Chemical fingerprints indicate group membership in a highly social communal breeding bird
Data files
May 29, 2023 version files 286.06 KB
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ANI-FEATH_mds.csv
4.38 KB
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ANI-GCMSsm_mds.csv
3.70 KB
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CAN-FEATH.csv
24.74 KB
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CAN-GCMSsm.csv
12.06 KB
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ChemSimRCode.txt
16.31 KB
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dclr2-bioenv-19Apr23.csv
2.19 KB
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dclr2-glandmatchoil-26aug22.csv
68.29 KB
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Fact-F.csv
2.64 KB
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Fact-P.csv
2.17 KB
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fbact-bioenv-19Apr23.csv
2.15 KB
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FeathBactNMDS.csv
100.40 KB
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FeathGCMS.csv
24.74 KB
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GCMS.csv
8.97 KB
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README_ChemicalSimilarity.md
13.31 KB
Oct 10, 2023 version files 287.20 KB
Abstract
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.
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:
> 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:
> 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
Methods
See README.md and main article text for details.
Usage notes
R, RStudio, Excel, Notepad (or other text reader).