Uniform Manifold Approximation and Projection for Clustering Taxa through Vocalizations in a Neotropical Passerine (Rough-Legged Tyrannulet, Phyllomyias burmeisteri)

Vocalizations from birds are a fruitful source of information for the classification of species. However, currently used analyses are ineffective to determine the taxonomic status of some groups. To provide a clearer grouping of taxa for such bird species from the analysis of vocalizations, more sen...

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Published inAnimals (Basel) Vol. 10; no. 8; p. 1406
Main Authors Parra-Hernández, Ronald M., Posada-Quintero, Jorge I., Acevedo-Charry, Orlando, Posada-Quintero, Hugo F.
Format Journal Article
LanguageEnglish
Published Switzerland MDPI AG 12.08.2020
MDPI
Subjects
Acoustics
acrochordopus
Algorithms
Bioacoustics
Biological research
Biology, Experimental
birds
Data analysis
Datasets
dimensionality reduction
Discriminant analysis
Graph representations
Identification and classification
information sources
Neotropics
Passeriformes
principal component analysis
Principal components analysis
sound
taxonomic complex
Taxonomy
tyrannidae
Variance analysis
Visualization
Colombia
Ecuador
Venezuela
Argentina
Uruguay
Panama
Brazil
Paraguay
Bolivia
Peru
Costa Rica
tyranniscus
dimensionality reduction
tyrannidae
acrochordopus
bioacoustics
sound
voices
taxonomic complex
tyranninae
white-fronted tyrannulet
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Abstract Vocalizations from birds are a fruitful source of information for the classification of species. However, currently used analyses are ineffective to determine the taxonomic status of some groups. To provide a clearer grouping of taxa for such bird species from the analysis of vocalizations, more sensitive techniques are required. In this study, we have evaluated the sensitivity of the Uniform Manifold Approximation and Projection (UMAP) technique for grouping the vocalizations of individuals of the Rough-legged Tyrannulet Phyllomyias burmeisteri complex. Although the existence of two taxonomic groups has been suggested by some studies, the species has presented taxonomic difficulties in classification in previous studies. UMAP exhibited a clearer separation of groups than previously used dimensionality-reduction techniques (i.e., principal component analysis), as it was able to effectively identify the two taxa groups. The results achieved with UMAP in this study suggest that the technique can be useful in the analysis of species with complex in taxonomy through vocalizations data as a complementary tool including behavioral traits such as acoustic communication.
AbstractList Vocalizations from birds are a fruitful source of information for the classification of species. However, currently used analyses are ineffective to determine the taxonomic status of some groups. To provide a clearer grouping of taxa for such bird species from the analysis of vocalizations, more sensitive techniques are required. In this study, we have evaluated the sensitivity of the Uniform Manifold Approximation and Projection (UMAP) technique for grouping the vocalizations of individuals of the Rough-legged Tyrannulet Phyllomyias burmeisteri complex. Although the existence of two taxonomic groups has been suggested by some studies, the species has presented taxonomic difficulties in classification in previous studies. UMAP exhibited a clearer separation of groups than previously used dimensionality-reduction techniques (i.e., principal component analysis), as it was able to effectively identify the two taxa groups. The results achieved with UMAP in this study suggest that the technique can be useful in the analysis of species with complex in taxonomy through vocalizations data as a complementary tool including behavioral traits such as acoustic communication.
Vocalizations from birds are a fruitful source of information for the classification of species. However, currently used analyses are ineffective to determine the taxonomic status of some groups. To provide a clearer grouping of taxa for such bird species from the analysis of vocalizations, more sensitive techniques are required. In this study, we have evaluated the sensitivity of the Uniform Manifold Approximation and Projection (UMAP) technique for grouping the vocalizations of individuals of the Rough-legged Tyrannulet Phyllomyias burmeisteri complex. Although the existence of two taxonomic groups has been suggested by some studies, the species has presented taxonomic difficulties in classification in previous studies. UMAP exhibited a clearer separation of groups than previously used dimensionality-reduction techniques (i.e., principal component analysis), as it was able to effectively identify the two taxa groups. The results achieved with UMAP in this study suggest that the technique can be useful in the analysis of species with complex in taxonomy through vocalizations data as a complementary tool including behavioral traits such as acoustic communication.Vocalizations from birds are a fruitful source of information for the classification of species. However, currently used analyses are ineffective to determine the taxonomic status of some groups. To provide a clearer grouping of taxa for such bird species from the analysis of vocalizations, more sensitive techniques are required. In this study, we have evaluated the sensitivity of the Uniform Manifold Approximation and Projection (UMAP) technique for grouping the vocalizations of individuals of the Rough-legged Tyrannulet Phyllomyias burmeisteri complex. Although the existence of two taxonomic groups has been suggested by some studies, the species has presented taxonomic difficulties in classification in previous studies. UMAP exhibited a clearer separation of groups than previously used dimensionality-reduction techniques (i.e., principal component analysis), as it was able to effectively identify the two taxa groups. The results achieved with UMAP in this study suggest that the technique can be useful in the analysis of species with complex in taxonomy through vocalizations data as a complementary tool including behavioral traits such as acoustic communication.
Vocalizations from birds are a fruitful source of information for the classification of species. However, currently used analyses are ineffective to determine the taxonomic status of some groups. To provide a clearer grouping of taxa for such bird species from the analysis of vocalizations, more sensitive techniques are required. In this study, we have evaluated the sensitivity of the Uniform Manifold Approximation and Projection (UMAP) technique for grouping the vocalizations of individuals of the Rough-legged Tyrannulet complex. Although the existence of two taxonomic groups has been suggested by some studies, the species has presented taxonomic difficulties in classification in previous studies. UMAP exhibited a clearer separation of groups than previously used dimensionality-reduction techniques (i.e., principal component analysis), as it was able to effectively identify the two taxa groups. The results achieved with UMAP in this study suggest that the technique can be useful in the analysis of species with complex in taxonomy through vocalizations data as a complementary tool including behavioral traits such as acoustic communication.
Simple Summary: Recognizing the different species can help us better understand the nature. One way to differentiate bird species is the bird song. There are mathematical techniques that extract information from the bird songs, potentially allowing automatic differentiation of species. However, there is still a lack of techniques that use the extracted information and accurately differentiate individuals of different species. For the first time, we have used a technique called Uniform Manifold Approximation and Projection (UMAP) to identify the two taxonomic groups of a bird named Rough-legged Tyrannulet Phyllomyias burmeisteri, which is a species that can be found all the way from Costa Rica to Argentina. Although there is evidence of the existence of two taxonomic groups, previous studies have shown them to be difficult to distinguish. We collected Rough-legged Tyrannulet bird songs of 101 birds from 11 countries. UMAP allowed us to make a transformation of the multiple measures obtained from the bird song of each bird into just two values. Plotting the UMAP values of each bird in a two-dimensional graph, it turns out that UMAP was able to clearly identify the two taxonomic groups, which has been named as Rough-legged Tyrannulet Phyllomyias burmeisteri and White-fronted Tyrannulet Phyllomyias zeledoni. UMAP can potentially help the identification of other species difficult to classify. Vocalizations from birds are a fruitful source of information for the classification of species. However, currently used analyses are ineffective to determine the taxonomic status of some groups. To provide a clearer grouping of taxa for such bird species from the analysis of vocalizations, more sensitive techniques are required. In this study, we have evaluated the sensitivity of the Uniform Manifold Approximation and Projection (UMAP) technique for grouping the vocalizations of individuals of the Rough-legged Tyrannulet Phyllomyias burmeisteri complex. Although the existence of two taxonomic groups has been suggested by some studies, the species has presented taxonomic difficulties in classification in previous studies. UMAP exhibited a clearer separation of groups than previously used dimensionality-reduction techniques (i.e., principal component analysis), as it was able to effectively identify the two taxa groups. The results achieved with UMAP in this study suggest that the technique can be useful in the analysis of species with complex in taxonomy through vocalizations data as a complementary tool including behavioral traits such as acoustic communication. Keywords: acrochordopus; bioacoustics; dimensionality reduction; sound; taxonomic complex; tyrannidae; tyranninae; tyranniscus; voices; white-fronted tyrannulet
Audience Academic
Author Parra-Hernández, Ronald M.
Acevedo-Charry, Orlando
Posada-Quintero, Jorge I.
Posada-Quintero, Hugo F.
AuthorAffiliation 7 Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA
2 Asociación Tolimense de Ornitología, Ibagué, Tolima 730005, Colombia
1 Institución Educativa Normal Superior Fabio Lozano Torrijos, Falan, Tolima 732001, Colombia
4 Facultad de Ciencias de la Educación y la Comunicación, Universidad Autónoma de Asunción, Asunción 001013, Paraguay
6 Asociación Colombiana de Ornitología, Bogotá, DC 111311, Colombia
3 Institución Educativa Técnica María Auxiliadora, Fresno, Tolima 731560, Colombia; jorge.posada@sedtolima.edu.co
5 Colección de Sonidos Ambientales, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Claustro de San Agustín, Villa de Leyva, Boyacá 154001, Colombia; oacevedo@humboldt.org.co
AuthorAffiliation_xml – name: 3 Institución Educativa Técnica María Auxiliadora, Fresno, Tolima 731560, Colombia; jorge.posada@sedtolima.edu.co
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– name: 5 Colección de Sonidos Ambientales, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Claustro de San Agustín, Villa de Leyva, Boyacá 154001, Colombia; oacevedo@humboldt.org.co
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– name: 2 Asociación Tolimense de Ornitología, Ibagué, Tolima 730005, Colombia
Author_xml – sequence: 1
  givenname: Ronald M.
  surname: Parra-Hernández
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  fullname: Posada-Quintero, Jorge I.
– sequence: 3
  givenname: Orlando
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  surname: Acevedo-Charry
  fullname: Acevedo-Charry, Orlando
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  givenname: Hugo F.
  orcidid: 0000-0003-4514-4772
  surname: Posada-Quintero
  fullname: Posada-Quintero, Hugo F.
BackLink https://www.ncbi.nlm.nih.gov/pubmed/32806680$$D View this record in MEDLINE/PubMed
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Issue 8
Keywords tyranniscus
dimensionality reduction
tyrannidae
acrochordopus
bioacoustics
sound
voices
taxonomic complex
tyranninae
white-fronted tyrannulet
Language English
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SSID ssj0000753151
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Snippet Vocalizations from birds are a fruitful source of information for the classification of species. However, currently used analyses are ineffective to determine...
Simple Summary: Recognizing the different species can help us better understand the nature. One way to differentiate bird species is the bird song. There are...
SourceID doaj
pubmedcentral
proquest
gale
pubmed
crossref
SourceType Open Website
Open Access Repository
Aggregation Database
Index Database
Enrichment Source
StartPage 1406
SubjectTerms Acoustics
acrochordopus
Algorithms
Bioacoustics
Biological research
Biology, Experimental
birds
Data analysis
Datasets
dimensionality reduction
Discriminant analysis
Graph representations
Identification and classification
information sources
Neotropics
Passeriformes
principal component analysis
Principal components analysis
sound
taxonomic complex
Taxonomy
tyrannidae
Variance analysis
Visualization
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Title Uniform Manifold Approximation and Projection for Clustering Taxa through Vocalizations in a Neotropical Passerine (Rough-Legged Tyrannulet, Phyllomyias burmeisteri)
URI https://www.ncbi.nlm.nih.gov/pubmed/32806680
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Volume 10
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