Plotting for change: an analytic framework to aid decisions on which lineages are candidate species in phylogenomic species discovery

A recent study argued that coalescent-based models of species delimitation mostly delineate population structure not species, and called for the validation of candidate species using biological information additional to the genetic information, such as phenotypic or ecological data. Here we introduce a framework to interrogate genomic datasets and coalescent-based species trees for the presence of candidate species in situations where additional biological data are unavailable, unobtainable, or uninformative. For de novo genomic studies of species boundaries, we propose six steps: (a) visualize genetic affinities among individuals to identify both discrete and admixed genetic groups from first principles, and to hold aside individuals involved in contemporary admixture for independent consideration; (b) apply phylogenetic techniques to identify lineages; (c) assess diagnosability of those lineages as potential candidate species; (d) interpret the diagnosable lineages in a geographic con...