In the presentation of phylogenetic trees, the geometric shape of the trees often seems somehow arbitrary and is more driven by aesthetics than by informative reasons.
But wouldn't it make sense to give the geometry (distances and angles) specific meanings? Or is this already done (when it's done right)?
Some basic principles:
- The vertical axis represents time (on a linear, logarithmic, or "anti-logarithmic" scale).
- The horizontal axis represents the amount of genetic change (measured in appropriate units).
- The line of one species (= population with virtually identical DNA) goes vertically from bottom to top.
- The line ends when the species becomes extinct.
- A new species branches off of an existing species by a horizontal line perpendicular to the line of the latter.
- The length of the new (horizontal) line reflects the amount of genetic change.
- At its end the line continues vertically.
- There are no other branchings along the horizontal line.
By these principles and with perfect knowledge (and a good measure of genetic change) we would have a perfect rectangular tree like this:
But our knowledge isn't perfect: we know little to nothing about lots of intermediate species which didn't leave traces. Hypotheses about these unknown species can be reflected by inclined lines whose slopes can tell for example:
a) Their have been many pronounced genetic changes in a short period of time after the new species branched off. (grey: hypothesized intermediate species)
b) Their have been few small genetic changes in a long period of time after branching off.
I'm looking for discussions/considerations of this kind of drawing phylogenetic trees (papers, web pages, or simply good search terms).
An interesting - and new to me - point of view is given in Joseph Ahrens' answer to this Quora question:
What slowly becomes clear to me: It's about the interpretation of straight line segments, maximal straight lines, of horizontal vs. vertical lines, and nodes (= branching points) in phylogenetic trees, especially: which of them is to interpreted as a species?