Histories of molecules: Reconciling the past

•Molecular phylogeny has transformed evolutionary biology, but many conflicts between trees still exist.•The branching order of early animals and eukaryotes is still unresolved.•Explanations of these unreconciled trees cite molecular clock anomalies, secondary simplifications, and rapid radiations.•Models are central to phylogenetic reconstruction.•Both unreconciled and reconciled evolutionary reconstructions give fresh insight into how historical science works.

Molecular data and methods have become centrally important to evolutionary analysis, largely because they have enabled global phylogenetic reconstructions of the relationships between organisms in the tree of life. Often, however, molecular stories conflict dramatically with morphology-based histories of lineages. The evolutionary origin of animal groups provides one such case. In other instances, different molecular analyses have so far proved irreconcilable. The ancient and major divergence of eukaryotes from prokaryotic ancestors is an example of this sort of problem. Efforts to overcome these conflicts highlight the role models play in phylogenetic reconstruction. One crucial model is the molecular clock; another is that of ‘simple-to-complex’ modification. I will examine animal and eukaryote evolution against a backdrop of increasing methodological sophistication in molecular phylogeny, and conclude with some reflections on the nature of historical science in the molecular era of phylogeny.