DOI: 10.5061/dryad.vdncjsxwq
title: Neotropical birds respond innately to unfamiliar acoustic signals dataset

description: Here we included the files for Sandoval and Wilson manuscript entitled
 "Neotropical birds respond innately to unfamiliar acoustic
 signals." which is publish in The American Naturalist. The name of
 each file is followed by a description of the file's contents in the
 file Read me. :  SWanalysis.R - The R script used to produce all
 statistical analyses and figures presented in the manuscript. This file is
 dependent on the following files described below: SWtreeF2.nex SWnames.csv
 SWtreePGLM.nex SWdataPGLM.csv SWtrialData.csv SWsppData.csv SWcallF1.wav
 SWsongF1.wav
description: SWanalysis.R - The R script used to produce all statistical
 analyses and figures presented in the manuscript. This file is dependent
 on the following files described below:
 SWtreeF2.nex SWnames.csv
 SWtreePGLM.nex SWdataPGLM.csv
 SWtrialData.csv SWsppData.csv
 SWcallF1.wav SWsongF1.wav
   SWtreeF2.nex --- A nexus file containing
 10,000 phylogenetic trees. Trees were generated from birdtree.org using
 all the species that overlapped with at least one of the playback sites
 used in our study. Although 692 species are sympatric with the sites, only
 689 are shown in the trees because three species recognized by the
 American Ornithological Society's checklists (Arremon atricapillus,
 Buteo plagiatus, Momotus subrufescens) were not included in the
 phylogenies provided by birdtree.org. Trees were created using the Hackett
 backbone.   SWnames.csv --- A data
 file containing taxonomic information used to create Figure 2 in the
 manuscript. It includes the following variables: AOS:
 species names shown in Figure 2, based on the American Ornithological
 Society birdtree: species names used in the phylogenies
 created by birdtree.org AOSorder: taxonomic order of
 each species, based on the American Ornithological Society
 colour: numbers (Alphabet colour palette) to colour code species
 of the same taxonomic order  
 SWtreePGLM.nex --- A nexus file containing 10,000 phylogenetic
 trees. Trees were generated from birdtree.org using the 38 species that
 responded to the chick-a-dee call treatment of at least one trial (shown
 in red in figure 2 of the paper), as well as 38 phylogenetically matched
 non-respondent species (shown in blue in figure 2 of the paper). These
 trees are used in the phylogenetic logistic regressions presented in the
 paper. Trees were created using the Hackett backbone.
   SWdataPGLM.csv --- A data file containing
 species traits used in the phylogenetic logistic regressions. The
 following variables are shown for each species that responded to the
 chick-a-dee calls of at least one trial (N = 38 species), and for 38
 phylogenetically matched species that did not respond:
 birdtree: species names used by birdtree.org
 respond: whether the species responded to the chick-a-dee calls
 of at least one trial corr: median cross-correlation
 coefficients (0-1) comparing a species' calls to chick-a-dee
 calls mass: mean body mass of the species
 (grams)   SWtrialData.csv --- A data
 file containing the raw data collected during 414 trial-treatments. These
 data are used in the analysis of whether experimental treatment affected
 the number of resident species that approached the playback speaker.
 Variables in the datafile include: migrants: North
 American migrants were either present or absent
 country: trials were conducted in Brazil, Colombia, or Costa
 Rica site: trials were conducted at 21 sites in Brazil,
 27 sites in Colombia, and 30 sites in Costa Rica block:
 a block included three playback treatments played at a given site over ~20
 minutes trt: playback treatments included a chick-a-dee
 call, fee bee song, and silence latency: time (s) from
 start of playback until first bird approached within 5 m of
 speaker dist: minimum distance (m) of any bird to
 speaker during the trial-treatment spp: number of
 resident species to approach within 5 m of speaker during
 trial-treatment inds: sum of # individuals of each
 resident species within 5 m of speaker during trial-treatment
   SWsppData.csv --- A data file containing the
 raw data collected during the 88 trials in which at least one resident
 species responded during at least one of the three treatments. For each
 trial-treatment, data are included separately for each species that
 ultimately responded to any of the three treatments in the trial. These
 data are used in the analyses of whether experimental treatment affected a
 given species' probability of response, their latency to respond, and
 their minimum approach distance. Variables in the datafile
 include: migrants: North American migrants were either
 present or absent country: trials were conducted in
 Brazil, Colombia, or Costa Rica site: trials were
 conducted at 21 sites in Brazil, 27 sites in Colombia, and 30 sites in
 Costa Rica block: a block included three playback
 treatments played at a given site over ~20 minutes trt:
 playback treatments included a chick-a-dee call, fee bee song, and
 silence latency: time (s) from start of playback until
 first bird of the species approached within 5 m of speaker
 dist: minimum distance (m) of the species to speaker during the
 trial-treatment focal: scientific name of the species;
 taxonomy follows American Ornithological Society
 respond: did focal species approach within 5 m of speaker during
 the treatment (0=no; 1=yes)  
 SWcallF1.wav --- Audio recording (44.1 kHz sampling rate, 16-bit
 amplitude encoding, WAVE format) of a chick-a-dee call used to create
 Figure 1a.   SWsongF1.wav --- Audio
 recording (44.1 kHz sampling rate, 16-bit amplitude encoding, WAVE format)
 of a fee bee song used to create Figure 1b.  
 SWsounds.csv --- A list of audio files obtained from public
 libraries of sound. One call within each recording was used either as a
 playback stimulus or in a spectrogram cross-correlation to determine the
 structural similarity between the species' call and the chick-a-dee
 call. Cross correlation coefficients were then used in a phylogenetic
 logistic regression predicting a species' probability of response.
 Variables in the data file include: species: scientific
 name of the species; taxonomy follows American Ornithological
 Society ID: the catalogue numbers of recordings from
 Macaulay Library (ML) and Xeno Canto (XC) onset: time
 (s) within recording when call begins offset: time (s)
 within recording when call ends role: each call was
 used either as a stimulus or in the phylogenetic logistic regression
 (PGLR)