Raw data used in Hall et al 2025 - Prevalence and implications of sex reversal in free-living birds

https://doi.org/10.5061/dryad.9w0vt4bs0

Description

This dataset contains one Excel file (with multiple sheets), one PDF, and a collection of individual image files representing photographs of birds and gel results.

Excel file - "Raw_Data_All_Species__Hall_et_al_Dryad_.xlsx"

This Excel file contains 5 separate sheets, one for each species used in the study (Australian magpie, crested pigeon, laughing kookaburra, rainbow lorikeet, and scaly-breasted lorikeet). Each sheet consists of the same columns of data, with one individual bird per row. The columns are as follows:

• Sample: Unique identifier for each individual sampled.
• Source: Institution or organization where the sample originated (e.g., wildlife hospital, research project).
• Source Acc#: Accession or intake number assigned by the source institution.
• Location: Geographic location where the individual was found or admitted from.
• Admission cause: Reason for the individual’s admission (e.g., injury, illness, orphaned).
• Date: Date of admission or sampling (format: YYYY-MM-DD).
• Bill: Length of the bill (in mm).
• Wing: Length of the wing (in mm).
• Tarsus: Length of the tarsus (in mm).
• Plumage/Beak: Notes on plumage or beak condition, coloration, or abnormalities.
• Gonads M/F: Sex of the individual based on gonadal inspection (M = male, F = female).
• Active Y/N: Whether the gonads were active (Y = yes, N = no).
• Right gonad length: Length of the right gonad (in mm).
• Right gonad width: Width of the right gonad (in mm).
• Left gonad length: Length of the left gonad (in mm).
• Left gonad width: Width of the left gonad (in mm).
• Largest follicle (F) mm: Diameter of the largest follicle in females (in mm).
• Sample Taken: Whether a biological sample was collected (Y/N).
• Photo taken: Whether a photo was taken of the individual or sample (Y/N).
• Comment morphology: Notes on physical characteristics or anomalies.
• Sample location: Body part or tissue type from which the sample was taken.
• DNA extracted: Whether DNA was successfully extracted from the sample (Y/N).
• PCR: Whether PCR was performed on the sample (Y/N).
• Comment: Additional notes or observations.
• DNA sex: Sex determined via molecular (DNA-based) methods. Entries with no result are marked as "ND" (Not Determined).
• Phenotype/DNA match Y/N: Whether the phenotypic sex matched the DNA sex (Y = yes, N = no).

Note: All previously empty cells have been updated to display either "ND" (Not Determined) or "N/A" (Not Applicable) for clarity.

PDF file - "Scanned_Laboratory_Book.PDF"

This is a scanned copy of all pages of the laboratory book used for notes, gel photos, and protocols used in the study. It serves as evidence for proper lab techniques, including verification of results, optimization of PCR protocols, number of gel runs, and use of primer sets.

Photographs

All photographs have been uploaded as individual image files rather than organized into folders. Each image filename includes a species code and an ID number. The species codes are as follows:

• CP = Crested Pigeon
• LK = Laughing Kookaburra
• SBL = Scaly-breasted Lorikeet
• RL = Rainbow Lorikeet
• AM = Australian Magpie

These images include photographs of birds, gonads, and PCR gel results. They correspond to individuals listed in the Excel dataset and can be cross-referenced by ID.

Description of Image Data

This dataset includes gel electrophoresis images and raw photographs used to determine and validate the sex of avian specimens across multiple species. The image files are organized into the following categories:

Gel Electrophoresis Images

These files document the results of PCR amplification using sex-linked primers (CHD1 and P2/P8), commonly employed in avian molecular sexing. The gels were visualized using agarose gel electrophoresis and imaged using a GelDoc system.

• CHD1*: Includes gels from multiple runs using CHD1 primers, such as:
  • 13_10pm_2nd runCHD1
  • 13-10-2021_1st_RLCHD1
  • CHD1_Primers_allSpp_Gradient_50-57
    These images show banding patterns that differentiate male and female birds based on the presence of one (ZZ) or two (ZW) CHD1 bands.
• GELDOC* / geldoc*: These files contain gel images from various dates and sample sets. Each image typically includes multiple lanes representing individual bird samples, with banding patterns interpreted to assign sex. File names often include species codes:
  • RL = Rainbow Lorikeet
    • e.g., geldoc 2021-10-15_RL_SBL_Publication
  • SBL = Scaly-breasted Lorikeet
    • e.g., geldoc 2021-10-22_SBL_Publication
  • LK = Laughing Kookaburra
    • e.g., geldoc 2021-11-05_Kookaburra_Publication
  • CP, AM, and others may refer to additional species or individual identifiers.

These gels were used to confirm sex assignments based on molecular markers, with results cross-validated against phenotypic data.

Photographs_raw_of_all_birds_and_gonads

This folder contains unprocessed photographs of each bird specimen and their dissected gonads. These images serve as phenotypic confirmation of sex assignments made via molecular methods. Each photo is labeled with the bird ID and includes either whole-body images or close-ups of gonadal tissue. Species represented include:

• Rainbow Lorikeet (RL)
• Scaly-breasted Lorikeet (SBL)
• Laughing Kookaburra (LK)
• Australian Magpie (AM)
• Crested Pigeon (CP)

Code/software

Microsoft Excel or other reader for .xlsx files

Adobe Acrobat or other reader for .pdf files

Any viewer suitable for .jpg and .tif image files

Access information

Data were derived from the following sources:

• Biological and morphological data were collected from wildlife admitted to Currumbin Wildlife Hospital, RSPCA Wacol, and Australia Zoo Wildlife Hospital between 2020–2021.
• Sample metadata includes measurements and observations recorded during routine veterinary assessments and necropsies.
• DNA extraction and PCR results were generated at the University of the Sunshine Coast, Sippy Downs, Australia.
• Photographs of individuals and/or sampled tissues were taken during processing and are included in the dataset as supplementary files or referenced by filename in the dataset.
• All data were collected under appropriate ethical approvals and permits, where applicable.