Biochemical and genomic underpinnings of carotenoid color variation across a hybrid zone between South Asian flameback woodpeckers

Coloration and patterning have been implicated in lineage diversification across various taxa, as color traits are heavily influenced by sexual and natural selection. Investigating the biochemical and genomic foundations of these traits therefore provides deeper insights into the interplay between genetics, ecology, and social interactions in shaping the diversity of life. In this study, we assessed the pigment chemistries and genomic underpinnings of carotenoid color variation in naturally hybridizing Dinopium flamebacks in tropical South Asia. We employed reflectance spectrometric analysis to quantify species-specific plumage coloration, High-Performance Liquid Chromatography (HPLC) to elucidate the feather carotenoids of flamebacks across the hybrid zone, and Genome-Wide Association Study (GWAS) using next-generation sequencing data to uncover the genetic factors underlying carotenoid color variation in flamebacks. Our analysis revealed that the red mantle feathers of D. psarodes pri..., , , # Biochemical and Genomic Underpinnings of Carotenoid Color Variation across a Hybrid Zone between South Asian Flameback Woodpeckers

Dataset DOI: [10.5061/dryad.gqnk98szb](10.5061/dryad.gqnk98szb)

## **Raw Data Availability**

Please note that the raw Genotype-by-Sequencing (GBS) data used for the GWAS analysis are publicly available on the NCBI Sequence Read Archive (SRA) under the accession number SUB14620227.

## **Description of the Dataset and File Structure**

### Genomic Data Processing and Analysis:

**GWAS_using_GEMMA_pipeline.rtf -**
This document provides a detailed overview of the pipeline used to conduct the Genome-Wide Association Study (GWAS) analysis using GEMMA.

### Phenotypic Data Analysis:

All pigment concentration data and reflectance spectrometric measurements were analyzed using R.
For a full demonstration of the data processing and visualization steps, please visit the website:
[Data Analysis and Visualization – Flameback](https://rashikaranasinghe.github.io/D...,