Whole-genome analyses resolve early branches in the tree of life of modern birds

TLDR

Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein‑coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous‑Paleogene mass extinction event about 66 million years ago. The study aimed to clarify the evolutionary history of modern birds by performing a genome‑scale phylogenetic analysis of 48 Neoaves species. The authors used phylogenomic methods designed for genome‑scale data to analyze 48 Neoaves species. The analysis produced a highly resolved tree that identified the first divergence in Neoaves into Passerea and Columbea, placed core landbirds’ ancestor as an apex predator with independent gains of vocal learning, and grouped pigeons and flamingoes as sister clades.

Abstract

To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.