Despite tremendous efforts in the past decades, relationships among main avian lineages
remain heavily debated without a clear resolution. Discrepancies have been attributed
to diversity of species sampled, phylogenetic method and the choice of genomic regions
1-3 . Here we address these issues by analysing the genomes of 363 bird species 4
(218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods,
we present a well-supported tree but also a marked degree of discordance. The tree
confirms that Neoaves experienced rapid radiation at or near the Cretaceous-Palaeogene
boundary. Sufficient loci rather than extensive taxon sampling were more effective
in resolving difficult nodes. Remaining recalcitrant nodes involve species that are
a challenge to model due to either extreme DNA composition, variable substitution
rates, incomplete lineage sorting or complex evolutionary events such as ancient hybridization.
Assessment of the effects of different genomic partitions showed high heterogeneity
across the genome. We discovered sharp increases in effective population size, substitution
rates and relative brain size following the Cretaceous-Palaeogene extinction event,
supporting the hypothesis that emerging ecological opportunities catalysed the diversification
of modern birds. The resulting phylogenetic estimate offers fresh insights into the
rapid radiation of modern birds and provides a taxon-rich backbone tree for future
comparative studies. Using intergenic regions and coalescent methods to analyse
the genomes of 363 bird species, the authors present a well-supported tree confirming
that Neoaves experienced rapid radiation at or near the Cretaceous-Palaeogene boundary.
