From genomes to graphs: Why macroevolution still matters in the pangenome era

Abstract

As genomics moves from multilocus data sets to pangenomes and graph genome representations, the main challenge is no longer only to detect variation but also to explain how genomic features are distributed across lineages. Pangenomes and graph genomes reveal structural variants, alternative haplotypes, lineage‐specific sequences, and complex patterns of lineage sharing. These signals, however, do not by themselves show whether a pattern reflects common ancestry, retained ancestral polymorphism, introgression, recurrent origin, or analytical artifact. This problem is especially acute in clades shaped by hybridization, introgression, and polyploidy, where a single bifurcating tree may be useful for some questions but misleading for others. Here, we argue that the pangenome era increases the need for explicit macroevolutionary coordinates. We propose a conservative evidence ladder that treats conflict first as an observation, evaluates incomplete lineage sorting and analytical artifacts before stronger process claims are made, and then considers introgression, backbone‐level reticulation, and, when necessary, polyploid‐aware interpretation. For many downstream questions, the output may be a compressed reticulate backbone rather than a fully elaborated network. Such a backbone should be auditable and retain only those departures from treeness that change comparative, functional, breeding‐oriented, or taxonomic interpretation. Examples from crop pangenomes, Rosaceae, and other conflict‐rich systems illustrate how macroevolutionary reasoning can improve the interpretation of micro‐scale genomic signals in the pangenome era.