Chapter 19 What is a time tree?
We’re tackling the topic of time trees, which are basically phylogenetic trees where the branches have been scaled to show time since divergence. Short branches mean very little time has passed since the most recent common ancestor, while longer branches mean a long time has passed. Without realizing it, you have probably looked at trees you’ve built earlier in the class and assumed the branches indicate time as well as the number of mutations or changes seen in your alignment. This is really only true when the branches have been scaled.
Absolute time trees, which are trees whose branches have been scaled based on a known calibration point, have been considered controversial in the past, though they’ve gained acceptance in the past ten years. Relative time trees (trees that have been scaled relative to the root of the tree, although the age of the root is unknown) were accepted fairly quickly, particularly when dealing with closely-related species.
19.1 Molecular clocks
What makes time trees possible are the use of a molecular clock. This is the idea that DNA mutations happen in a fairly regular fashion that we can describe and simulate using mathematical models. The simplest version of a clock is to take the number of differences between two species and divide them by the time since they diverged. The resulting number is mu, or the mutation rate. In 1963, Emanuel Margoliash introduced the genetic equidistance idea, writing: “It appears that the number of residue differences between cytochrome c of any two species is mostly conditioned by the time elapsed since the lines of evolution leading to these two species originally diverged. If this is correct, the cytochrome c of all mammals should be equally different from the cytochrome c of all birds. Since fish diverges from the main stem of vertebrate evolution earlier than either birds or mammals, the cytochrome c of both mammals and birds should be equally different from the cytochrome c of fish. Similarly, all vertebrate cytochrome c should be equally different from the yeast protein.”
Not all trees show clocklike patterns. In some cases, the number of mutations is much greater on a branch due to selection pressure. In other cases, very long branches will appear to stop developing new mutations due to saturation (sites are changing more than once, but we can only detect one change). Recent work has developed new clock models to get around these issues.
A molecular clock can only say how long tree branches are relative to each other, but cannot estimate actual ages of nodes or times to most recent common ancestors (MRCA). In order to do that, you need to apply calibration points.
19.2 Calibration points
Calibration points are phylogenetic splits which researchers have managed to date with some accuracy. There are three major sources for calibration dates: the fossil record, geologic events, and independent molecular data. The fossil record can be used to estimate the latest point at which a split might have occurred and is considered the gold standard of calibration methods. However, not everything can be captured by the fossil record, so we rely on other methods to fill in the missing spaces. Geologic events are quite useful when working with species that are endemic (or exclusively found) to a location like volcanic islands. A geologic split estimate is the earliest possible date for a split to have occurred. One of the most famous geologic event used for dating is the formation of the Hawaiian islands. We have fairly firm dates for when each of the islands arose, so we can date with some certainty the date when species arrived on each island.
Independent molecular data calibration is the only source of calibration for many taxa, but dates estimated using this approach also have the greatest uncertainty, as they are indirectly based on either fossil record or geologic event dating of related taxa.