Hemiplasy helps explain high rates of apparent morphological convergence in neoavian birds

The clade Neoaves, which comprises more than 95% of extant bird diversity, is thought to have undergone a rapid episode of diversification following the end-Cretaceous mass extinction.^1,2,3,4,5,6 Relatedly, interrelationships among the major neoavian subclades remain challenging to disentangle, with contradictory topologies arising from virtually all phylogenomic datasets.^{2,3,5,6,7,8,9,10,11} Irrespective of alternative hypotheses of neoavian relationships, patterns of morphological variation across Neoaves reveal rampant homoplasy, traditionally interpreted as the result of evolutionary convergence.^{12,13,14,15,16,17,18} Here, we suggest an alternative interpretation for the extensive patterns of apparent morphological homoplasy across the neoavian radiation, linked to the clade's rapid pace of diversification in the aftermath of the end-Cretaceous mass extinction. We show extremely high hemiplasy risk factors¹⁹ that map to branches near the origin of Neoaves, suggesting that many instances of apparent morphological convergence among major neoavian lineages, unless associated with clear selective drivers, are better interpreted as a result of high levels of morphological incomplete lineage sorting during the clade's rapid early Cenozoic radiation. This explanation is congruent with the ongoing difficulty of inferring a stable bifurcating phylogenetic topology at the base of Neoaves^8,9,10,20 and holds fundamental implications for phylogenetic inference, fossil placement near the origin of Neoaves, and interpretations of morphological character state evolution. We highlight conserved polymorphism combined with rapid cladogenesis as a driver of the extensive patterns of apparent convergence in comparative morphological datasets and suggest that this phenomenon also underlies extensive patterns of homoplasy observed in other clades that have undergone rapid episodes of diversification, such as placental mammals.