Accurate species delimitation is a central assumption in studies of biodiversity, systematics, biogeography and ecology. In algae, morphology-based species delimitation is often problematic, and hence DNA sequence data are becoming the standard for delimiting species. The idea that species are separately evolving metapopulation lineages, along with theoretical progress in phylogenetic and population genetic analyses, has led to the development of new methods of species delimitation.
In a paper that we recently submitted to the European Journal of Phycology we review these recent developments in DNA-based species delimitation methods, and discuss how they have and will continue to change our understanding of algal species boundaries.
Single-locus (DNA barcoding) approaches have proven effective for rapid and large-scale assessment of algal species diversity. However, species delimitation based on single gene trees falls short due to gene tree – species tree incongruence, caused by confounding processes like incomplete lineage sorting, trans-species polymorphism, hybridisation and introgression. Data from unlinked loci and multispecies coalescent methods, which combine principles from phylogenetics and population genetics, may now be able to account for these complicating factors.
Although we realize that many algal taxonomists may feel uncomfortable with the idea of delimiting species based solely on DNA sequence data, we argue that DNA sequence data serve as a reliable source of data for testing species boundaries even in the absence of additional phenotypic evidence. The hundreds of new species discovered using DNA sequences have profoundly reshaped our ideas on algal diversity and present a telling case of our inability to accurately assess species diversity based on phenotypic characters alone.
Because speciation is a process and not a single event in time, uncertainty about species boundaries is inevitable in recently diverged lineages. One of the strengths of DNA-based species delimitation methods is that this uncertainty can be taken into account and quantified by incorporating probabilistic tests for species boundaries that provide statistical support plus a level of uncertainty regarding species boundaries.
In species delimitation approaches, it is important to keep in mind the moving target that we are trying to circumscribe, a species. The question of species definition and delimitation is tied to the process of speciation, which has idiosyncratic components involving multiple populations, individuals with different life cycles and reproductive successes, different selective histories, and which contains a large component of stochasticity. Elucidating the relative importance of these components in the speciation process defines the beauty of systematic biology. The use of molecular markers in species delimitation has pointed phycologists toward more realistic species boundaries. We anticipate that multispecies coalescent methods based on multi-locus data will further refine our view on algal species, especially in recently diverged lineages, in which factors such as incomplete lineage sorting, hybridisation and introgression may confound species boundaries. These methods will increase the statistical rigour and objectivity of species delimitation, and are likely to result in the recognition of less inclusive entities, which in turn will have implications for estimates of algal species diversity. Resetting species boundaries towards a point where they truly reflect the biological reality will make the study of speciation processes more expedient. But quite likely, the question of “what is a species?” will remain with us as long as we want to study the process of evolution that produces these apparent discontinuities that we call “species”.