Plotting evolutionary divergence and time

Evolutionary studies have always been based in some way on the phenotype / genotype distance between organisms, usually taken as representing divergence or convergence through evolutionary time. In phylogenetics, this aspect of evolution is usually secondary to the discovery of pathways of historical descent, which are based on patterns of character distribution among organisms rather than on their degree of character divergence.

Nevertheless, evolutionary biologists have long wanted a diagram that links the phenotype / genotype distance between organisms with evolutionary time. One could thereby visualize the presumed historical patterns of phenotype / genotype divergence (and convergence). This should produce a diagram that looks something like a phylogenetic tree (or a coalescent tree), except that one axis would explicitly represent time and the other would explicitly represent phenotype / genotype distance.

Mike Keesey, at the consistently interesting blog A Three-Pound Monkey Brain, has attempted to produce such a thing. The particular example shown here is based on All Known Great Ape Individuals (Messinian to Present).

The figure is intended to include all known hominid fossil individuals (Hominidae), with the horizontal axis representing a distance matrix based on craniodental characters — varying from orangutan-like skull and teeth on the left to human-like on the right. Since the vertical axis represents fossil age, the diagram shows the morphological divergence of human-like individuals (including Neandertals) from earlier forms.

The diagram itself is somewhat of a work in progress, and Mike notes several limitations of the data (eg. absence of fossil gorillas and Pliocene stem-orangutans, lack of postcranial characters, the problematic assignment of names) as well as the analysis (eg. there's a random element to the plotting). Moreover, summarizing morphological divergence in only one axis is a major simplification, and so the diagram should not be over-interpreted.

Nevertheless, this looks very promising for those people who are interested in visualizing the process of evolutionary divergence. This could be especially useful if data are available for genetic distances rather than phenotypic ones. With the increasing availability of genome data for hominids, for example, the temporal relationships among Humans, Neandertals and Denisovans should be much easier to visualize (see Why do we still use trees for the Neandertal genealogy?). If nothing else, ancestral polymorphism would be clearly displayed!