To date, most annotation of avian genomes derives from information from other species, and this necessarily misses lineage-specific characteristics that define what it is to be a bird. In addition, sequence diversity between and within avian species needs to be associated with its physiological, evolutionary and ecological consequences.
Several specific examples of mutations or polymorphisms responsible for major phenotypic changes now have been elucidated, but enormous gaps remain in our ability to link genotype to phenotype, especially for those traits that are uniquely avian.