Data from: Divergence in vocalizations indicates cryptic speciation in Camptostoma tyrannulets
Data files
Nov 27, 2024 version files 113.14 KB
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Camptostoma_Lima_and_Vaz.zip
107.46 KB
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README.md
5.67 KB
Abstract
The tyrant flycatcher genus Camptostoma currently comprises two visually similar species: the Northern Beardless-Tyrannulet (C. imberbe), ranging from the southern United States to Costa Rica, and the Southern Beardless-Tyrannulet (C. obsoletum), found from Costa Rica to Uruguay. Vocal and genetic differences suggest that the Southern Beardless-Tyrannulet may include multiple species, but no analysis of acoustic trait variation has been conducted within the genus. We analyzed a geographically comprehensive sample of sound recordings to measure geographic variation in vocalizations across the genus, testing the hypothesis that the Southern Beardless-Tyrannulet includes multiple species. We find that Camptostoma comprises eight vocally distinct populations, two within the Northern and six within the Southern Beardless-Tyrannulet. These populations exhibit diagnostic differences in multiple different vocalizations, including vocalization types that are typically species-specific in the Tyrannidae. Their range limits and contact zones largely corresponded with known dispersal barriers, ecotones, and suture zones, with little evidence of gene flow between adjacent populations. Our results strongly suggest that Camptostoma comprises as many as eight vocally distinct biological species, underscoring the underestimated diversity of species in birds with conservative plumage evolution.
README: Divergence in vocalizations indicates cryptic speciation in Camptostoma tyrannulets
https://doi.org/10.5061/dryad.612jm64dm
Description of the data
This repository is associated with Lima, R. D. & Vaz, R. V. (2024). Divergence in vocalizations indicates cryptic speciation in Camptostoma tyrannulets. Ornithology. In Press. https://doi.org/10.1093/ornithology/ukae058
It contains the data and scripts necessary to reproduce all analyses and figures in the paper. Descriptions of each file are provided below:
File camptostoma_daysong_measurements.csv
This comma-separated spreadsheet contains "daytime song" trait measurement data. Each row is a unique sample (i.e., one measured vocalization). Empty cells indicate unavailable data; for instance, a vocalization with only four notes will have empty cells for measurements pertaining to a fifth note, which is absent in this sample.
- sample: Unique accession number for the sound recording used for measurement.
- group: One of eight vocally distinct populations identified in the associated study.
- country: Country of recording.
- locality: Locality of recording.
- latitude: Latitude in decimal degrees.
- longitude: Longitude in decimal degrees.
- dur.n*x*: duration of the nth note, in seconds (e.g., dur.n1 is the duration of the 1st note).
- dur.i*x*: duration of the nth interval between notes, in seconds (e.g., dur.i1 is the duration of the 1st interval).
- total.dur: total duration of the vocalization, in seconds.
- n.notes: number of notes.
- overall.pace: pace of the vocalization (notes per second).
- mean.dur.note: mean note duration in the vocalization.
- mean.dur.int: mean duration of intervals between notes in the vocalization.
- freqamp.n*x*: frequency amplitude of the nth note, in hertz (e.g., freqamp.n1 is the frequency amplitude of the 1st note).
- mean.freqamp: mean frequency amplitude in the vocalization.
- peakfreq.n*x*: peak frequency of the nth note, in hertz (e.g., peakfreq.n1 is the peak frequency of the 1st note).
- mean.peakfreq: mean peak frequency in the vocalization.
File camptostoma_dawnsong_measurements.csv
This comma-separated spreadsheet contains "dawn song" trait measurement data. The file's structure and variables are the same as described above for the file "camptostoma_daysong_measurements.csv."
File camptostoma_commoncall_measurements.csv
This comma-separated spreadsheet contains trait measurement data for the "common call".
- sample: Accession number for the sound recording used for measurement.
- variant.measured: One of five variants of the "common call" described in the paper, indicating which variant was measured in the sample concerned.
- group: One of eight vocally distinct populations identified in the associated study.
- country: Country of recording.
- locality: Locality of recording.
- latitude: Latitude in decimal degrees.
- longitude: Longitude in decimal degrees.
- dur: duration of the only note, in seconds.
- freqamp: frequency amplitude of the only note, in hertz.
- peakfreq: peak frequency of the only note, in hertz.
File camptostoma_abruptcall_measurements.csv
This comma-separated spreadsheet contains trait measurement data for the "abrupt call".
- sample: Accession number for the sound recording used for measurement.
- group: One of eight vocally distinct populations identified in the associated study.
- country: Country of recording.
- locality: Locality of recording.
- latitude: Latitude in decimal degrees.
- longitude: Longitude in decimal degrees.
- dur: duration of the only note, in seconds.
- freqamp: frequency amplitude of the only note, in hertz.
- peakfreq: peak frequency of the only note, in hertz.
File camptostoma_peeepeee_measurements.csv
This comma-separated spreadsheet contains trait measurement data for the "peee-peee" variant of the "complex call". The file's structure and variables are the same as described above for the file "camptostoma_daysong_measurements.csv."
File camptostoma_peeetrill_measurements.csv
This comma-separated spreadsheet contains trait measurement data for the "peee-trill" variant of the "complex call". The file's structure and variables are the same as described above for the file "camptostoma_daysong_measurements.csv."
File camptostoma_peeedit_measurements.csv
This comma-separated spreadsheet contains trait measurement data for the "peee-dit" variant of the "complex call". The file's structure and variables are the same as described above for the file "camptostoma_daysong_measurements.csv."
File camptostoma_trill_measurements.csv
This comma-separated spreadsheet contains trait measurement data for the "trill call". The file's structure and variables are the same as described above for the file "camptostoma_daysong_measurements.csv."
File camptostoma_altitude_data.csv
Altitude data for all sound recordings used in the study, needed to reproduce Supplementary Material Figure S13.
- sample: Accession numbers for sound recordings.
- group: One of eight vocally distinct populations identified in the associated study.
- latitude: Latitude in decimal degrees of where the recording was made.
- longitude: Longitude in decimal degrees of where the recording was made.
- altitude: Altitude in meters above sea level of where the recording was made.
File Camptostoma_analysis.R
R code to reproduce all analyses and figures.