The biodiversity of the Neotropics is considerable, but it is likely underestimated owing to gaps in sampling effort and a focus on using morphological features of animals to determine species differences rather than divergence in their mating signals and behavior. Recent multi-trait analyses incorporating morphological, plumage, and vocal data have allowed for more accurate quantification of tropical biodiversity. We present a comprehensive study of morphological features, plumage, and vocalizations of the Neotropical resident Rufous-capped Warbler (Basileuterus rufifrons). This species’ taxonomic status is controversial because the B. r. salvini subspecies is intermediate in plumage coloration between the neighboring B. r. delattrii and B. r. rufifrons subspecies. Using morphological and spectral plumage measurements of field and museum specimens, as well as analyses of vocalizations from field recordings and sound libraries, we compared phenotypes of all eight currently recognized Rufous-capped Warbler subspecies, with an emphasis on delattrii, rufifrons, and salvini. We found that delattrii and rufifrons differ significantly in morphology and plumage, and that salvini is similar to rufifrons in morphology and some plumage features. Vocalizations fall into two distinct groups, delattrii and rufifrons-salvini, which differ in multiple spectro-temporal characteristics with no overlap between them, even among individuals in the delattrii-rufifrons zone of sympatry. Our results therefore suggest that Rufous-capped Warblers comprise two distinct groups: Rufous-capped Warblers (B. r. rufifrons and salvini as well as B. r. caudatus, dugesi, and jouyi) and Chestnut-capped Warblers (B. r. delattrii as well as B. r. actuosus and mesochrysus). Future genomic analysis of samples from multiple sites in Mexico and Central America will further refine our assessment of range-wide phenotypic and genetic divergence in this species complex.

Morphology data: Wing, tail, tarsus, and bill measurements were collected from museum specimens and live birds caught in the field.

Plumage coloration data: Spectrometry measurements were collected from 10 body regions for each museum specimen included in the analysis.

Song data: Recordings of singing birds were obtained in the field, and from the Macaulay and University of Florida natural sound archives. The audio files were high-pass filtered and spot-filtered to remove non-target background sounds. The associated audio files included are minimally processed versions (unprocessed or high-pass filtered only).

Morphology:

Data spreadsheets: (1) RCWA_morphology.csv (all analyses except DFA for females: all subspecies); (2) FemalesDFA.csv (DFA for females: all subspecies)

R script: RCWA_morphology.R

Plumage coloration:

Data spreadsheets: (1) RCWA museum data summary_all.csv (raw spectral data); (2) RCWA.spec_processed_2.csv (data summarized by individual)

R script: (1) RCWA spectral analysis_3spp.R (3-subspecies analysis); (2) RCWA spectral analysis_plumage_grps.R (plumage groups analysis)

Raw data (folder): AUK-19-195 RCWA spectrometry (spectrometry data)

Song:

Data spreadsheets: (1) RCWA_vocal analysis.csv (measurements summarized for each song); (2) RCWA songs_average.csv (data summarized by individual)

R script: RCWA_vocal analysis.R

Raw data (folder): RCWA song audio files