Four main challenges that can underpin ongoing, intransigent debates about species limits in birds are reviewed: allopatry (population subdivision vs. speciation), geographically widespread introgression of mitochondrial DNA (mtDNA), recent speciation, and selection. Examples from birds of the Australian region show how these challenges, their interplay, and the molecular-phenotypic discordance they generate can clarify or mislead species limits. Examples of how phylogenetic frameworks help reject or retain hypotheses of species limits under these challenges are given. Although mtDNA's strengths and limitations are well known, an underappreciated limitation of mtDNA is geographically widespread introgression that homogenizes mtDNA diversity across species, subspecies, or population boundaries and across hundreds of kilometers. The resulting discordance between mtDNA and phenotype can be profound. If undetected, the setting of species limits and evolutionarily significant units are misled. An example shows how recent genomic analyses can detect and solve the problem. Other examples concern legacy mtDNA-only datasets. These are often essentially unfinished studies leaving residual uncertainty in species limits. Examples illustrate when the possibility of large-scale introgression across species boundaries needs to be considered, and how genomic scale data offer solutions. Researchers must carefully parse 3 questions: has there been introgression of mtDNA and, if so, which population genetics-based driver has caused introgression, and do species limits need altering? Understanding of allopatry, mtDNA introgression, recent speciation, and selection must be properly integrated if species limits are to be robustly understood and applied with maximum benefit in downstream applications such as conservation and management.
LAY SUMMARY
Biologists still debate what species are and how we should best demarcate one species from another.
The debates reflect a curious aspect of ongoing evolution: although we expect each species to have its own unique DNA, that is often not the case for many pieces of DNA that we look at.
My paper reviews some of the major reasons why each species may not have its own unique DNA.
I focus on birds of the Australian region but the lessons apply to ornithologists everywhere.
This is important because we want to use DNA wisely to work out which populations and individuals belong to which species.
Then we can best conserve and manage the biodiversity that nurtures us in so many ways.
I hope my article will guide ornithologists everywhere in how they might deal with the thorny issues associated with these debates.
