Skip to content

Research at St Andrews

Quantifying similarity in animal vocal sequences: which metric performs best?

Research output: Contribution to journalArticle

Abstract

1. Many animals communicate using sequences of discrete acoustic elements which can be complex, vary in their degree of stereotypy, and are potentially open-ended. Variation in sequences can provide important ecological, behavioural, or evolutionary information about the structure and connectivity of populations, mechanisms for vocal cultural evolution, and the underlying drivers responsible for these processes. Various mathematical techniques have been used to form a realistic approximation of sequence similarity for such tasks.
2. Here, we use both simulated and empirical datasets from animal vocal sequences (rock hyrax, Procavia capensis; humpback whale, Megaptera novaeangliae; bottlenose dolphin, Tursiops truncatus; and Carolina chickadee, Poecile carolinensis) to test which of eight sequence analysis metrics are more likely to reconstruct the information encoded in the sequences, and to test the fidelity of estimation of model parameters, when the sequences are assumed to conform to particular statistical models.
3. Results from the simulated data indicated that multiple metrics were equally successful in reconstructing the information encoded in the sequences of simulated individuals (Markov chains, n-gram models, repeat distribution, and edit distance), and data generated by different stochastic processes (entropy rate and n-grams). However, the string edit (Levenshtein) distance performed consistently and significantly better than all other tested metrics (including entropy, Markov chains, n-grams, mutual information) for all empirical datasets, despite being less commonly used in the field of animal acoustic communication.
4. The Levenshtein distance metric provides a robust analytical approach that should be considered in the comparison of animal acoustic sequences in preference to other commonly employed techniques (such as Markov chains, hidden Markov models, or Shannon entropy). The recent discovery that non-Markovian vocal sequences may be more common in animal communication than previously thought, provides a rich area for future research that requires non-Markovian based analysis techniques to investigate animal grammars and potentially the origin of human language.
Close

Details

Original languageEnglish
Pages (from-to)1452-1461
JournalMethods in Ecology and Evolution
Volume6
Issue number12
Early online date7 Aug 2015
DOIs
Publication statusPublished - Dec 2015

    Research areas

  • Sequence, Animal communication, Vocal, Edit distance, Markov, Stochastic processes

Discover related content
Find related publications, people, projects and more using interactive charts.

View graph of relations

Related by author

  1. Animal cultures matter for conservation

    Brakes, P., Dall, S. R. X., Aplin, L. M., Bearhop, S., Carroll, E. L., Ciucci, P., Fishlock, V., Ford, J. K. B., Garland, E. C., Keith, S. A., McGregor, P. K., Mesnick, S. L., Noad, M. J., Notarbartolo di Sciara, G., Robbins, M. M., Simmonds, M. P., Spina, F., Thornton, A., Wade, P. R., Whiting, M. J. & 5 othersWilliams, J., Rendell, L., Whitehead, H., Whiten, A. & Rutz, C., 26 Feb 2019, In : Science. 5 p., eaaw3557.

    Research output: Contribution to journalArticle

  2. Cultural revolutions reduce complexity in the songs of humpback whales

    Allen, J. A., Garland, E. C., Dunlop, R. A. & Noad, M. J., 21 Nov 2018, In : Proceedings of the Royal Society B: Biological Sciences. 285, 1891, 6 p., 20182088.

    Research output: Contribution to journalArticle

  3. Culturally transmitted song exchange between humpback whales (Megaptera novaeangliae) in the southeast Atlantic and southwest Indian Ocean basins

    Rekdahl, M. L., Garland, E. C., Carvajal, G. A., King, C. D., Collins, T., Razafindrakoto, Y. & Rosenbaum, H., Nov 2018, In : Royal Society Open Science. 5, 15 p., 172305.

    Research output: Contribution to journalArticle

  4. Beluga whales in the western Beaufort Sea: current state of knowledge on timing, distribution, habitat use and environmental drivers

    Stafford, K. M., Ferguson, M. C., Hauser, D. D. W., Okkonen, S. R., Berchok, C. L., Citta, J. J., Clarke, J. T., Garland, E. C., Jones, J. & Suydam, R. S., Jun 2018, In : Deep Sea Research Part II: Topical Studies in Oceanography. 152, p. 182-194

    Research output: Contribution to journalArticle

  5. Using agent-based models to understand the role of individuals in the song evolution of humpback whales (Megaptera novaeangliae)

    Mcloughlin, M., Lamoni, L., Garland, E. C., Ingram, S., Kirke, A., Noad, M. J., Rendell, L. & Miranda, E., 2018, In : Music & Science. 1, 17 p.

    Research output: Contribution to journalArticle

Related by journal

  1. A 2.6-gram sound and movement tag for studying the acoustic scene and kinematics of echolocating bats

    Stidsholt, L., Johnson, M., Beedholm, K., Jakobsen, L., Kugler, K., Brinkløv, S., Salles, A., Moss, C. F. & Madsen, P. T., Jan 2019, In : Methods in Ecology and Evolution. 10, 1, p. 48-58 11 p.

    Research output: Contribution to journalArticle

  2. Model selection with overdispersed distance sampling data

    Howe, E. J., Buckland, S. T., Després-Einspenner, M-L. & Kühl, H. S., Jan 2019, In : Methods in Ecology and Evolution. 10, 1, p. 38-47

    Research output: Contribution to journalArticle

  3. State-switching continuous-time correlated random walks

    Michelot, T. & Blackwell, P. G., 14 Feb 2019, In : Methods in Ecology and Evolution. Early View

    Research output: Contribution to journalArticle

  4. inlabru: an R package for Bayesian spatial modelling from ecological survey data

    Bachl, F. E., Lindgren, F., Borchers, D. L. & Illian, J. B., 21 Mar 2019, In : Methods in Ecology and Evolution. Early View, 7 p.

    Research output: Contribution to journalArticle

  5. Estimating effective detection area of static passive acoustic data loggers from playback experiments with cetacean vocalisations

    Nuuttila, H. K., Brundiers, K., Dähne, M., Koblitz, J. C., Thomas, L., Courtene-Jones, W., Evans, P. G. H., Turner, J. R., Bennell, J. D. & Hiddink, J. G., Dec 2018, In : Methods in Ecology and Evolution. 9, 12, p. 2362-2371

    Research output: Contribution to journalArticle

Related by journal

  1. Methods in Ecology and Evolution (Journal)

    Michael Blair Morrissey (Member of editorial board)
    1 Jan 20171 Jan 2020

    Activity: Publication peer-review and editorial work typesEditor of research journal

  2. Methods in Ecology and Evolution (Journal)

    Theoni Photopoulou (Editor)
    2017 → …

    Activity: Publication peer-review and editorial work typesEditor of research journal

  3. Methods in Ecology and Evolution (Journal)

    Oscar Eduardo Gaggiotti (Member of editorial board)
    1 Sep 2014 → …

    Activity: Publication peer-review and editorial work typesEditor of research journal

ID: 198207159