Phylogeny of waterfowl (Anseriformes) constructed using genome sequences provides insights into topological incongruences.

The evolutionary history of waterfowl (Anseriformes) has long been a focal point of avian research. However, previous phylogenetic investigations have focused primarily on morphology or mitochondrial DNA or have lacked sufficient taxon sampling. Accompanied by observed phylogenetic incongruence and incomplete resolution, waterfowl phylogenetic branching patterns remain uncertain at various taxonomic ranks. To further validate phylogenetic relationships among higher waterfowl taxa and assess presence of conflicting signal, we assembled and analyzed 24 waterfowl genomes representing all waterfowl families and several subfamilies. Utilizing both newly acquired and previously obtained genomes, we constructed and analyzed seven DNA data classes, which yielded highly resolved phylogenetic trees including a time-calibrated tree. Most of these trees consistently and completely resolved the phylogenetic relationships of the included waterfowl species. Despite these efforts, our analysis across chromosomes uncovered four instances of phylogenetic incongruous signal. After minimizing tree estimation error through focus on whole-genome alignment dataset and by sequence simulation, analyses revealed that incomplete lineage sorting and gene introgression essentially contributed to all gene-tree discordance. The variable impact of both factors across distinct waterfowl nodes reflects an underlying complexity that warrants further interpretation. This study not only presents a strongly-supported and well-resolved phylogenetic backbone for the major waterfowl lineages, but also provides foundational data for subsequent comparative genomics studies of a more expanded set of waterfowl taxa.