DOI: 10.5061/dryad.w6m905qw1
title: Data and R analysis code: Asian elephants distinguish sexual status and identity of unfamiliar elephants using urinary odours

description: Despite the ubiquity of odours in mammals, few studies have documented the
 natural olfactory abilities of many “non-model” species such as the Asian
 elephant. As Asian elephants are endangered, we may apply odours to more
 effectively manage threatened populations. We implemented a
 habituation–discrimination paradigm for the first time in Asian elephants
 to test the ability of elephants to discriminate between unfamiliar male
 elephant urine, hypothesizing that elephants would successfully
 distinguish non-musth from musth urine and also distinguish identity
 between two closely related individuals. We conducted two bioassay series,
 exposing three female and three male zoo-housed elephants to the same
 urine sample (non-musth urine in the first series, and urine from an
 unfamiliar individual in the second) over five days. On the sixth day, we
 simultaneously presented each elephant with a novel sample (either musth
 urine or urine from a second unfamiliar individual) alongside the
 habituated urine sample, comparing rates of chemosensory response to each
 sample to indicate discrimination. All elephants successfully
 discriminated non-musth from musth urine, and also urine from two
 unfamiliar half-brothers. Our results further demonstrate the remarkable
 olfactory abilities of elephants with promising implications for
 conservation and management.
description: This README file was generated on 2023-12-01 by Chase LaDue. GENERAL
 INFORMATION 1. Title of Dataset: Data and R analysis code: Asian elephants
 distinguish sexual status and identity of unfamiliar elephants using
 urinary odours 2. Author Information A. Principal Investigator Contact
 Information Name: Chase LaDue Institution: Oklahoma City Zoo and Botanical
 Garden Address: 2000 Remington Place, Oklahoma City, OK USA Email:
 chase.ladue@gmail.com B. Co-investigator Contact Information Name: Rebecca
 Snyder Institution: Oklahoma City Zoo and Botanical Garden Address: 2000
 Remington Place, Oklahoma City, OK USA Email: rsnyder@okczoo.org 3. Date
 of data collection: June to July 2023 4. Geographic location of data
 collection: Oklahoma City Zoo and Botanical Garden, USA 5. Information
 about funding sources that supported the collection of the data: No
 external funding. SHARING/ACCESS Information 1. Licenses/restrictions
 placed on the data: CC0 1.0 Universal (CC0 1.0) Public Domain 2. Links to
 publications that cite or use the data: LaDue, C. A., & Snyder, R. J.
 (2023). Asian elephants distinguish sexual status and identity of
 unfamiliar elephants using urinary odours. Biology Letters. 3. Links to
 other publicly accessible locations of the data: None 4.
 Links/relationships to ancillary data sets: None 5. Was data derived from
 another source? No A. If yes, list source(s): NA 6. Recommended citation
 for this dataset: LaDue, C. A., & Snyder, R. J. (2023). Data and R
 analysis code: Asian elephants distinguish sexual status and identity of
 unfamiliar elephants using urinary odours. Dryad Digital Repository.
 https://doi.org/10.5061/dryad.w6m905qw1 DATA & FILE OVERVIEW 1. File
 List: A) Behavior.Data.csv B) Consistency.Data.csv C) Reliability.Data.csv
 2. Relationship between files, if important: * To test for
 habituation/discrimination and generate plots: Behavioral data
 (`Behavior.Data.csv`) are analyzed using `Behavior.Data.Analysis.R`
 script. See comments within script for explanations. * To test for
 observer reliability and consistency: Data (`Reliability.Data.csv` and
 `Consistency.Data.csv`) are analyzed using
 `Reliability.Consistency.Analysis.R` script. See comments within script
 for explanations. 3. Additional related data collected that was not
 included in the current data package: None 4. Are there multiple versions
 of the dataset? No A. If yes, name of file(s) that was updated: NA i. Why
 was the file updated? NA ii. When was the file updated? NA
 #########################################################################
 DATA-SPECIFIC INFORMATION FOR: Behavior.Data.csv 1. Number of variables:
 22 2. Number of cases/rows: 144 3. Variable List: * SessionID: ID number
 of observation session/bioassay * Animal.Code: unique identifier for each
 of six animals in study (F = female, M = male) * Trial.Set: Musth = musth
 discrimination series; Individual = individual discrimination series *
 Series.Day: day of respective bioassay series (Day 1 through Day 6) *
 Sample.identifier: kind of sample towards which chemosensory response was
 directed (habituated sample is habituated urine, control sample is
 vanillin mixture, novel sample is new urine; see reference for
 description) * Sample.Position: relative position of each sample on each
 day of bioassay (near or far; left or right) * Sniff: number of sniffs
 observed during bioassay * Check: number of checks observed during
 bioassay * Place: number of places observed during bioassay * Flehmen:
 number of flehmens observed during bioassay * Chemosensory.behavior: sum
 total of sniffs, checks, places, and flehmens observed during bioassay *
 Proximity.Count: number of times elephant was in proximity to sample
 during bioassay * Sniff.min: number of sniffs observed during bioassay,
 standardized per minute of observation * Check.min: number of checks
 observed during bioassay, standardized per minute of observation *
 Place.min: number of places observed during bioassay, standardized per
 minute of observation * Flehmen.min: number of flehmens observed during
 bioassay, standardized per minute of observation *
 Chemosensory.behavior.min: sum total of sniffs, checks, places, and
 flehmens observed during bioassay, standardized per minute of observation
 * Sniff.prox: number of sniffs observed during bioassay, standardized per
 instance of proximity * Check.prox: number of checks observed during
 bioassay, standardized per instance of proximity * Place.prox: number of
 places observed during bioassay, standardized per instance of proximity *
 Flehmen.prox: number of flehmens observed during bioassay, standardized
 per instance of proximity * Chemosensory.behavior.prox: sum total of
 sniffs, checks, places, and flehmens observed during bioassay,
 standardized per instance of proximity 4. Missing data codes: None 5.
 Specialized formats or other abbreviations used: None
 #########################################################################
 DATA-SPECIFIC INFORMATION FOR: Consistency.Data.csv 1. Number of
 variables: 2 2. Number of cases/rows: 72 3. Variable List: * Standard:
 number of chemosensory behaviors per minute towards a sample observed by
 expert observer * Reliability: number of chemosensory behaviors per minute
 towards a sample observed by test observer (to check for data consistency)
 4. Missing data codes: None 5. Specialized formats or other abbreviations
 used: None
 #########################################################################
 DATA-SPECIFIC INFORMATION FOR: Reliability.Data.csv 1. Number of
 variables: 22 2. Number of cases/rows: 144 3. Variable List: * SessionID:
 ID number of observation session/bioassay * Animal.Code: unique identifier
 for each of six animals in study (F = female, M = male) * Trial.Set: Musth
 = musth discrimination series; Individual = individual discrimination
 series * Series.Day: day of respective bioassay series (Day 1 through Day
 6) * Sample.identifier: kind of sample towards which chemosensory response
 was directed (habituated sample is habituated urine, control sample is
 vanillin mixture, novel sample is new urine; see reference for
 description) * Sample.Position: relative position of each sample on each
 day of bioassay (near or far; left or right) * Sniff: number of sniffs
 observed during bioassay * Check: number of checks observed during
 bioassay * Place: number of places observed during bioassay * Flehmen:
 number of flehmens observed during bioassay * Chemosensory.behavior: sum
 total of sniffs, checks, places, and flehmens observed during bioassay *
 Proximity.Count: number of times elephant was in proximity to sample
 during bioassay * Sniff.min: number of sniffs observed during bioassay,
 standardized per minute of observation * Check.min: number of checks
 observed during bioassay, standardized per minute of observation *
 Place.min: number of places observed during bioassay, standardized per
 minute of observation * Flehmen.min: number of flehmens observed during
 bioassay, standardized per minute of observation *
 Chemosensory.behavior.min: sum total of sniffs, checks, places, and
 flehmens observed during bioassay, standardized per minute of observation
 * Sniff.prox: number of sniffs observed during bioassay, standardized per
 instance of proximity * Check.prox: number of checks observed during
 bioassay, standardized per instance of proximity * Place.prox: number of
 places observed during bioassay, standardized per instance of proximity *
 Flehmen.prox: number of flehmens observed during bioassay, standardized
 per instance of proximity * Chemosensory.behavior.prox: sum total of
 sniffs, checks, places, and flehmens observed during bioassay,
 standardized per instance of proximity 4. Missing data codes: None 5.
 Specialized formats or other abbreviations used: None