Unmasking hidden genetic, vocal, and size variation in the Masked Flowerpiercer along the Andes supports two species separated by Northern Peruvian Low
Data files
May 29, 2023 version files 170.13 KB
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ORNITH-23-023_AlternVSMainSongData.csv
31.36 KB
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ORNITH-23-023_DataAnalysis.R
17.98 KB
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ORNITH-23-023_MainSongData.csv
98.22 KB
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ORNITH-23-023_MorphoData.csv
16.27 KB
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README_ORNITH-23-023_UnmaskingDiglossaNPL.md
6.30 KB
Dec 05, 2023 version files 170.20 KB
Abstract
Genetic divergence among isolated populations is not always reflected in phenotypic differentiation. We investigated the genetic and phenotypic differentiation in Diglossa cyanea (Thraupidae; Masked Flowerpiercer), a widely distributed species in the tropical Andes. We found strong evidence for two main lineages separated by the Marañón River valley in the Northern Peruvian Low (NPL). These two lineages show a deep sequence divergence in mitochondrial DNA (mtDNA; ~6.7% uncorrected p-distance, n = 122), spectral frequency and song structure (with exclusive final whistles in southern populations, n = 88), and wing length (the northern populations are smaller, n = 364). The two divergent D. cyanea mitochondrial lineages were not sister to each other, suggesting a possible paraphyly with respect to D. caerulescens (Bluish Flowerpiercer) that remains to be tested with nuclear genomic data. No genetic variation, size difference or song structure was observed within the extensive range of the southern group (from the NPL to central Bolivia) or within all sampled northern populations (from the NPL to Venezuela). These vocal differences appear to have consequences for song discrimination, and species recognition, according to a previously published playback experiment study. We propose that the southern taxon be elevated to species rank as D. melanopis, a monotypic species (with the proposed name Whistling Masked-Flowerpiercer). In turn, we provide a redefinition of D. cyanea (Warbling Masked-Flowerpiercer), which is now restricted to the northern half of the tropical Andes as a polytypic species with three subspecies (tovarensis, obscura, and cyanea). Based on our results, the subspecies dispar should be treated as a junior synonym of cyanea. Our study highlights the need to continue amassing complementary datasets from field observations, experiments, and collection-based assessments to better characterize the evolutionary history, biogeography, bioacoustics, and taxonomy of Neotropical montane birds.
README: Data from "Unmasking hidden genetic, vocal, and size variation in the Masked Flowerpiercer along the Andes supports two species" ORNITH-23-023
File name: README_ORNITH-23-023_UnmaskingDiglossaNPL.md
- Dataset Title: Data for the article "Unmasking hidden genetic, vocal, and size variation in the Masked Flowerpiercer along the Andes supports two species"
- Authors: Silvia C, Martínez-Gomez, Carlos Esteban Lara, J. Van Remsen Jr., Robb Brumfield, Andrés M. Cuervo
- Date created: 2023-05-23
- Date modified: 2023-05-29
- Persistent identifier: DOI: 10.5061/dryad.fj6q5740r
- Description: This dataset contains the raw vocal and morphometrical data, in addition to the R script used for the vocal and morphological analyses of the mentioned study.
Data and File Overview
=========================
- Files:
- ORNITH-23-023_MainSongData.csv
- ORNITH-23-023_AlternVSMainSongData.csv
- ORNITH-23-023_MorphoData.csv
- ORNITH-23-023_DataAnalysis.R
The folowing description is complementary to the METHODS section in the paper. We recomend to read the paper carefully before using these files to avoid potential confusion.
The three .csv files contain raw data used in in the R Script to reproduce all Bayesian Linear Mixed Models and Linear Models used for the vocal and body size analyses of this paper.
The complete methodological details, such as specimens or vocalization sources and workflow to interpret the results of this script can be found within the article text and its supplementary material.
Details for: ORNITH-23-023_MainSongData.csv
- Description: Raw vocal data for all five variables used in the analysis on the main song part of the study. All data were extracted from the analyzed recordings in RavenPro 1.6 as detailed in the article.
- Format: .csv
- Dimensions: 476 rows x 14 columns
- Variables:
- Gr: Binomial code for geographic group in relation to North Peruvian Low (NPL): 0= North; 1= South
- Group: Geographic group in relation to North Peruvian Low (NPL): N= North; S= South
- Country: Recording's locality. BO= Bolivia; CO= Colombia; EC= Ecuador; PE= Peru; VE= Venezuela
- Lat: Latitude (Recording's locality)
- Long: Longitude (Recording's locality)
- Subsp: Subspecies according to Dickinson & Christidis (2014) and The Clements Checklist of Birds of the World v.2022
- Rec: Recording ID of songs with its respective ML (Macaulay Library) or XC (Xeno-canto) identifier. Each Recording refers to an individual.
- Song: Each song bout of each individual (multiple belonging to same Recording), numbered from 1 to 11 after Recording ID. There can be multiple and different amounts of song bouts per individual/Recording.
- Section: Song section as described in the article: F= Full song; S1= Section 1; S2= Section 2
- Dur: Duration (s)
- PeakF: Peak Frequency (Hz)
- HighF: Maximum Frequency (Hz)
- LowF: Minimum Frequency (Hz)
- DeltaF: Bandwidth (Hz)
Details for: ORNITH-23-023_AlternVSMainSongData.csv
- Description: Raw data for the same five vocal variables for both, main and alternative songs for all the studied individuals or individuals.
- Format: .csv
- Dimensions: 165 rows x 13 columns
- Variables:
- Gr: Binomial code for geographic group in relation to North Peruvian Low (NPL): 0= North; 1= South
- Group: Geographic group in relation to North Peruvian Low (NPL): N= North; S= South
- Country: Recording's locality. BO= Bolivia; CO= Colombia; EC= Ecuador; PE= Peru; VE= Venezuela
- Lat: Latitude (Recording's locality)
- Long: Longitude (Recording's locality)
- Rec: Recording ID of songs with its respective ML (Macaulay Library) or XC (Xeno-canto) identifier. Each Recording refers to an individual.
- Song: Each song bout of each individual (multiple belonging to same Recording), numbered from 1 to 11 after Recording ID. There can be multiple and different amounts of song bouts per individual/Recording.
- Section: Song section as described in the article. Note that the only song section is F= Full song, because other sections of the song (S1, S2) were not comparable. We left this column to avoid confusions on the source of the data.
- Dur: Duration (s)
- PeakF: Peak Frequency (Hz)
- HighF: Maximum Frequency (Hz)
- LowF: Minimum Frequency (Hz)
- DeltaF: Bandwidth (Hz)
Details for: ORNITH-23-023_MorphoData.csv
- Description: Wing length (WL) data for all the skin specimens we analyzed in this study, respectively identified by their biological collecion code and geographical information.
- Format: .csv
- Dimensions: 365 rows x 8 columns
- Variables:
- Skin_ID: Museum acronyms with unique ID for respective skin (see acronyms and museum names in Supplementary Material of the article)
- Group: Geographic group in relation to North Peruvian Low (NPL): N= North; S= South
- Subspecies: Subspecies according to Dickinson & Christidis (2014) and The Clements Checklist of Birds of the World v.2022
- Country: Specimen's locality. BO= Bolivia; CO= Colombia; EC= Ecuador; PE= Peru; VE= Venezuela
- Lat: Latitude (specimen's locality)
- Long: Longitude (specimen's locality)
- Sex: identified sex; F= Female; M= Male
- WL: Wing length (mm) - wing chord; see article for details
Details for: ORNITH-23-023_DataAnalysis.R
- Description: R file with the codes used to fit the vocal and morphometric models.
- Format: .R
- Length: 458 lines
Contact information
======================
If you need further information please contact us:
Silvia C. Martínez-Gomez, scmartinezg@unal.edu.co
Andrés M. Cuervo, amcuervom@unal.edu.co
References
=============
Clements, J. F., T. S. Schulenberg, M. J. Iliff, T. A. Fredericks, J. A. Gerbracht, D. Lepage, S. M. Billerman, B. L. Sullivan, and C. L. Wood. 2022. The eBird/Clements checklist of Birds of the World: v2022. Downloaded from https://www.birds.cornell.edu/clementschecklist/download/
Dickinson, E. C., and L. Christidis. 2014. The Howard & Moore Complete Checklist of the Birds of the World. 4th. Edition, Vol. 2: Passerines. 4th. Edition, Vol. 2 edition. Aves Press, Eastbourne, United Kingdon.
Methods
Please see the README.md file (README_ORNITH-23-023_UnmaskingDiglossaNPL.md) and the accompanying published article: Silvia C Martínez-Gómez, Carlos Esteban Lara, J V Remsen, Robb T Brumfield, Andrés M Cuervo. Unmasking hidden genetic, vocal, and size variation in the Masked Flowerpiercer along the Andes supports two species separated by Northern Peruvian Low. Ornithology, Volume 140, Issue 4, 5 October 2023, ukad028, https://doi.org/10.1093/ornithology/ukad028