A Little More Land

Phylogenetic trees are tree-like diagrams showing the relationships among a group of creatures, often with their most recent common ancestor serving as the base of the trunk (rooted versus unrooted). They illustrate how groups of organisms originated, divided, and endured or died off over time. An example of a very low resolution (i.e. only showing a very high level grouping of the organisms represented) tree of the entirety of life may be found here.

Phylogenetic trees are formed using a number of genetic analyses, in combination with various heuristic methods. While they have a number of limitations and their formulation isn’t a trivial matter, they serve an important role in phylogenetics and evolutionary biology in general. Ever since Darwin’s tree-like diagrams in the Origin of Species, they have been used to illustrate the history and branching of groups of organisms, as well as particular genes and traits.

Phylogenetic supertrees are, intuitively enough, large phylogenetic trees. More importantly, they are formed of multiple, smaller, phylogenetic trees that share some nodes (i.e. leaves of the tree, taxons) in common. This seems simple to imagine, but they are difficult to construct, and often require significant computing power. The end result can appear quite stunning. Here is an example (this is a relatively large PDF; but it is worth it) of such a supertree, in this case of the entire 5000-member class Mammalia, created in a study last year concerning the relationship of the dinosaurs to the rise of mammals. The study found that the extinction of the dinosaurs did not cause an explosion in mammal diversity. The standard view had held that once dinosaurs died out as a result of an asteroid or comet striking the earth some 65 Myr ago, mammals were free to diversify, without the fierce and entrenched competition that dinosaurs provided. The conclusion of the study becomes apparent when viewing the tree diagram, which is marked with a dotted ring at the K-T Boundary time (the time corresponding to when it is hypothesized that a large asteroid or comet struck the earth). One can see that well before this time, the major groups of mammals had already formed. Nearly 28 Myr before, in fact. It is only 10 Myr after the dinosaurs were off the scene that mammal diversity greatly increased, due to various climatic changes. What made such a large and convincing tree possible was the combination by the authors of hundreds of other studies and trees. “If we had done this from scratch, we would have had to get molecular and morphological data for 4,000 different species”, said Dr. Kate Jones, co-author of the study in Nature.

And this is what gives phylogenetic supertrees their power. As diagrams, they appear simply as larger phylogenetic trees, which they are. But forming them through analysing and re-coding pre-existing studies and phylogenetic trees means that researchers can formulate a wide-ranging and potentially revolutionary tree that simply would not have been possible with only the smaller trees alone.

Another example of an powerful supertree is found in a study published just last month regarding dinosaur diversity and how it was affected by the KTR (”Cretaceous Terrestrial Revolution”; see bottom of this page). The diagram (again, large file, but worth it) was computed using over 155 previous phylogenetic trees, and shows the relationships among some 440 out of the 600 known dinosaur species. The paper’s lead author Graeme Lloyd describes it thus: “Our supertree summarises the efforts of two decades of research by hundreds of dinosaur workers from across the globe and allows [one] to look for unusual patterns across the whole of dinosaurs for the first time.” It reveals that the period of perceived increased dinosaurian diversity at the end of the Cretaceous was a resulting of various sampling biases. Dinosaurs experienced the greatest diversity during the first one-third of their existence. They diversified at a constant rate through the end of the Cretaceous, neither in a state of decline nor increasing along with the KTR.

Through clever techniques and modern computing power, the results of many disparate research projects can be synthesized into profoundly impacting illustrations that get us even closer to what life’s true family tree might resemble.

Tags: Evolutionary Biology, Genetics