DOI: 10.5061/dryad.wwpzgmsqb
title: Chemical fingerprints indicate group membership in a highly social communal breeding bird

description: Gregarious species must distinguish group members from non-group members.
 Olfaction is important for group recognition in mammals but rarely studied
 in birds, despite birds using olfaction in social contexts from species
 discrimination to kin recognition. Olfactory-based recognition requires
 that groups have a signature odour, so we tested for preen oil and feather
 chemical similarity among group-living smooth-billed anis (Crotophaga
 ani). Physiology affects body chemistry, so we also tested for an effect
 of egg-laying competition, as a proxy for reproductive status, on female
 chemical similarity. Finally, the fermentation hypothesis for chemical
 recognition posits that host-associated microbes drive host odour, so we
 tested for covariation between ani chemicals and microbiota. Group members
 were more chemically similar than non-group members, regardless of body
 region, demonstrating that gregarious bird species can have group chemical
 signatures. Females in groups with less egg-laying competition had more
 similar preen oil, but not feather, chemicals, suggesting preen oil
 conveys information about reproductive status. There was no overall
 covariation between chemicals and microbes; instead, subsets of microbes
 could mediate olfactory cues in birds. Preen oil and feather chemicals
 showed little overlap, suggesting they convey different information. These
 findings will guide experimental work on olfaction in gregarious birds.
description: See README.md and main article text for details.
description: R, RStudio, Excel, Notepad (or other text reader).
description: Reference Information === Provenance for this README --- * File name:
 README\_ChemicalSimilarity.md * Author: Leanne A Grieves * Other
 contributors: Allyson L Brady, Greg F Slater, James S Quinn * Date
 created: 2023-05-26 * Date modified: 2023-05-26 Dataset Version and
 Release History --- * Current Version: * Number: 1.0.0 * Date: 2023-05-26
 * Persistent identifier: DOI: PENDING * Summary of changes: n/a * Embargo
 Provenance: n/a * Scope of embargo: n/a * Embargo period: n/a Dataset
 Attribution and Usage --- * Dataset Title: Data for the article
 "Chemical fingerprints indicate group membership in a highly social
 communal breeding bird" * Persistent Identifier: PENDING * Dataset
 Contributors: * Creators: Leanne A Grieves, Allyson L Brady, Greg F
 Slater, James S Quinn * Date of Issue: 2023 * Publisher: McMaster
 University * License: Use of these data is covered by the following
 license: * Title: CC0 1.0 Universal (CC0 1.0) * Specification:
 https://creativecommons.org/publicdomain/zero/1.0/; the authors
 respectfully request to be contacted by researchers interested in the
 re-use of these data so that the possibility of collaboration can be
 discussed. * Suggested Citations: * Dataset citation: &gt; Grieves,
 L.A., G.B. Gloor, and J.S. Quinn. 2023. Data for the article
 "Chemical fingerprints indicate group membership in a highly social
 communal breeding bird", Dryad, Dataset, PENDING * Corresponding
 publication: &gt; Grieves, L.A., G.B. Gloor, and J.S. Quinn. 2023.
 Chemical fingerprints indicate group membership in a highly social
 communal breeding bird. The American Naturalist. In Revision. DOI: PENDING
 Contact Information --- * Name: Leanne A Grieves * Affiliations:
 Department of Biology, School of Earth, Environment and Society, McMaster
 University * ORCID ID: 0000-0002-6836-2177 * Email: grievel@mcmaster.ca *
 Alternate Email: lagrieves@gmail.com * Address: e-mail preferred *
 Alternative Contact: postdoctoral co-PI * Name: James S Quinn *
 Affiliations: Department of Biology, McMaster University * Email:
 quinn@mcmaster.ca * Address: Life Sciences Building 435, McMaster
 University, Hamilton, ON L8S 4L8 *** Additional Dataset Metadata ===
 Acknowledgements --- * Funding sources: Natural Sciences and Engineering
 Research Council of Canada (NSERC) postdoctoral fellowship awarded to LAG
 and discovery grant to JSQ. Dates and Locations --- * Dates of data
 collection: Field data collected between October and December 2021 *
 Geographic locations of data collection: Fieldwork conducted in Cabo Rojo
 National Wildlife Refuge, Puerto Rico (see publication for details) *
 Other locations pertaining to dataset contents: Wet lab work performed by
 LAG at McMaster University. *** Methodological Information === * Methods
 of data collection/generation: see manuscript for details Links to other
 publicly accessible locations of the data === * DOI: PENDING *** Data and
 File Overview === Summary Metrics --- * File count: 14 * Total file size:
 13.4 MB * Range of individual file sizes: 2.1 KB - 799 KB * File formats:
 .csv, .txt, .pdf Table of Contents --- * CAN-FEATH.csv * Fact-F.csv *
 ANI-FEATH\_mds.csv * CAN-GCMSsm.csv * Fact-P.csv * ANI-GCMSsm\_mds.csv *
 GCMS.csv * dclr2-glandmatchoil-26Aug22.csv * dclr2-bioenv-19Apr23.csv *
 FeathGCMS.csv * FeathBactNMDS.csv * fbact-bioenv-19Apr23.csv *
 SI-GroupChemicalSimilarity-19Apr23.pdf * ChemSimRCode.txt Setup --- *
 Unpacking instructions: n/a * Relationships between files/folders:
 Detailed in file useage * Recommended software/tools: RStudio 2023.03.0; R
 version 4.0.3 File Usage --- * Main analyses: ChemSimRCode.txt * Require
 files * CAN-FEATH.csv * Fact-F.csv * ANI-FEATH\_mds.csv * CAN-GCMSsm.csv *
 Fact-P.csv * ANI-GCMSsm\_mds.csv * GCMS.csv *
 dclr2-glandmatchoil-26Aug22.csv * dclr2-bioenv-19Apr23.csv * FeathGCMS.csv
 * FeathBactNMDS.csv * fbact-bioenv-19Apr23.csv * ChemSimRCode.txt
 File/Folder Details === Details for: CAN-FEATH.csv --- * Description: a
 file containing GCMS peak proportional data for all feather chemicals
 extracted from smooth-billed anis included in the study. * Format(s): .csv
 * Size(s): 24.1 KB * Dimensions: 80 rows x 46 columns * Variables: * Whole
 number: chromatogram peak number * X#####F: smooth-billed ani sample (F
 suffix denotes a feather sample) * Additional info: * Each peak was
 assigned a number and the peak area was extracted from chromatogram
 output. Each column is an individual, each row is a peak, and each cell
 value is the proportion of a given peak in relation to the total
 chromatogram peak area. Details for: FACT-F.csv --- * Description: a file
 containing metadata associated with each smooth-billed ani feather sample
 * Format(s): .csv * Size(s): 2.6 KB * Dimensions: 48 rows x 10 columns *
 Variables: * Col 1: unique identification code for each individual sampled
 (F suffix denotes feather sample) * ID: unique identification code for
 each individual sampled (suffix denoting sample type removed) * Group:
 breeding group sample was collected from * Status: breed = breeding, comp
 = egg laying competition, NoNest = no nest found * Type: sample type
 (feather or preen oil, only feathers included in this file) * Sex: sex of
 individual sampled * JulDate: Julian date * Comp: Rank score for egg
 laying competition * FComp: Term assigned to rank score reflecting level
 of competition * Prop.Lost: Proportion of total eggs laid lost to egg
 laying competition Details for: ANI-FEATH\_mds.csv --- * Description: a
 file containing the mds scores for each bird included in the study (from
 non-metric multidimensional scaling analysis) * Format(s): .csv * Size(s):
 4.3 KB * Dimensions: 48 rows x 13 columns * Variables: * points.1: mds
 score 1 (x coord) * points.2: mds score 2 (y coord) * stress: nmds scaling
 stress value * ID: unique identification code for each individual sampled
 (no suffix denoting sample type) * Group: breeding group sample was
 collected from * Status: breed = breeding, comp = egg laying competition,
 NoNest = no nest found * Type: sample type (feather or preen oil, only
 feathers included in this file) * Sex: sex of individual sampled *
 JulDate: Julian date * Comp: Rank score for egg laying competition *
 FComp: Term assigned to rank score reflecting level of competition *
 Prop.Lost: Proportion of total eggs laid lost to egg laying competition
 Details for: CAN-GCMSsm.csv --- * Description: a file containing
 chromatogram peak proportional data for all preen oil chemicals extracted
 from smooth-billed anis included in the study. * Format(s): .csv *
 Size(s): 11.7 KB * Dimensions: 42 rows x 41 columns * Variables: * Whole
 number: chromatogram peak number * X#####: smooth-billed ani sample (no
 suffix denotes a preen oil sample) * Additional info: * Each peak was
 assigned a number and the peak area was extracted. Each column is an
 individual, each row is a peak, and each cell value is the proportion of a
 given peak in relation to the total chromatogram peak area. Details for:
 Fact-P.csv --- * Description: a file containing the metadata for all
 samples * Format(s): .csv * Size(s): 2.1 KB * Dimensions: 42 rows x 10
 columns * Variables: * Col 1: unique identification code for each
 individual sampled (no suffix denotes preen oil sample) * ID: unique
 identification code for each individual sampled (suffix denoting sample
 type removed) * Group: breeding group sample was collected from * Status:
 breed = breeding, comp = egg laying competition, NoNest = no nest found *
 Type: sample type (feather or preen oil, only preen oil included in this
 file) * Sex: sex of individual sampled * JulDate: Julian date * Comp: Rank
 score for egg laying competition * FComp: Term assigned to rank score
 reflecting level of competition * Prop.Lost: Proportion of total eggs laid
 lost to egg laying competition Details for: ANI-GCMSsm\_mds.csv --- *
 Description: a file containing the mds scores for each bird included in
 the study (from non-metric multidimensional scaling analysis) * Format(s):
 .csv * Size(s): 3.6 KB * Dimensions: 42 rows x 13 columns * Variables:
 \*Col 1: Sample ID (unique identification code for each individual sampled
 ) * points.1: mds score 1 (x coord) * points.2: mds score 2 (y coord) *
 stress: nmds scaling stress value * ID: unique identification code for
 each individual sampled (no suffix denoting sample type) * Group: breeding
 group sample was collected from * Status: breed = breeding, comp = egg
 laying competition, NoNest = no nest found * Type: sample type (feather or
 preen oil, only feathers included in this file) * Sex: sex of individual
 sampled * JulDate: Julian date * Comp: Rank score for egg laying
 competition * FComp: Term assigned to rank score reflecting level of
 competition * Prop.Lost: Proportion of total eggs laid lost to egg laying
 competition Details for: GCMS.csv --- * Description: a file containing
 only the preen oil proportional peak data from samples that have matched
 microbial (16S) data collected from the preen gland * Format(s): .csv *
 Size(s): 8.8 KB * Dimensions: 41 rows x 31 columns * Variables: * Whole
 number: peak number * X#####: smooth-billed ani sample (no suffix denotes
 a preen oil sample) Details for: dclr2-glandmatchoil-26Aug22.csv --- *
 Description: a file containing clr-transformed 16S sequences collected
 from the preen gland for smooth-billed anis with matched preen oil
 chemical data * Format(s): .csv * Size(s): 66.6 KB * Dimensions: 176 rows
 x 31 columns * Variables: * SV: amplicon sequence variants * Sample:
 smooth-billed ani sample (no suffix denotes a preen oil sample) Details
 for: dclr2-bioenv-19Apr23.csv --- * Description: a file containing
 clr-transformed 16S sequences for only the top 5 microbial sequence
 variants (SVs) that maximized correlations between preen oil and preen
 gland bacteria after bioenv analysis * Format(s): .csv * Size(s): 2.1 KB *
 Dimensions: 6 rows x 31 columns Variables: * SV: amplicon sequence
 variants * Sample: smooth-billed ani sample (no suffix denotes a preen oil
 sample) ## Details for: FeathGCMS.csv * Description: a file containing
 only the feather proportional peak data from samples that have matched
 microbial (16S) data collected from body feathers * Format(s): .csv *
 Size(s): 274 KB * Dimensions: 80 rows x 47 columns * Variables: * Whole
 number: peak number * X#####F: smooth-billed ani sample (F suffix denotes
 a feather sample) Details for: FeathBactNMDS.csv *** * Description: a file
 containing clr-transformed 16S sequences collected from body feathers for
 smooth-billed anis with matched feather chemical data * Format(s): .csv *
 Size(s): 98 KB * Dimensions: 48 rows x 171 columns Variables: * SV:
 amplicon sequence variants * Sample: smooth-billed ani sample (F suffix
 denotes a feather sample) ## Details for: fbact-bioenv-19Apr23.csv *
 Description: a file containing clr-transformed 16S sequences for only the
 top 3 microbial sequence variants (SVs) that maximized correlations
 between feather chemicals and bacteria after bioenv analysis * Format(s):
 .csv * Size(s): 66.6 KB * Dimensions: 48 rows x 4 columns Variables: * SV:
 amplicon sequence variants * Sample: smooth-billed ani sample (F suffix
 denotes a feather sample) ## Details for:
 SI-GroupChemicalSimilarity-19Apr23.pdf * Description: a .pdf file
 containing supplementary materials (Figures and Tables) referred to in
 main article text. See main article for more details * Format(s): .pdf *
 Size(s): 524 KB * Dimensions: na Read file for details ## Details for:
 ChemSimRCode.txt * Description: a text file containing the R code used for
 all analyses presented in this paper. The file is currently formatted for
 use with R * Format(s): .txt * Size(s): 18.2 KB * Dimensions: na * See
 file annotations for details *** END OF README