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

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## Abstract

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## Simple Summary

## Abstract

## 1. Introduction

## 2. Materials and Methods

#### 2.1. Species Model

#### 2.2. Dataset

#### 2.3. The Uniform Manifold Approximation and Projection (UMAP)

## 3. Results

## 4. Discussion

## 5. Conclusions

## Supplementary Materials

## Author Contributions

## Funding

## Acknowledgments

## Conflicts of Interest

## References

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**Figure 1.**Distribution of Rough-legged Tyrannulet (sensu lato). Records used in the bioacoustics analysis with Uniform Manifold Approximation and Projection (UMAP) are represented by a pink square (Table S1). Hollow circles are other acoustic records, not used here in the analysis. Country codes alpha-2 represent the countries with records.

**Figure 2.**Illustration of UMAP process. Original data points (

**left**), 22% of the distance to 5th neighbor (

**center**), and 100% of the distance to 5th neighbor (

**right**). Beyond the intersection with the first neighbor, the radius begins to get blurred, assigning less weight to subsequent connections [40].

**Figure 3.**UMAP visualization and k-medoids clustering of the N = 101 samples of Rough-legged Tyrannulet (sensu lato) included in the study. Two clusters are identified using markers: Group A with blue circles, Group B with red x-mark. Each individual is labeled with the country of precedence using country codes alpha-2.

**Figure 4.**Comparison of results using UMAP, principal components analysis (PCA), and t-distributed stochastic neighbor embedding (t-SNE). Each individual is labeled with the country of precedence using country codes alpha-2, and groups are marked using text color: Group A in blue, Group B in red.

**Figure 5.**Segregation by the distribution of two different acoustic groups within the Rough-legged Tyrannulet complex.

**Figure 6.**Elevation comparison between two groups of Rough-legged Tyrannulet (sensu lato). Rough-legged Tyrannulet (sensu strictu; Phyllomyias burmeisteri) and White-fronted Tyrannulet (P. zeledoni) differed in median elevation. White violin plots show the density of records in the elevation axis. Box plots show the interquartile range (IQR) from the first and third quartile (25 and 75% data), while whiskers extend up to ±1.5 × IQR.

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**MDPI and ACS Style**

Parra-Hernández, R.M.; Posada-Quintero, J.I.; Acevedo-Charry, O.; Posada-Quintero, H.F.
Uniform Manifold Approximation and Projection for Clustering Taxa through Vocalizations in a Neotropical Passerine (Rough-Legged Tyrannulet, *Phyllomyias burmeisteri*). *Animals* **2020**, *10*, 1406.
https://doi.org/10.3390/ani10081406

**AMA Style**

Parra-Hernández RM, Posada-Quintero JI, Acevedo-Charry O, Posada-Quintero HF.
Uniform Manifold Approximation and Projection for Clustering Taxa through Vocalizations in a Neotropical Passerine (Rough-Legged Tyrannulet, *Phyllomyias burmeisteri*). *Animals*. 2020; 10(8):1406.
https://doi.org/10.3390/ani10081406

**Chicago/Turabian Style**

Parra-Hernández, Ronald M., Jorge I. Posada-Quintero, Orlando Acevedo-Charry, and Hugo F. Posada-Quintero.
2020. "Uniform Manifold Approximation and Projection for Clustering Taxa through Vocalizations in a Neotropical Passerine (Rough-Legged Tyrannulet, *Phyllomyias burmeisteri*)" *Animals* 10, no. 8: 1406.
https://doi.org/10.3390/ani10081406