now let's look at how we would actually use this in an actual case so here's our three three organisms in our in group an elephant an eagle and a snake we're using a salamander a amphibian as an out group it's in a different class of vertebrates than a reptile a bird and a mammal and we're trying to determine the relationship among the the snake the eagle and the elephant now we're going to look at various characters and determine the character states remember the character state is whether something is present or absent whether it's large or small whether it's green or blue so for example we can look at whether these organisms have cells and now this is obvious obviously all of these organisms are cells all organ living organisms have cells this is a primitive condition yes cells are present in all of them so that is not helpful at all now do all of these organisms have vertebrae yes these are all vertebrates they have a backbone and so this is not helpful this is also a primitive condition for all of the organisms including the out group so vertebrae are present vertebrae is the character vertebrae present is the character state also not helpful now here's another character ectothermy ectothermy is what's commonly called cold-bloodedness and the organisms here that are ectothermic would be the salamander and the snake now here's where we need to be very careful the salamander and the snake are ectothermic they're cold-blooded the eagle and the elephant are endothermic they're warm-blooded now remember that primitive characters cannot be used to infer phylogeny so which of these organisms show ectothermy well the answer is the salamander and the snake is this evidence of a close relationship between the salamander and the snake and the answer is no this does not provide evidence of a close relationship of the salamander and the snake and the reason is for the same reason that the vertebrae and the cells do not show a close relationship between the salamander and the snake and that is because it is a primitive character yes the salamander and the snake are ectothermic but so are the fish that are also more primitive vertebrates and everything else that came before it so ectothermy does not show a close relationship between those two organisms between those two organisms it's simply something that was inherited from all of their ancestors so ectothermy is not helpful it's it's a primitive character now ectothermy was not inherited by all of the descendants of these organisms so if we look on the tree these organisms are ectothermic and endothermy was developed in some of the descendants of those organisms but the primitive condition was ectothermy now here's another characteristic the amniote egg the egg that was able to be laid on land that surrounds the embryo with an amnion and amnion amniotic fluid and we already discussed that the amniote egg is found in these three amniote vertebrates reptiles birds and mammals it's found in a modified form in mammals because they retain the embryo in in the uterus but all three of those have an amniote egg does this help us determine the relationships among the in group well we're getting closer but it doesn't help us tell what which of these three organisms is most closely related to to each other it does provide evidence that the in group is a clade distinct from the out group but it still doesn't answer a question it still doesn't address the red question mark here now hair which of these organisms has hair well the answer is just the elephant it's a mammal it has hair does this help us it's a derived character is it a shared derived character for these organisms no it's an odd epimorphy it's a unique derived character if we had more than one mammal here we could say it's a shared derived character for those mammals if we had an elephant and an aardvark and a pig or something we could say it's a shared derived character for those animals but we only have an elephant that we're looking at in this study so this is an autopimorphy feathers that's another odd epimorphy it doesn't help us it's a new character that arose in the ancestor of the birds and since we only have one bird here that doesn't help us in determining which of these organisms is most closely related now a diopside skull what is a diopside skull well a diopsid skull is one that has two temporal openings on the on the side of the skull and it's something you would learn about in comparative anatomy but the organisms that have a diapsid skull it turns out are the snake and the bird reptiles and birds are diapsids and so this is a shared derived character it is a synapomorphy that tells us that reptiles and birds are closely related it provides evidence that reptiles and birds shared a common ancestor by itself is that enough evidence no but we have other characters that provide that evidence beta keratin in the epidermis for example and many many other characters that we could show that are synapomorphies for this clade a clade that includes birds and uh reptiles now what about endothermy endothermic warm bloodedness we found in birds and we found that in mammals is that evidence for a close relationship between birds and mammals that's different from the tree that we have here and the answer is yes that is evidence for a different tree we can say that endothermy would be evidence for a relationship between the elephant and the eagle but overall we have far more evidence that shows a close relationship between the eagle and the snake now i don't have all of the evidence here i'm only showing two but there would be many many many others that we could put here so the most reasonable interpretation of the evidence is that endothermic developed twice independently in those two lineages it makes more sense to say that endothermic developed in the ancestor of the mammals and developed independently in the ancestor of the birds than to say that all of these characters developed independently in two different lineages so endothermy is what we would call a homoplasy or a homoplastic character now as an example of that take a look at this tree this is the accepted phylogeny for these particular organisms that we might consider a tuna a lizard a monkey a hippopotamus and a whale and these are some characters the dorsal fin pectoral girdle limb skeleton lungs cervical thoracic vertebrae and so on two through five are tetrapod synapomorphies these are tetrapods the lizard and the mammals and these are mammalian character napa morphe shared derived characters that provide evidence for a close relationship among mammals including these three mammals and a dorsal fin what about a dorsal fin well a dorsal fin is found in a whale and it's found in detuna and the accepted phylogeny has this as a homoplasy dorsal fin developed twice independently is this evidence of a relationship between tuna and a whale yes we can say it's evidence of that but the evidence is drowned out by the much greater evidence for this phylogeny now we could look at an alternative phylogeny where we say that the dorsal fin shows a close relationship between the tuna and the whale and that characters two through nine developed independently in all of these organisms and in the whale but this is a less likely scenario than the previous tree which shows only the dorsal fin developing independently makes sense that an organism that lives in the water would need to have a dorsal fin same thing with this hypothetical phylogeny showing a close relationship between a bird and a human based on bipedalism both the bird and the human are bipedal that could be said to be evidence for a close relationship but then we would have to say that these are homoplasies all these other characteristics are homoplasies the more parsimonious tree the more sensible tree says that all of these mammalian characteristics arose only once and that bipedalism developed independently twice just like the dorsal fin in the previous tree and just like endothermy in the tree that we looked at previously so in this case this is this is what we call a homoplasy developed independently this is a homoplastic character and these are homologous characters these are characters that are shared due to common descent homology refers to characters that are shared among organisms because of a common ancestor homoplasy are characters that are shared because they evolved independently and in any tree any phylogeny you are going to find both homologous characters and homoplastic characters the correct tree what we infer to be the correct tree will be the one that has the fewest homoplasies this is the maximum parsimony tree the most parsimonious tree is the one with the fewest homoplasies and so it's most likely to be the correct tree