DOI: 10.5061/dryad.6hdr7sr92
title: Data from: Cryptic hybridization dynamics in a three-way hybrid zone of Dinopium flamebacks on a tropical island

description: 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 their respective northern arid and southern wet habitats. The
 discovery of two genetically distinct but phenotypically similar D.
 benghalense populations in northern Sri Lanka highlights the process of
 cryptic population differentiation within island ecosystems. These
 populations trace their ancestry back to a common ancestor, similar to the
 Indian form D. b. tehminae, which colonized Sri Lanka from mainland India
 during the late Pleistocene. Subsequent divergence within the island,
 driven by selection, isolation-by-distance, and genetic drift, led to the
 current three populations. Our findings provide evidence of cryptic
 diversification and within-island population divergence, highlighting the
 complexity of hybridization and speciation processes. These findings
 further emphasize the intricate nature of evolutionary dynamics in island
 ecosystems.
description: # 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** This file includes R
 scripts for generating SNP-based PCA, genomic cline analysis, and
 phenotypic cline analysis. ### Data Files * **Fst_groups_III.txt** The
 file provides the sample information (sample IDs, capture locations, and
 Fst groups based on sampling location). *
 **PhenoCline_sample_data_n_109_new_LocalityData.csv** This file contains
 the locality data used to generate the phenotypic cline. Columns include
 "Locality_new" (sampling location IDs) and
 "googleearth.dist_km" (distance for each sampling location from
 Point Calimere). *
 **admix_data.k3_locality_data_added_with_mean_ancestry.csv** This file
 contains the locality data used for genomic cline analysis. Columns
 include "Locality" (sampling location IDs),
 "distance_km" (distance for each sampling location from Point
 Calimere), "ancestry_D.psarodes" (mean D. psarodes ancestry
 proportion at each sampling location), and "nSamples" (number of
 samples captured at each sampling location). *
 **PhenoCline_sample_data_n_109_new.csv** This file contains the phenotypic
 data of each flameback sample used to generate the phenotypic cline.