Relationships of Birds – Molecules versus Morphology

AbstractMolecules and morphology frequently point to different phylogenies of modern birds, hence making birds unique models to study reasons for such conflicts. Molecules generally make a less biased tool for phylogenetic inference, but evolutionary interpretation of a phylogeny requires knowledge from both morphology and fossils. In the past decade, considerable progress has been made in reconciling molecular and morphological phylogenies, the examples of which are discussed here. Despite this progress and a wealth of new data now available, key features of the avian phylogenetic tree remain unresolved. This pattern more likely reflects the short time interval during which the majority of modern bird lineages diversified. Much improved insight about the early evolution of modern birds more likely will come from (1) genomic data, provided that biases at this scale are understood and (2) well‐preserved fossils that represent the stem of distinct bird lineages. At present, such data are too incomplete to resolve most key nodes in the diversification of modern birds.Key Concepts:Phylogenies represent the best interpretation of the evolutionary history of a chosen taxon set.At increasing taxonomic level, both DNA sequence‐based and morphological variation are expected to increase.DNA sequence variation at neutral markers is produced and enhanced by the process of random mutation; therefore, it is a function of time.Morphological variation is enhanced by selection for certain phenotypes; therefore, it is a function of the environment.Evolutionary convergence is less likely at the molecular level than at the morphological level.If underlying changes at the molecular/morphological level are modelled appropriately (e.g. alignment, substitution bias and character weighting), reconstruction of phylogeny from either molecular or morphological data should yield the same result.Rampant phylogenetic conflict at the ordinal level in modern birds can be explained by ordinal diversification taking place over a short time interval. During this interval, morphological key innovations were quickly selected for, but augmentation of molecular differences was small.Phylogenetic conflict in modern birds is exacerbated by lack of molecular resolution, imperfect taxonomic sampling, uncertainty about extent of morphological homoplasy and paucity of well‐preserved fossils plesiomorphic for clades Palaeognathae, Neognathae and Neoaves.