First let's start looking at the tree of life and how doe we build a tree of life. And so we need, we need, to have some sort of [UNKNOWN] to understand this. And a tree of life is basically just a three taxon statement. Now taxa are simply another word for a species that has a name and groups of species. So, Homo sapiens, is an, is a name. It's a species and it's also a taxon. Mamalia, including all mammals. That's a taxon and it's the proper name. But we look at them in terms of three taxon statements and we ask, is A and B more closely related to each other than either of them are to C? And then we might ask are A B and C more closely related? To each other than they are to another thing out here called D. Now these parts of the tree, right there and right there, we call clades, because this is a cladogram and a clade refers to a segment of the tree of life in which it encompasses all of the descendence of this node, right there. Now, we can derive these big file of genetic kinds of questions to problems, from the notion of speciation. So we can start, with an inter interbreeding population here, where the little dots are males and the openings are say females and they interbreed but then a barrier arises. And these populations begin, to become isolated and in isolation they begin to diverge. So now we need to discuss some more terminology. Very important terminology. So, we, we have the word clade. And a clade is a group of related species. And so on a tree, this is a clade and it's called monophyletic. It came from a single origin. Over here, if we classified these groups here, this is a non monophyletic group because it comes from different parts of the tree. From different clades of the tree. And, so the goal of phylogenetic analysis is to discover these monophyletic groups. And, this has been the history of tree of life research for, for decades now. And we do not want names on non-monophyletic groups because the information content is tied up into shared similarity with monophyletic groups. Now there's other tree language that will be very helpful for us. Two taxa, two species, two mammal, two orders, two families, that are each other's closest relative are called sister taxa. And there are nodes on internal branches and then there's these long terminal branches and the tips of the tree of which we have our taxa. And here is the root of the tree right there. And so, there's always going to be root at. We, we, we use an outgroup. We were really interested in understanding the relationships of this ingroup. Another aspect of phylogenetic trees is how to read em. So if we look at this tree right up here, F and G are each others sister group, E is their sister group, D is the sister group to E F G. C is the sister group to D E F G. B is their sister group and A is the sister group to everything else. Okay, now we rotate these, some of these branches and we go to this tree and it looks real different, and to somebody that doesn't pay attention they say the relationship is different but then look very carefully and you see F and G are each others sister group. E is their sister group and D is their sister group, so you have this played right here and right here. And C is their sister group and then you have B on the outside and A down at the bottom. Now, you can rotate them again and you can come up to these relationships. And you can rotate em again and come up with these relationships, yet they're all. The same tree, they look different but their all the same tree, they signify the same phylogenetic relationships. Now there's another thing that's very important, people have a tendency to think we are the most exalted creatures on earth and we are at the top of the phylogenetic tree, but that's not That's not a way of looking at trees. We can change these trees around. Here, it looks like we go from the poor fish to a frog, to a lizard, to a mouse and then we get up to the humans at the top of the tree. But there really is no top of the tree in many ways. So, we do some rotation of those limbs and we find out, well. Humans are right in the middle, alright? So it's important not to use trees to say something is necessarily more primitive or more advanced than anything else. Now let's talk about how we're going to build trees. We have three hypotheses here. For three taxa, that's all the hypothesis that you can have for three taxa. So you can have A and B are more closly related than they are to C. A and C more closely related than they are to B, and B and C more closely related to each other than either is to A. Now, hypotheses are tested by derived characters. And primitive characters cannot be used to test hypothesis. Now, on the next slide, I'll be showing you that. But, we want to find characters here, here, or here. That test these different hypothesis. And we want to look at ingroups and outgroups. So these three taxa are called an ingroup and we also want to go out and we want to look at an outgroup too, to understand their character distribtution relative to those. Now, here's the way it works. We create, we have a root of tree, because were testing these 3 taxon a b and c and so were looking for shared derived characters and these black bars indicate shared derived characters so, character 3 Brings A and B together. Character two brings A, B, and C together. And character one brings all of them together because it's all shared. But now you can see that character one because it's in all of these, it's a primitive character and we call shared primitive characters symplesiomorphies, shared derived character, synapomorphy. Just this jargon. But it's used all the time by evolutionary biologists. So we can see that character 1 is shared by all of them. So character 1 can't tell me if A and B are more closely related to each other than they are to C. Because they all share it, so primitive characters do not. Give you much, give you any information about what's related, and then finally we'll also talk about homoplasy, which simply means the character is or isn't in multiple instances and we'll have a good example of that on the next slide. So here's a kind of busy slide, but it tells you all you need to know in some ways about how we might go about building phylogenetic trees. And so we have a bunch of tacksuff, A, B, C, D and we want to know How are they inter-related? In specifically, were very much interested in the 3 taxa statement here. Is it D, C, B, A, D, B, C, A with an out-group B, C, D with a as an out-group again? So the relationships of these three taxa, D, B, and C. So that's what we're very interested in right now. So we have a character matrix and A, has a primitive condition, unfilled primitive condition. And then, there is a distribution of character states, that we interpret to be derived. And they're scattered and then they're shared in different ways. So we, we can take the three different, alternative cletergram. These are the three [INAUDIBLE]. And then we can plot these on these different trees. So for instance, here is character one and it's found in B, C, D. So we can put that right there. Well, it's found in this one we can put that right there and we can put it right there. Then character two is only found pari, in taxon B and that's an odd apomorphy. So it's going to be there, it's going to be there and it's going to be there. But now when we get to character three, it's found in C and D. Well, we can put that on that tree. But C and D are not related to one another. So, if D has that character and C has that character, on this tree, that character has evolved twice. And we can do the same thing for character four. We can put character four on c on all of them because it's only found in character four. And then we have another character, five, that's found in C and D. And so we, we put, there's character five there. There's character five there. 5 there, and 5 there, and 6 is found in B and C. So, this tree, here, has B and C together, so character 6 evolved once in that shared common ancestor, but evolved twice there, and twice there. Now, if we count up the character changes, we see this tree only took seven changes, or steps, on the tree. This one took nine, this one took eight. So, this tree right here is more parsimonious and that means it just took the fewest changes. And we want to choose in science those hypotheses that explain something with the fewest assumptions. That's what we have to understand, because as we add more characters, then our preferred tree could change and that's the nature of science. Your constantly trying to test these characters. And we ply optimality criteria, so I was applying what is called minimizing the branch length, so the minimizing of the number of changes. And so I was using the minimim number of steps, or changes, on those trees, under what we call the critrium of maximum parsiomoney, or simple character parsimony. But there are other ways in which scientists now look at trees. Mostly with respect to DNA distances. So there's all kinds of tree-based, model-based approaches that can be used to to generate phylogenetic trees from, say, DNA sequences. So here's a tetrapod tree and it just, to make it very simple, all tetrapods from frogs to lizards, birds, and then mammals all have four legs, hence called tetrapods. Before then, they didn't have four legs, but these have four legs, and therefore as synapomorphies, they're grouped together. All of these organisms from here on up, are called amniotes because of the way of the membranes that are in, in surrounding the eggs and some of the them have, mammals of course, have mammary glands, they have hair, they also have single bones in the lower jaw compared other of these tetrapods. So there are different characters we can place on here and there are special biochemical characters that unite birds and the squaw-mate reptiles, lizards and snakes. And then within mammals, there are carnassial teeth, which bring the carnivores together, that, you know, the cheetah and the jaguar, for instance, together. Now you can see from this thee, you can see that it's highly predictive, so if a colleague of yours goes out and says, oh, I just discovered a new mammal. Well, from what you know about the phylogenetic relationships of mammals, you can make a predication. Well, they're going to have mammary glands. They're going to have have hair and so forth. And this is really important for the discovery of new life forms, because if we start classifying those, then we can start predicting what are their properties. And that's exceedingly important and we'll get into that in future lectures.
