EEB 122: Principles of Evolution, Ecology and Behavior?

Lecture?15. Phylogeny and Systematics

https://oyc.yale.edu/ecology-and-evolutionary-biology/eeb-122/lecture-15

The?Tree of Life?shows you that since about 3.5 billion years ago, there have been three large clades that have developed.?It provides a very basic structure?of relationships.?It provides an extremely useful, overarching structure. How did phylogenetic biologists actually get this picture, and are they still changing it??They got it with the methods of inference that I'm going to sketch today, and they're still changing it. ?

Darwin?said, "The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile is largely the truth."?He could see immediately that the tree isn't given but should be??discovered. In the not very distant past, it was?an extremely controversial area of science, and that it was revolutionized both by the advent of DNA sequence data, and by the development of powerful mathematical and computer methods for determining relationship.

Monophyletic is a group that contains all of the descendants from a single common ancestor and nothing that is not descended from that common ancestor; paraphyletic groups are groups that do not contain all of the species descended from the most recent common ancestor; and polyphyletic groups really are a hodgepodge of stuff that shouldn't be in that sort of bin, under that category at all, basically independent evolutionary lines are being incorrectly lumped together.?

Sharing a more recent common ancestor defines relationship,?which?wasn't really clearly articulated until Zimmermann laid it down as a principle in 1931.?Magnolias and Apple trees are more closely related to each?other than?either is to a gingko.?The basis of a lot of this inference is the concept of homology and analogy. They were defined by Richard Owen in the early nineteenth century, before Darwin's?Origin of Species. The idea of homology is that a trait is identical in two or more species because they are descended from a common ancestor. So they got it because their ancestor had it. Homoplasy, or convergence, is similarity for any reason other than common ancestry. So convergence in morphological traits, mutation to the same sequence, in DNA, will lead to homoplasy. So homology is helpful, and homoplasy is confusing in determining phylogenies.?

Here's a good?monophyletic?group.?The timber wolf is in the genus Canis, and all domestic dogs are descended from wolves, which is a nice example of really rapid evolution. On the branch going up to the?Caninae, is?digitigrady, which means that at that point they started chasing after things that were running fast, and evolution, just like?it did with horses, started to cause them to be selected?to?run on their toes. So they got?longer legs by running on their toe tips, rather than on the pads of their feet directly. And bone cracking came in right about here, so they could get the marrow out of bones.?The?whole thing starts taking off about 40,000,000 years ago, in the?Eocene. And Canis, the dog genus itself, is about 5,000,000 years old; it's about as old as Homo.?

Reptiles is paraphyletic. It's got turtles, lizards and crocodiles in it, but it doesn't have the birds. So reptiles is an inaccurate term. This is the monophyletic group--lizards, crocodiles and birds--and we don't have an everyday language term for it.

Here's a polyphyletic group. If we define a group called the homoeothermic tetrapods, which?contains the birds and the mammals, it would be a false group, because phylogenetically the birds have many things which are more closely related to them than the mammals do. And this group is polyphyletic. It has contributions from two different sources. Another good example of a polyphyletic group would be if you decided to link together all of the things that look like cactuses in Africa and South America. The ones in South America are cactuses, but the ones in Africa are euphorbs; they look just like cactuses.?They are convergent, they came together.?

Then this central concept, homology. Here are the forelimbs of turtles, humans, horses, birds, bats and seals,?spanning quite a bit of the tetrapods; vertebrates that are living on land. All in an ancestral condition together, you can see how evolution has changed their proportions and?thickness, but it hasn't changed their spatial relationships to each other.?

• If you go through the development,?the same nerves coming out of the backbone are running to the same parts of the limb, and all of those conditions have been held together, over evolutionary time.

• If you look at the HOX genes that are controlling their development, the DNA sequences in the HOX genes, that are telling it whether to make a humerus, a radius, an ulna or digits, are actually homologous in their DNA sequence.?So there's a molecular homology that underlies the morphological homology.

If you look at molecular sequences, here's a gene called aniridia in humans, and a gene called eye-less in fruit flies,?only six of the sixty amino acids of?the?protein sequence?are different. The two sequences are 90% identical. There are search algorithms, like BLAST, that go out and look for these sorts of similarities or?molecular homology.

A good molecular homology is the fruit fly homeobox complex and the human HOX complex?where the sequence of the genes along the chromosome, and the parts of the body that are being controlled by those genes developmentally, are similar in humans and in fruit flies, and actually unite everything that you see here. So this sort of thing is a signal of shared ancestry, and it's the kind of molecular information used to construct the broader Tree of Life. So this is something that is linking together arthropods, annelids, mollusks, echinoderms and chordates.?

analogy or convergence is a misleading kind of information, because that means that natural selection has taken things that were evolutionarily independent, and which have sister groups, have relatives, that don't look anything like this, and then shaped both of those things to come together to a common form. The definition of analogy is two things that look very much alike, even though they have many relatives that look quite different and are distant on the tree.?

• The dolphin and the ichthyosaur have a very similar fusiform body, and this is because of strong selection to swim rapidly in the ocean and to chase down fish and squid; which they both did. And the analogy goes deeper than that. As you probably know, the dolphin has live birth, it's viviparous. So is the ichthyosaur. The dolphin is more closely related to a kangaroo than it is to an ichthyosaur, and an ichthyosaur is more closely related to a hummingbird than it is to a dolphin; nevertheless they look similar. So that's analogy.?

• Pentastomids were a mysterious group of creatures, and they turn out to be closely related to fish lice, an?isopod.?Pentastomids are related to fish lice. They are not related to beetles, or to nematode worms. It?probably was accomplished by things like crocodiles eating things like fish. And when the parasite that was living on the fish got ingested by the crocodile,?it could fall of the fish and stay in the mouth of the crocodile and crawl up its nose and?can survive.

• There used to be a group called carnivorous plants, the pitcher plants and the sundews?are plants that are adapted to living under very low nitrogen conditions, and they need nitrogen to make all of their proteins, and they get it by killing insects and other things. Some of them can even kill a small frog.?They are?polyphyletic. Pitcher plants have evolved independently at least three times; flypaper traps at least five times.?

• Seals and otters are carnivores, and it turns out that whales, including the toothed whales, the active carnivorous dolphins and sperm whales?are ungulates. So there was an ungulate that used go around eating plants and it went into the water and it started to?eati?fish, squid; and some of them eat a lot of crustacea, if they filter feed.This is a chunk of the Tree of Life that shows you the radiation of the ungulates. Both the toothed and the baleen whales are nested within the ungulates, and their closest relatives are the hippos.?

• Sycamores, or plane trees, are the classic tree which is used to decorate the European plaza. They have a leaf that looks like a maple leaf, and they have?white bark but with blotches on it.?They are in fact more closely related to water lilies.?

Those are things that were buried in the DNA sequences, that were not Apparent in the morphology, and they are not only testimony to the power of molecular systematics, they are testimony to the power of natural selection to change the shape of things in ways that are profoundly altering and create all sorts of mis-impressions about relationship.?Appearances are deceptive and detective work is needed.

How do you build a phylogenetic tree??You need to have some characters; so those are states of traits. They could be nucleotide sequences. It could be whether the thing has scales or fur, or it could be whether it has a three or four-chambered heart. It could be a lot of things.?And the characters that are informative are shared derived characters. The characters that give you phylogenetic information are the ones that everything in a group shares with each other, and it's different from the ancestor.?Synapomorphy?is?derived from the?Greek.?Syn?means shared;?apo?means derived; and?morph?means trait. So?a shared-derived trait is a synapomorphy.?

You can only define derived by comparison with primitive. So primitive is like what it used to be, and derived is what it is now, somewhere on the tree, and you can't do that without a tree. So there's kind of a paradox. You don't have a tree, and if you don't have it, you don't have a way to determine what came first, and therefore you don't know about character polarization. Character polarization means knowing which state is primitive and which is derived; that polarizes that series of trait states. So there are number of ways out of this logical dilemma.?

• One is you look at all possible trees?and you choose the ones that are simplest. So that's the principle of parsimony. And it's a logical principle; it's not an empirical principle, and it's not necessarily the way that evolution operates.

• Or you could choose the tree that would make it most likely that you would have observed the character data that you actually did observe; that's called the principle of maximum likelihood.

• In fact, in the computer programs and in the theoretical arguments that go on in phylogenetics, these are two of the main themes, and many of the methods combine them, in various ways.?

Having a forelimb that has a humerus, a radius, an ulna, carpals and metacarpals, in that sequence, really doesn't help us to distinguish bats from turtles. They've all got it, but that's not telling you whether they're closely related to each other or not, because they all got it from a common ancestor; it's not derived.?

However, that structure distinguishes the tetrapods from the lobe-finned fishes. It becomes useful as a shared-derived marker?of a group; which is?one of the reasons why?we're confident that the tetrapods is a good group, and that the vertebrates didn't come out of the water multiple times. In this context it's marking a trait that originated once in their common ancestor; it's shared by all of them and?not found in their closest relatives.?

The informative traits are the ones that are shared and derived. And what is shared and what is derived, and therefore what is informative, depends on the context; it depends on the part of the tree that you're sitting in.