Phylogenomics of a genus of ‘Great Speciators’ reveals rampant incomplete lineage sorting, gene flow, and mitochondrial capture in island systems

The flora and fauna of island systems, especially those in the Indo-Pacific, are renowned for their high diversification rates and outsized contribution to the development of evolutionary theories. The total diversity of geographic radiations of many Indo-Pacific fauna is often incompletely sampled in phylogenetic studies due to the difficulty in obtaining single-island endemic forms across the Pacific and the relatively poor performance of degraded DNA when using museum specimens for inference of evolutionary relationships. New methods for the production and analysis of genome-wide datasets sourced from degraded DNA are facilitating insights into the complex evolutionary histories of these influential island faunas. Here, we leverage whole genome resequencing (20X average coverage) and extensive sampling of all taxonomic diversity within Todiramphus kingfishers, a rapid radiation of largely island-endemic ‘Great Speciators.’ We find that whole genome datasets do not outright resolve th..., , , # Data from: Phylogenomics of a genus of ‘Great Speciators’ reveals rampant incomplete lineage sorting, gene flow, and mitochondrial capture in island systems

[https://doi.org/10.5061/dryad.cfxpnvxg8](https://doi.org/10.5061/dryad.cfxpnvxg8)

## Description of the data and file structure

Whole genome resequencing data for all taxonomic diversity within Todiramphus kingfishers. Raw reads are available on genbank (Bioproject PRJNA1174201).

This dataset has:

**One zipped datasets file.** This zipped file contains a folder structure of the four types of molecular markers analyzed and output files. UCE and BUSCO folders have the locus-specific alignments in a subfolder with IQtree output, which can be used to produce input files for ASTRAL.

1. UCE: 90% complete matrix. In the concatenated subfolder, the concatenated matrix (todi116_90per.phylip) and a character set matrix for a partitioned analysis is available. In the gene-trees subfolder, the 4,845 fasta formatted locus-specific align...,