Data from: Phylogenomics of a genus of ‘Great Speciators’ reveals rampant incomplete lineage sorting, gene flow, and mitochondrial discordance 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 the evolutionary relationships of this clade: four
types of molecular markers (UCEs, BUSCOs, SNPs, and mtDNA) and
tree-building methods did not find a single well-supported and concordant
species-level topology. We then uncover evidence of widespread incomplete
lineage sorting and both ancient and contemporary gene flow and
demonstrate how these factors contribute to conflicting evolutionary
histories. Our complete taxonomic sampling allowed us to further identify
a novel case of mitochondrial capture between two allopatric species,
suggesting a potential historical (but since lost) hybrid zone as islands
were successively colonized. Taken together, these results highlight how
increased genomic and taxon sampling can reveal complex evolutionary
patterns in rapid island radiations.