Data from: Cryptic hybridization dynamics in a three-way hybrid zone of Dinopium flamebacks on a tropical island
Data files
Jan 29, 2025 version files 75.74 KB
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admix_data.k3_locality_data_added_with_mean_ancestry.csv
1.38 KB
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barcodes_Dinopium_Chrysocolaptes_GBS_plate2.rtf
1.74 KB
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barcodes_Dinopium_Chrysocolaptes_GBS_plate3.rtf
2.05 KB
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barcodes_Dinopium_Sphyrapicus_GBS_plate1.rtf
1.56 KB
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Flameback_Bioinfomatic_data_analysis_script.rtf
16.69 KB
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Flameback_GBS_analysis_script.R
38.39 KB
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Fst_groups_III.txt
6.73 KB
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PhenoCline_LocalityData.csv
2.26 KB
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PhenoCline_sample_data_n_109_new.csv
2.82 KB
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README.md
2.12 KB
Abstract
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.
README: 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.