Data and analysis scripts for Borrero et al.: Sexual dimorphism in pollen foraging and sensory traits in Heliconius butterflies

# Reference Information

## Provenance for this README

- File name: README_himera_sensory_ecology.md  
- Authors: José Borrero  
- Other contributors: David F. Rivas-Sánchez, , Daniel Shane Wright, Stephen H. Montgomery, Alexander Keller,  Richard M. Merrill  
- Date created: 2025-12-01  
- Date modified: 2025-12-01  

## Dataset Version and Release History

- **Current Version**
  - Number: 1.0.0  
  - Date: 2025-12-01  
  - Persistent identifier: DOI: 10.5281/zenodo.17777739  
  - Summary of changes: Initial public release of *H. himera* sensory ecology and brain dimorphism datasets; includes brain morphology, eye morphology, reflectance-age calibration, pollen metabarcoding, and microhabitat recapture datasets.

- **Previous Versions**
  - None (this is the first release)

- Embargo Provenance: n/a  
  - Scope of embargo: n/a  
  - Embargo period: n/a  

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# Sexual dimorphism in pollen foraging and sensory traits in Heliconius butterflies
### Data & Analysis Repository

This repository contains datasets and analysis scripts used across multiple components of the *Heliconius himera* sensory ecology project, including brain morphology, eye morphology, wing reflectance, pollen metabarcoding, and recapture microhabitat analyses.  
Files are grouped below by theme and briefly described.

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# Data and File Overview

## 1. Brain Morphology & Sexual Dimorphism

### **Data**
- **Cyr_him_combined_brain_volumes.csv**  
  Combined neuropil volume dataset for *H. cydno* and *H. himera* with log-transformed measurements and metadata.

- **Hhimera_eyemorph.csv**  
  Eye morphology dataset (ommatidia counts, eye area) for *H. himera*.

- **TableS1_Hhim-brain-dimorphism.xlsx**  
  Curated neuropil volume summary table for sexual dimorphism analysis.

- **himera_lrt_table.csv**  
  Likelihood-ratio test results for neuropil linear mixed models.
  
  - **smatr_table_himera.csv**  
  Table containing slope, intercept, and elevation shift outputs from SMATR.

### **Scripts**
- **Brains_sex_him.r**  
  Main statistical pipeline for modelling sexual dimorphism in brain structure. 

- **smatr_eyes_himera.R**  
  SMATR major axis analysis of eye scaling relationships.

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## 2. Reflectance Spectrometry & Age Prediction

### **Data**
- **reflectance_age.csv**  
  Area-under-curve reflectance measures used to train age prediction models.

- **Vilcabamba_samples_age.csv**  
  Known-age dataset for wild *H. himera* from Vilcabamba used to validate reflectance–age mapping.

### **Scripts**
- **reflectance_age_modeling_full.R**  
  End-to-end reflectance-based age modelling script (model fitting, validation, diagnostics).

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## 3. Pollen Metabarcoding & Foraging Ecology

### **Data**
- **asv_vilcabamba_table.merge.txt**  
  Merged ITS2 amplicon sequence variant (ASV) table from proboscis and gut samples.

- **samples_metadata_vilcabamba.csv**  
  Metadata for sequenced samples (sex, body part, date, barcode, etc.).

### **Scripts**

- **metabarcoding_tools_0-1a.R**  
  Helper functions for data cleaning, ASV processing, and taxonomic lookup.
- **R_ITS2_vilcabamba.R**  
  ITS2 metabarcoding pipeline including filtering, taxonomic assignment, and diversity analyses.

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## 4. Microhabitat & Recapture Data

### **Data**
- **recaptures_logger_1h.csv**  
  Temperature and relative humidity recorded approximately one hour after recapture events.

- **Vilcambamba_recapture_data.csv**  
  Spatial and environmental capture–recapture dataset (coordinates, canopy cover, flight height, temperature, humidity).
  
  ### **Scripts**

- **Pollen_loads.R**  
  Quantification of pollen loads, taxonomic richness, and Shannon diversity.

# Reproducibility Notes

- Analyses were performed using **R v4.2–4.4**.  
- Required packages include:  
  `tidyverse`, `lme4`, `smatr`, `vegan`, `phyloseq`, `ggplot2`,  
  and others listed within individual scripts.  
- Scripts are modular and will run when corresponding datasets are placed in the working environment.  
- Raw sequencing FASTQ files are **not** included in this dataset release.  
- All coordinate data have been processed to remove sensitive location information where needed.

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# Dataset Metadata

## Dataset Title
**Sexual dimorphism in pollen foraging and sensory traits in Heliconius butterflies**  
*(Formal publication title will be updated upon manuscript acceptance.)*

## Persistent Identifier
To be assigned (10.5281/zenodo.17777739).

## Dataset Contributors

- José Borrero (Creator)
- David F. Rivas-Sánchez
- Daniel Shane Wright  
- Stephen H. Montgomery  
- Alexander Keller
- Richard M. Merrill  

## Date of Issue
2025-12-01

## Publisher
To be updated depending on repository (Dryad, Zenodo, institutional repository).

## License
- **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 re-use of these data to discuss potential collaboration.

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# Contact Information

### Primary Contact
- **Name:** José Borrero  
- **Affiliation:** Department of Evolutionary Biology, LMU Munich  
- **ORCID:** https://orcid.org/0000-0003-0164-496X  
- **Email:** jose.borrero@lmu.de   

### Alternate Contact (PI)
- **Name:** Richard M. Merrill  
- **Affiliation:** Department of Evolutionary Biology, LMU Munich  
- **ORCID:** https://orcid.org/0000-0003-4527-9298  
- **Email:** merrill@bio.lmu.de  
- **Address:** LMU Biozentrum Martinsried, Großhaderner Straße 2, 82152 Martinsried, Germany

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# Additional Information

## Funding
This research was funded by a European Research Council (ERC) Starter Grant (851040) to R.M.M.
    
## Dates and Locations of Data Collection
- Field data were collected from 2023.  
- Geographic location: Vilcabamba, Ecuador (Andean dry forest habitat).  
- Laboratory analyses were performed at LMU Munich.

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# Setup

- Recommended software: RStudio (2023 or later), R v4.2–4.4  
- Scripts are written in base R and tidyverse conventions.  

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# Table of Contents

- README.md  
- Brains_sex_him.r  
- smatr_eyes_himera.R  
- reflectance_age_modeling_full.R  
- R_ITS2_vilcabamba.R  
- metabarcoding_tools_0-1a.R  
- Pollen_loads.R  
- All associated datasets (.csv, .txt, .xlsx)

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**END OF README**