Monday, 26 August 2013

Cladistics - How we understand relationships of animals

After writing this blog for a year, I've come across a number of terms that I've had to define as many non-biology people may not understand them. Then I thought maybe it would be a good idea to give a quick review of some of these and how they relate to palaeontology. So here goes...

The first important thing to understand is where modern taxonomy or classification of plants and animals comes from. The first important word is taxon. A taxon is a single group of animals. This group can be any group from species to phylum, depending on what is being talked about (for a review on the modern classification system of animals, check out our post 'Where do dinosaur names come from?'). So as an example, lets use Tyrannosaurus rex. It's classification is as follows:
Tyrannosaurus rex
Kingdom Animalia
Phylum Chordata
Class Reptilia
Order Dinosauria (this isn't completely accurate, but we will use it here as an example)
Family Tyrannosauridae
Genus Tyrannosaurus
Species Tyrannosaurus rex

In this case, taxon can refer to the species, genus, family, order, etc., as long as you are only referring to that one group. There are even subgroups, like subfamily, tribe, etc. and are also referred to as a taxon. If someone wanted to refer to a number of groups at once, we use the term taxa. That could be a number of genera (plural of genus) within a family, or something like that. 

The next important thing to talk about is cladistics, the main point of this post. Cladistics is a way of grouping organisms based on how many unique characteristics they share with each other. These characteristics must not be the ancestral state, or plesiomorphic, which means the character is retained from its ancestor. For example, most tetrapods have some type of front limb (like an arm or paddle), which is because fish have fins, and tetrapods evolved from fish. This character would therefore not be used to assess how closely related a tetrapod group is to another. In contrast, apomorphies, or derived characteristics are used to group closely related or separate distantly related organisms. To use the limb example again, snakes have lost their limbs, which is considered to be a derived characteristic. The loss of limbs could, therefore, be used in cladistics. 

As implied above, each character is coded into a character state using 0 as primitive, and 1-4 as derived. For example, using limbs again, an animal with front limbs would be coded as 0, as that is the basal state, whereas a snake would be coded as 1 for the derived state. This can become much more complicated where you could also have something like a state for a paddle-like limb for a swimming animal, and more. For a group of organisms and characters, you create a character matrix full of numbers (0-4 usually), which is then uploaded into a computer program like PAUP or TNT. Using a complex number of algorithms, these programs work out how closely or distantly related taxa are, and spit out a cladogram. Think of a cladogram as a kind of family tree, where the relationships between groups can be seen. 
An example of a character matrix for ceratopsian dinosaurs from Ryan et al. [1]. Each taxon has the same number of characters with states from 0-2. ? denotes where the state is unknown due to the lack of preservation, which is often the case in fossils.
An example of a cladogram made form the matrix above from Ryan et al. [1]. 
If the relationship is well supported and can be distinguished, there will be a branch of just 2 branches on each side. For example, you can see on the bottom that Chasmosaurus and Pentaceratops are split into two, suggesting these are very closely related, and well supported. In contrast, at the base of the "tree", you'll see that Protoceratops, Turanoceratops, Zuniceratops, and the large branch containing everything else are all coming off of the same line, meaning there isn't enough evidence to fully understand the relationship between those groups. A cladogram is made of clades, which can be any group of organisms that includes all descendants of a particular ancestor. For example, a clade may be the entire tree above, or could be the group in the middle that includes Centrosaurus, Coronosaurus, Styracosaurus and Spinops, or the small clade at the bottom with Chasmosaurus and Pentaceratops, and many many more. 
Another example of a cladogram for ceratopsians from Farke et al. [2]
Above is another representation of a cladogram, which may be more easy to understand. When comparing this one with the one from Ryan et al. [1]  you can see some differences. First of all, Protoceratops is no longer included in that group that was unresolved in the first one, however, Zuniceratops, Turanoceratops, and everything else is still not clear. Chasmosaurus and Pentaceratops still make up a group (seen towards the top) while Avaceratops, Albertaceratops, and the rest are now unresolved. 

The final term that I think is useful to talk about is 'sister groups'. When something is considered to be a sister group to something else, it means that these are closer to each other than anything else. It also means that these groups can swap places on the cladogram and it would not change the meaning. Looking at the above cladogram, Pachyrhinosaurus canadensis is sister to Pachyrhinosaurus lakustai. The group that includes both Pachyrhinosaurus species is in turn sister to Achelosaurus, and the group that includes all three is in turn sister to Einiosaurus, which makes that group sister to Rubeosaurus. That whole group is then sister to the group that includes Spinops, Styracosaurus, and Centrosaurus. In each of these sister groups, you could swivel the cladogram around and preserve the relationships, while showing them in a different order. 

Cladograms can be made of both morphological (as in the features you can see from looking at a skeleton or animal) or molecular (those that come from DNA studies). Of course in palaeontology, we are restricted to morphological studies as no DNA is present.

I know that might have been a bit complicated to wrap your head around, but I think it's a really important lesson to understanding palaeontological literature, and what some of these words mean! If you have any suggestions for next week's blog, let me know!

1. Ryan, M. J., et al. 2012. A new ceratopsid from the Foremost Formation (middle Campanian) of Alberta. Canadian Journal of Earth Science 49: 1251-1262.
2. Farke, A. A. et al. 2011. A new centrosaurine from the Late Cretaceous of Alberta, Canada, and the evolution of parietal ornamentation in horned dinosaurs. Acta Palaeontologica Polonica 56: 691-702. -> Available free online here.

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