Phylogroups

Phylogroups are groups of organisms that are inferred to share a recent common ancestor based on phylogenetic analysis. They are used to describe the evolutionary structure within a population, species, or higher taxonomic groups by organizing sequences or strains into lineages that reflect their histories.

Phylogroups are typically identified by analyzing genetic data and applying tree- or cluster-based methods. Data sources can include core genome sequences, multiple housekeeping genes (as in multilocus sequence typing, MLST), single-nucleotide polymorphisms, or whole-genome comparisons. The resulting phylogenetic or clustering assignments place isolates into discrete groups that are interpreted as lineages with common ancestry.

In microbiology and related fields, the term is often used to denote natural lineages within a taxon. For example, Escherichia coli has commonly referenced phylogroups such as A, B1, B2, and D, which can differ in ecology, virulence, and other traits. Phylogroups are not formal taxonomic ranks like genus or species; rather, they summarize population structure and evolutionary relationships that may be nested within or across traditional classifications.

Limitations include the dependence of group definitions on the chosen data set and methods, as well as the confounding effects of recombination and horizontal gene transfer, which can blur phylogenetic signals. Consequently, different studies may assign different phylogroups to the same organisms. Despite these caveats, phylogroups are useful for epidemiology, outbreak tracing, ecological studies, and broader questions about evolutionary history.

See also: clade, monophyly, phylogeny, population structure.