Conducting large-scale phylogeographic studies to understand processes affecting population structure and genetic diversity across multiple species is difficult because the key genetic (NCBI) and spatial (GBIF) repositories are disconnected. In this issue of Molecular Ecology Resources, Pelletier et al. (2022) demonstrate the power of connecting these in the program phylogatR. This program assembled 87,852 species and 102,268 sequence alignments in a taxonomic hierarchy, yielding multiple sequence alignments per species, mainly for animals (88%), composed mostly of mtDNA data. The authors discuss several caveats with these alignments and provide flags identifying particular problems associating locality and genetic data with certain taxa (e.g., multiple localities per individuals). They provide a test that nucleotide diversity should increase with area, but find a significant relationship in only 32% of taxa with no clear taxonomic or ecological factors accounting for this. To examine the potential of this program, I tested the idea that the degree of population expansion should increase with latitude given potential environmental stability in the tropics and instability in temperate regions. In under two hours, I downloaded all squamates (lizards and snakes) and regressed Tajima’s D on latitude and found a weak but significant negative relationship, indicating a potential association between latitude and population expansion. The phylogatR database is a powerful resource for researchers wanting to test the relationship between genetic diversity and some aspect of space or environment.

Species-level taxonomy is derived from methodological sources (data and techniques) that assess the existence of spatio-temporal evolutionary lineages via various species concepts. These concepts determine if observed lineages are independent given a particular methodology supposedly connected to ontology, which relates the metaphysical concept to what “kind” of thing a species is. Often, species concepts fail to link methodology and practice back to ontology. This lack of coherence is in part responsible for the persistence of the rank of subspecies, which in modern usage often functions as a placeholder between the evolutionary events of divergence or collapse. Thus, prospective events like lineage merger or collapse determine if a subspecies is subsumed into an existing species, or achieves species rank given unknowable future information. This is conditioned on evidence that the lineage already has a detectably distinct evolutionary history. Ranking these lineages as subspecies seems attractive given the observation that many lineages do not exhibit intrinsic reproductive isolation. We argue that the use of subspecies is indefensible on philosophical and empirical grounds. Ontologically, the rank of subspecies is either identical to that of species or undefined in the context of evolutionary lineages representing spatio-temporally defined individuals. Some species concepts more inclined to consider subspecies, like the Biological Species Concept, are disconnected from ontology and do not consider genealogical history. Even if ontology is ignored, methods addressing reproductive isolation are often indirect and fail to capture the range of scenarios linking gene flow to species identity over space and time. The use of subspecies and reliance on reproductive isolation as a basis for an operational species concept can also conflict with ethical issues governing the protection of species. We provide a way forward for recognizing and naming species that links theoretical and operational species concepts regardless of the magnitude of reproductive isolation.