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!

References

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.

Crown Group Mammals

Last week we introduced mammal evolution and discussed the earliest mammals and how they came to be. This week, we'll talk about crown group mammals, including some modern groups and when they evolved. In order to do that, we must first explain what is meant by "crown group". Crown group mammals include extant (still living today) mammals and their relatives, sharing a last common ancestor. 

Looking at the base of the cladogram (think of it as a kind of family tree) of crown mammals, we have monotremes. Monotremes are the most basal mammals alive today, and they include just five animals: one species of platypus, and four species of echidna. Very few monotreme fossils have been found, and the earliest are all from the Cretaceous of Australia. The earliest, Teinolophus, was already a fully evolved platypus, suggesting monotremes evolved earlier, possibly in the Jurassic. Monotremes are considered to be basal mammals because of many features, including the fact that they still lay eggs, unlike other mammals. 

The very strange duck-billed platypus. Image by Maksim

Moving up the "tree" we have a group of mammals called multituberculates. This fully extinct group is characterised by small rodent-like animals that have very distinct molars with tubercles. They lived from the Late Jurassic to the Oligocene (153-35 million years ago), and their position within Mammalia is often debated. Some scientists believe they are in this position, between monotremes and Theria (marsupials and placental mammals), while others don't agree that they are crown group mammals at all, and think they are more primitive than monotremes.

After a few minor extinct groups, we have the therians. This includes the two mammal groups we typically think of: the marsupials and placental mammals. Marsupials are the living representatives of Metatheria, which also include some fossil taxa. The first metatherian, Sinodelphys, lived during the Late Cretaceous of China, about 125 million years ago. Modern groups like opossums evolved during the Late Cretaceous, while diprotodonts (kangaroos, koalas, wallabies, etc.) first appeared in the fossil record during the Oligocene, about 25 million years ago. This is likely review for many people, but marsupials mainly differ from placental mammals in way of their reproduction. Marsupials do not have a placenta, and have very short gestational periods, causing them to "give birth" to very young, under developed offspring. The offspring are then kept in the mother's pouch, where they continue to develop for several months. 

Artists impression of Diprotodon, an extinct marsupial. Image by Nobumichi Tamura

Finally, this brings us to the Eutheria, and specifically, placental mammals. Fossils like Juramaia (160 million years ago) and Eomaia (125 million years ago) have been attributed to Eutheria, while other studies have suggested the earliest true eutherian is Maelestes that lived 91 million years ago. Relationships of modern placental mammals are messy, mainly due to the fact that studies based on physical characters do not agree with those based on molecular features and DNA. Some extant groups of interest include the Xenarthra (anteaters, tree sloths and armadillos) which evolved during the Late Cretaceous, Insectivora (including hedgehogs, moles, and are not to be confused with rodents) also in the Late Cretaceous, while rodents (mice, rats, squirrels, and porcupines) didn't evolve until the Paleocene (approximately 61 million years ago). Bats didn't appear until the Eocene (52 million years ago), with their evolution being fairly unclear as no transitional fossils have yet been found. The major groups of modern mammals all had started to evolve by the Miocene, 20 million years ago, with aardvarks being the last group to evolve. 

Fossil of Icaronycteris, the earliest known fossil of a bat. Image by Andrew Savedra

Skeleton of a modern bat, which is not significantly different from the early fossil bat above. Image by Mnolf. 

And I think that's about it for today on mammals. There are so many more groups of mammals, we could be talking about them for days! So I think this is it for now. Keep watching and maybe we'll touch on mammals a bit more soon!

Early Mammal Evolution

This week on Mesozoic Mondays, we're going to talk about early mammal evolution. Those of you who have been reading this blog since the beginning may remember our post on Dimetrodon, the early mammal relative. You may remember even further back to our post on What is a dinosaur, and about the importance of temporal fenestrae, or the holes in the back of the skull, throughout  the evolution of animals. Mammals are what we call synapsids, which are the group of animals that have just one temporal fenestra. As previously mentioned, Dimetrodon was also a synapsid, one of the earliest relatives of modern mammals. 

The very beginning of mammal evolution takes us back to the Carboniferous, when the first amniotes (animals with an amniotic egg) evolved into two separate lineages: the synapsids, which eventually give rise to mammals; and the sauropsid branch, which gave rise to lizards, snakes, dinosaurs and eventually birds. The first big group of synapsids were the pelycosaurs, like Dimetrodon. They were the largest land animals to live during the Early Permian, and gave rise to therapsids. Therapsids had larger temporal fenestrae, and included some very strange animals like dinocephalians, and the carnivorous gorgonopsids.

Struthiocephalus, a dinocephalian from the Permian

The gorgonopsid Arctops. Image by Nobumichi Tamura

Remembering back to the blog post on mass extinctions, you may remember that the largest mass extinction to have ever happened was at the Permian-Triassic boundary. Therapsids, like all groups, were very hard hit, but the cynodonts survived, and eventually gave rise to modern mammals. Cynodonts first evolved in the Late Permian, and have several mammal-like features including a reduction in the number of lower jaw bones (modern mammals have one bone while reptiles have many). They continued to evolve into the Triassic by further evolving precise occlusion of their teeth, the mammalian ear started to evolve, and their olfactory lobes increased in size to provide better sense of smell. 

Like all evolutionary transitions, the line between mammalian ancestors and true mammals can be hard to distinguish. Early mammals were small, typically the size of a rat or mouse. Their size, the environment they lived in, and delicate bones mean that they were not commonly preserved and are rarely found in the fossil record. Some of the earliest mammals, or mammaliaforms as some scientists call them, include the morganucodontids. These mouse-sized animals like Morganucodon were transitional between cynodonts and true mammals, seen by the lower jaws with two bones, and bony venomous spurs like modern monotremes (platypus and echidna). 

Morganucodon, a Late Triassic mammaliaform. Image by FunkMonk

Early mammals were evolving alongside dinosaurs, and therefore were restricted to ecological niches not occupied. They were generally small, and required little food and sustenance. Although mammals were typically thought of being "in the shadow" of dinosaurs throughout the Mesozoic, there is evidence that they were capable of defending themselves, and feeding on dinosaurs. 

That's all for the initial evolution of mammals, and we hope you've enjoyed it. Stay tuned for additional posts on further evolution of mammals, including the evidence we have of mammals defending themselves and feeding on dinosaurs!