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 exceptional diversification and for shaping key evolutionary theories. Yet, phylogenetic studies often undersample the full diversity of these geographic radiations. This gap stems both from the challenges of collecting single-island endemics and from the poor performance of degraded DNA when using museum specimens to infer evolutionary relationships. Advances in generating genome-wide data sets with degraded DNA from museum samples are overcoming these obstacles. Here, we leveraged 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 found that four types of molecular markers (UCEs, BUSCOs, SNPs, and mtDNA) and tree-building methods did not recover a single well-supported and concordant species-level topology. Instead, we revealed pervasive incomplete lineage sorting and both ancient and contemporary gene flow, processes contribute to conflicting evolutionary histories. Complete taxonomic sampling uncovered a novel case of mitochondrial discordance between two allopatric species, consistent with a historical (but since lost) hybrid zone during successive island colonizations. Together, these results underscore how dense genomic and taxonomic sampling can reveal complex evolutionary dynamics in rapid island radiations.