Incorporating the speciation process into species delimitation
Fig 1
The Protracted Birth Death (PBD) model of the speciation process [26, 27] implemented in DELINEATE separately models lineage splitting and completion of speciation events, such that “speciation” is an extended process.
For example, considering a phylogeny of population lineages inferred under the MSC [1, 28], the lineage splitting events correspond to the formation of new isolated population lineages (not species) through restrictions in gene flow in an ancestral population (e.g., V1). These lineages may themselves give rise to other population lineages (V2 through V9), or go extinct (X1 through X3). Population lineages develop into an independent species at a fixed background rate, providing they are not otherwise lost (i.e., there is duration between the initiation and completion of speciation). Changes in status from incipient to full or good species are marked by speciation completion events, shown by the blue bars. Under the PBD, a “species” is thus made up of one or more population lineages not separated from one another by a speciation event. In this example, five speciation completion events divide the seven extant populations into four species: {A, B}, {C}, {D, E}, and {F, G}.