Cryptic hybridization dynamics in a three-way hybrid zone of Dinopium flamebacks on a tropical island

Island ecosystems have emerged as vital model systems for evolutionary and speciation studies due to their unique environmental conditions and biodiversity. This study investigates the population divergence, hybridization dynamics, and evolutionary history of hybridizing golden-backed and red-backed Dinopium flameback woodpeckers on the island of Sri Lanka, providing insights into speciation processes within an island biogeographic context. Utilizing genomic analysis based on next-generation sequencing, we revealed that the Dinopium hybrid zone on this island is a complex three-way hybrid zone involving three genetically distinct populations: two cryptic populations of golden-backed D. benghalense in the north and one island-endemic red-backed population of D. psarodes in the south of Sri Lanka. Our findings indicate asymmetric introgressive hybridization, where alleles from the southern D. psarodes introgress into the northern D. benghalense genome while phenotype remains adapted to th..., , , # Data Processing for Cryptic Hybridization Dynamics in a Three-Way Hybrid Zone of *Dinopium* Flamebacks on a Tropical Island

Please note that the raw GBS data for plates 1, 2, and 3 are available on NCBI SRA under database number SUB14620227.

## Description of the Data and File Structure

### Genomic Data Processing and Analysis

* **barcodes_Dinopium_Sphyrapicus_GBS_plate1.rtf** - Barcode data file for Dinopium flamebacks GBS plate 1.
* **barcodes_Dinopium_Chrysocolaptes_GBS_plate2.rtf** - Barcode data file for Dinopium flamebacks GBS plate 2.
* **barcodes_Dinopium_Chrysocolaptes_GBS_plate3.rtf** - Barcode data file for Dinopium flamebacks GBS plate 3.
* **Flameback_Bioinformatic_data_analysis_script.rtf**
This file includes the scripts for raw Genotype-by-Sequencing (GBS) data processing, admixture mapping analysis, the construction of a maximum likelihood tree using *Treemix*, and the generation of a maximum-clade-credibility tree with SNAPP.
* **Flameback_GBS_analysis_script.R...