Given the availability of genomic data to identify separately evolving groups of organisms, many researchers establish species limits based on assessments of the extent of gene flow among populations and often use analytical approaches to identify species in which gene flow is explicitly disallowed. Strictly considering lack of—or limited—gene flow as the main or only criterion to delimit species involves two main complications in practice. First, approaches often used to analyze genome-wide data cannot by themselves distinguish species limits from within-species population structure, particularly in allopatric organisms. Second, recognizing as species only those lineages one can identify using such approaches fails to embrace the role of other evolutionary forces (i.e. various forms of selection) in defining evolutionary lineages. Using examples from various groups of birds, we call for the importance of considering evolutionary forces additional to gene flow in species delimitation and explain why genomic approaches commonly used in taxonomic studies may be insufficient by themselves to properly uncover species limits. By considering the processes that structure genotypic and phenotypic variation during speciation, we argue that rigorous analyses of phenotypic variation remain crucial for species delimitation in the genomics era because phenotypes uniquely inform us about the role of selection maintaining the cohesion of evolutionary lineages. Evolutionary theory describing the roles of gene flow, genetic drift and natural and sexual selection in the origin and maintenance of species calls for an integration of genomics with phenomics in avian species delimitation.
LAY SUMMARY
State-of-the-art approaches to delimit bird species using genomic data do not properly account for all the evolutionary forces that generate avian diversity.
A dominant paradigm followed by ornithologists to delimit bird species relies on inferences of reproductive isolation between populations.
We review evidence from genetic and genomic studies in avian taxonomy and show these have significant limitations because many species are less reproductively isolated (i.e. exchange more genes) than previously thought.
We argue that studies using phenotypic data and methods properly grounded on evolutionary theory offer unique insight to delimit species because they shed light on the role of selection in generating and maintaining biodiversity.
Because species play a central role in biology, delimiting species using genomic and phenotypic data on equal footing is necessary to effectively capture the reality of species as the products of evolution.
