A Genomic Perspective on Species Delimitation

Genomic species delimitation is transforming how we understand and define species by enabling a process-oriented and efficient approach to identifying species boundaries. This review outlines the two key steps in genomic species delimitation: ( a ) discovering species-level units and ( b ) assessing their validity. Validity can be evaluated by a diversity of approaches, including applying the multispecies coalescent to delineate the population–species boundary and using estimated gene flow as a proxy for reproductive isolation. We illustrate the utility of these methods across the tree of life through a comprehensive review of published articles and case studies on birds, siphonophores, and bacteria. Despite the many benefits of genomic species delimitation, challenges remain. In particular, genomic divergence does not always accurately reflect ecological divergence and reproductive barriers, and genome heterogeneity can complicate the overall understanding of genetic divergence. We discuss these challenges and potential solutions.