, Zsebők S, Gábor H et al (2016) A kulturális evolúció nyomai az örvös légykapó (Ficedula albicollis) énekében. Állattani közlemények 101:25–41. https://doi.org/10.20331/allkoz.2016.101.1-2.25
Weiss M, Hultsch H, Adam I et al (2014) The use of network analysis to study complex animal communication systems: a study on nightingale song. Proc R Soc B Biol Sci 281:20140460. https://doi.org/10.1098/rspb.2014.0460
Zsebők S, Herczeg G, Blázi G, Laczi M, Nagy G, Szász E, Markó G, Török J, Garamszegi LZ (2017) Short- and long-term repeatability and pseudo-repeatability of bird song: sensitivity of signals to varying environments. Behav Ecol Sociobiol 71:154. https://doi.org/10.1007/s00265-017-2379-0
Zsebők S, Herczeg G, Blázi G, Laczi M, Nagy G, Török J, Garamszegi LZ (2018) Minimum spanning tree as a new, robust repertoire size comparison method: simulation and test on birdsong. Behav Ecol Sociobiol 72:48. https://doi.org/10.1007/s00265-018-2467-9
Acknowledgements
We are grateful to the members of the Behavioural Ecology Research Group for assistance during the fieldwork, Erdők a Közjóért Alapítvány and Pilisi Parkerdő Zrt. Permission for the fieldwork was given by the Middle-Danube-Valley Inspectorate for Environmental Protection, Nature Conservation and Water Management.
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This study was supported by funds from the Ministry of Economy and Competitiveness, Spain (CGL2015-70639-P) and the National Research, Development and Innovation Office Hungary (NKFIH, K-115970 and PD-115730).
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All applicable international, national and/or institutional guidelines for the care and use of animals were followed.
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Communicated by S. Kipper.
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Zsebők, S., Blázi, G., Laczi, M. et al. “Ficedula”: an open-source MATLAB toolbox for cutting, segmenting and computer-aided clustering of bird song. J Ornithol 159, 1105–1111 (2018). https://doi.org/10.1007/s10336-018-1581-9
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DOI: https://doi.org/10.1007/s10336-018-1581-9