Improved versions of the Levenshtein distance method for comparing sequence information in animals’ vocalisations: tests using humpback whale song

Garland, Ellen C.; Lilley, Matthew S.; Goldizen, Anne W.; Rekdahl, Melinda L.; Garrigue, Claire; Noad, Michael J.

doi:10.1163/1568539x-00003032

Cited by 47 publications

(59 citation statements)

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“…The measured variables were subjected to a nonparametric CART with cross-validation using the rpart package in R (R Foundation for Statistical Computing, 2012), following the method of Garland et al (2012) and Rekdahl et al (2013). As we had no concurrent visual data to understand the number of animals within range of the recorder, multiple calls from an individual animal are likely included in the analysis.…”

Section: Quantitative Classification and Statistical Analysis Of Callmentioning

confidence: 99%

Beluga whale (Delphinapterus leucas) vocalizations and call classification from the eastern Beaufort Sea population

Garland

Castellote

Berchok

2015

The Journal of the Acoustical Society of America

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Beluga whales, Delphinapterus leucas, have a graded call system; call types exist on a continuum making classification challenging. A description of vocalizations from the eastern Beaufort Sea beluga population during its spring migration are presented here, using both a non-parametric classification tree analysis (CART), and a Random Forest analysis. Twelve frequency and duration measurements were made on 1019 calls recorded over 14 days off Icy Cape, Alaska, resulting in 34 identifiable call types with 83% agreement in classification for both CART and Random Forest analyses. This high level of agreement in classification, with an initial subjective classification of calls into 36 categories, demonstrates that the methods applied here provide a quantitative analysis of a graded call dataset. Further, as calls cannot be attributed to individuals using single sensor passive acoustic monitoring efforts, these methods provide a comprehensive analysis of data where the influence of pseudo-replication of calls from individuals is unknown. This study is the first to describe the vocal repertoire of a beluga population using a robust and repeatable methodology. A baseline eastern Beaufort Sea beluga population repertoire is presented here, against which the call repertoire of other seasonally sympatric Alaskan beluga populations can be compared.

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Section: Quantitative Classification and Statistical Analysis Of Callmentioning

confidence: 99%

Beluga whale (Delphinapterus leucas) vocalizations and call classification from the eastern Beaufort Sea population

Garland

Castellote

Berchok

2015

The Journal of the Acoustical Society of America

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“…The Levenshtein distance (LD) calculates the minimum number of changes (insertions, deletions, and substitutions) needed to transform one string of data into another (Kohonen, 1985;Helweg et al, 1998;Eriksen et al, 2005;Tougaard and Eriksen, 2006;Garland et al, 2012). The LD is calculated as ( Kohonen, 1985).…”

Section: Levenshtein Distance Analysismentioning

confidence: 99%

“…To allow multiple pairwise comparisons, raw LD scores were standardized to allow meaningful comparisons (see Kohonen, 1985;Tougaard and Eriksen, 2006;Garland et al, 2012). Two standardizations of the data were undertaken.…”

Section: Levenshtein Distance Analysismentioning

confidence: 99%

“…In order to investigate the similarity of multiple sets or groups of data, a variation on the LD equation, called the "Levenshtein distance similarity index" (LSI), was used (Helweg et al, 1998;Eriksen et al, 2005;Garland et al, 2012). This normalized the LD score by the length of the longest string as follows:…”

Section: Matrix Of Ld Similaritymentioning

confidence: 99%

“…To ensure an unbiased quantitative assignment of song type clusters, we removed all information regarding populations, years, and qualitatively assigned song types, and thus all preconceptions of what song types particular songs belonged to, for both levels of analysis. A handful of studies have investigated song sequence similarity in humpback whales using the Levenshtein distance method (Helweg et al, 1998;Eriksen et al, 2005;Tougaard and Eriksen, 2006;Garland et al, 2012). The Levenshtein distance technique and variants of this method provide a quantitative measure to investigate the similarity of multiple song sequences by grouping or clustering similar sequences together.…”

Section: Introductionmentioning

confidence: 99%

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Quantifying humpback whale song sequences to understand the dynamics of song exchange at the ocean basin scale

Garland

Noad

Goldizen

et al. 2013

The Journal of the Acoustical Society of America

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109

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Humpback whales have a continually evolving vocal sexual display, or "song," that appears to undergo both evolutionary and "revolutionary" change. All males within a population adhere to the current content and arrangement of the song. Populations within an ocean basin share similarities in their songs; this sharing is complex as multiple variations of the song (song types) may be present within a region at any one time. To quantitatively investigate the similarity of song types, songs were compared at both the individual singer and population level using the Levenshtein distance technique and cluster analysis. The highly stereotyped sequences of themes from the songs of 211 individuals from populations within the western and central South Pacific region from 1998 through 2008 were grouped together based on the percentage of song similarity, and compared to qualitatively assigned song types. The analysis produced clusters of highly similar songs that agreed with previous qualitative assignments. Each cluster contained songs from multiple populations and years, confirming the eastward spread of song types and their progressive evolution through the study region. Quantifying song similarity and exchange will assist in understanding broader song dynamics and contribute to the use of vocal displays as population identifiers.

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Sexually dimorphic phrase organization in the song of the indris (Indri indri)

Zanoli

Gregorio

Valente

et al. 2020

American J Primatol

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Animal acoustic communication often takes the form of complex sequences, composed of multiple distinct acoustic units, which can vary in their degree of stereotypy.Studies of sequence variation may contribute to our understanding of the structural flexibility of primates' songs, which can provide essential ecological and behavioral information about variability at the individual, population, and specific level and provide insights into the mechanisms and drivers responsible for the evolutionary change of communicative traits. Several methods have been used for investigating different levels of structural information and sequence similarity in acoustic displays. We studied intra and interindividual variation in the song structuring of a singing primate, the indri (Indri indri), which inhabits the montane rain forests of Madagascar. Indri groups emit duets and choruses in which they combine long notes, short single units, and phrases consisting of a variable number of units (from two to six) with slightly descending frequency. Males' and females' contributions to the song differ in the temporal and frequency structure of song units and repertoire size. We calculated the similarity of phrase organization across different individual contributions using the Levenshtein distance, a logic distance that expressed the minimum cost to convert a sequence into another and can measure differences between two sequences of data. We then analyzed the degree of similarity within and between individuals and found that: (a) the phrase structure of songs varied between reproductive males and females: female structuring of the song showed a higher number of phrases if compared to males; (b) male contributions to the song were overall more similar to those of other males than were female contributions to the song of other females; (c) male contributions were more stereotyped than female contributions, which showed greater individual flexibility.The picture emerging from phrase combinatorics in the indris is in agreement with previous findings of rhythmic features and song repertoire size of the indris, which also suggested that female songs are potentially less stereotyped than those of males. K E Y W O R D Slanguage evolution, Levenshtein distance, primates, singing, syntax

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Improved versions of the Levenshtein distance method for comparing sequence information in animals’ vocalisations: tests using humpback whale song

Cited by 47 publications

References 0 publications

Beluga whale (Delphinapterus leucas) vocalizations and call classification from the eastern Beaufort Sea population

Beluga whale (Delphinapterus leucas) vocalizations and call classification from the eastern Beaufort Sea population

Quantifying humpback whale song sequences to understand the dynamics of song exchange at the ocean basin scale

Sexually dimorphic phrase organization in the song of the indris (Indri indri)

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