The genomics of adaptation in birds

Organismal adaptations are the hallmark of natural selection. Studies of adaptations in avian systems have been central to key conceptual and empirical advances in the field of evolutionary biology and, over the past decade, leveraged the proliferation of a diversity of genomic tools. In this synthesis, we first discuss how the different genomic architectures of avian traits are relevant to adaptive phenotypes. A mutation's chromosomal location (e.g., microchromosomes or sex chromosomes) or its specific nature (e.g., nucleotide substitution or structural variant) will determine how it may evolve and shape adaptive phenotypes, and we review different examples from the avian literature. We next describe how the source of adaptive variation, whether from de novo mutations, existing genetic variation, or introgression from another species, can affect the evolutionary dynamics of a trait. Our third section reviews case studies where the genetic basis of key avian adaptive phenotypes (e.g., bill morphology or plumage coloration) have been revealed. We end by providing an outlook and identifying important challenges to this field, both by focusing on technical aspects, such as the completeness of genomic assemblies and the ability to validate genetic associations with new sources of data, as well as by discussing the existential threat posed to birds from habitat alteration and climate change.