At the interface of phylogenetics and population genetics: The potential of target enrichment in species delimitation under different evolutionary circumstances

Species are a central unit of biological diversity and are important aspect of efficient communication of biodiversity and conservation efforts. And yet, the process of species categorization, i.e., species delimitation, is not only inefficient due to the existence of many different species concepts, but is also subjective, owing to the personal preferences of taxonomists in adopting different concepts for species delimitation. In addition to this, species delimitation is also challenging for populations of species during the period from the beginning of, until the end of divergence, also known as the Gray Zone. This zone is typically long, and during this period species characteristics, for example external features of an organism, are not as informative, as they may not have fully developed yet, making it impossible to objectively define species boundaries. Moreover, given the fact that a majority of the Earth’s species remain undiscovered, it is crucial that methods be developed, to rapidly identify and delimit them. In 2003, a group of scientists proposed that species identification could entirely be carried out using DNA barcodes, which, in animals, is a short single standard stretch of mitochondrial DNA. These barcodes, while efficient in species identification, do not always work well for species delimitation. In my thesis, I explored several cases of closely related populations and species pairs of butterflies and moths from Europe and North America, with different geographic distributional relationships, including parapatry (narrow overlap in the geographic ranges where opportunities for gene flow occur) and allopatry (where species or populations of species are geographically isolated). I used both DNA barcoding and target enrichment, where hundreds to thousands of nuclear genomic markers can be recovered, as primary genetic data collection methods. The aim of my study was to test the efficiency of the target enrichment method in species delimitation under different modes of geographic distribution. The results I obtained suggest that target enrichment can efficiently delimit closely related species pairs with parapatric modes of distribution. In the case of allopatry, this method could provide an accurate picture of genetic relationships, but the inherent arbitrariness of delimitation under allopatry is a conceptual issue that remains unresolved. The comparison of the two types of genetic data – barcodes and target enrichment – revealed the discordance in some cases, which was revealed to have been caused by gene exchange between species in the past, or incomplete lineage sorting, which implies differences in divergence times between genes of species. Overall, my research shows that genomic approaches in which a consistent set of loci are recovered, have a high potential to standardize species delimitation principles across taxa.