Figure 1.

Stylized diagram depicting location in time and space of individuals of one ancestor (black) and two descendent species (dark and light grey) in relation to a hypothetical researcher (X) and their observations. Circles combining two shades depict instances of hybridization and introgression. Overlaid phylogenies (A: high genome coverage; B: barcode marker/organelle) show potentially conflicting topologies of relationships inferred as a result of different taxon and genome samplings. The majority of individuals that have ever belonged to the three hypothetical species are beyond the perception of the researcher. The researcher’s spatial location within part of the geographical range of one species also results in a bias in sampling towards the accessible minority. Both of these factors have a knock-on effect when it comes to inferring evolutionary relationships through phylogenetic analysis of different genomic regions taken from different groups of individuals. Historic introgression might cause two species to be lumped together when analysed with a barcode or organelle marker (b) for example, while spatially biased sampling within the more widespread species may imply a level of phylogenetic divergence that some researchers might treat as evidence of a third species (a), despite a lack of corresponding phenotypic or ecological change.