Understanding Phylogeny and Traits

When inferring or elucidating or discovering the phylogeny of a group of organisms, it's crucial to use shared derived traits as evidence of clades, as we have said. Now, remember that a clade is a group of related organisms that includes all the descendants of a common ancestor. And because they share a common ancestor, they will have a... new traits, new derived character states from that common ancestor. You can see here that feathers are a synapomorphy, a shared derived trait of the ostrich, the eagle, and the crow, and in fact all birds. The amnion, as we've said, is a synapomorphy, a shared derived trait of the amniotes, the reptiles, the mammals, and the birds. Tetrapod means four legs and the tetrapods include the amphibians as well as the amniotes. So the tetrapod limb is a synapomorphy for the tetrapods. But notice that the trait can be later lost in some groups. So do you see any organisms among the tetrapods that have lost the tetrapod limb that was found in the in the ancestor? Well, you know, of course the front limb is modified in the birds into a wing, and in the bats it's modified into a wing. The limbs have been completely lost in the snakes and in some other organisms that aren't shown here, but the ancestors had it, so the tetrapod limb is a synapomorphy. for the tetrapods, that is the amphibians, reptiles, mammals, and birds. Now, I want to discuss the importance of inferring phylogeny with shared derived characters rather than with primitive characters. You need to be able to understand and explain why we need to look for shared derived characters instead of just looking for shared characters. We'd have to look for primitive states to see what's new, what is derived. So consider these four organisms. Now we know we have two birds and three mammals. But what evidence leads us to say that we have here these two clades that are indicated with the blue and the yellow? We can look at the characteristics. of these organisms. We can say that birds have feathers, they have the right aortic arch that comes out of the heart towards the right side, they have air-filled bones, they have lungs that have air sacs, mammals of course have hair, they have a left aortic arch, mammals have mammary glands, they have red blood cells. that are non-nucleated. They have three middle ear bones, the hammer, anvil, and stirrup. Now, all of these happen to be good synapomorphies for these clades, but we might have chosen different characters that would lead us to different taxa. For example, we might have chosen these groupings, and we might have chosen characters that would lead us to these groups. So, for example, the chicken, the... crow, and the platypus share some important traits. The platypus and these birds, and in fact all birds, are oviparous, that is they are egg-laying. They have a cloaca. Cloaca is the Latin word for sewer. Cloaca is a single opening for the digestive, the urinary, and the reproductive systems. All three of these organisms have The interclavicle bone and the coracoid bone and exactly what those are. If you look at a bird the interclavicle is fused with the furcula or the wishbone and the coracoid is this bone that connects the sternum with the shoulder joint. So look for this the next time you eat a chicken breast. You don't have one but platypuses and birds do. Now all placental mammals such as humans, dogs, camels, and every other placenta A placental mammal has lost those two bones and there's no cloaca. Instead of a single opening in placental mammals, in the females at least, there are separate openings for the digestive, urinary, and reproductive system. Placental mammals are viviparous, that is, they nourish the young inside the body until birth. So what exactly is the problem with... these traits that we have chosen that lead us to this erroneous conclusion? Well, the problem is that we have chosen here primitive traits to define what we wanted to be a clade. Every one of these characters is something that was inherited from the ancestors of the birds and the mammals rather than something new that was derived in the hypothetical ancestor of the chicken, the crow, and the platypus. So, what do we do? Well, as you know, we need an outgroup to determine primitive states. In this case, the outgroup will need to be outside the common ancestor of the birds and the mammals. A turtle will do. So let's look at some of the primitive traits of a turtle. A turtle... is oviparous, it lays eggs. It has a cloaca, a single opening for all three of those systems. It has epidermal scales. It has both an interclavicle and a coracoid bone. It has, like most vertebrates, it has nucleated red blood cells. It has a single bone in the middle ear. It has a double aortic arch, both left and right, coming out of the heart. And of course it has an amnion. Now that we know what's primitive for our in-group, we can look for what's shared and derived. For birds, feathers instead of epidermal scales. Well, really it's in addition to epidermal scales. Some of the scales have been modified into feathers. Birds do have scales on their legs. Birds have a right aortic arch. They've really just lost the left aortic arch. out group had both left and right. We didn't say anything about the out group about the the bones or the lungs but the lungs with air sacs are new. For mammals, hair instead of the epidermal scales, red blood cells have lost their nuclei, the middle ear has added two middle ear bones instead of just one, and the right aortic arch has been lost from what was the double aortic arch, and a new characteristic, the mammary glands, has been developed in the mammals. Within the mammals, the placental mammals, represented here by the dog and the camel, have separate openings for the various systems instead of a common cloaca, and are viviparous, or bare-life young. and have lost those bones in the pectoral girdle. What about the other primitive traits? Simply retained in the descendants, unless they have acquired a derived state. The amnion, well, it's retained in everything. Mammals and birds. Oviparie, retained in the birds, and... in the monotremes, in the platypus. But placental mammals have something new. The cloaca, the cloaca retained in the birds and in the platypus, but lost in the placental mammals. What about the nucleated red blood cell, the single middle ear bone? All those are lost in the mammal, but birds retained them from their ancestors. So the loss of those characters are synapomorphies supporting the mammal clade. But, and this is very important, we can't suggest a turtle and bird clade and point to nucleated red blood cells, interclavicles, a coracoid bone, or a single middle ear bone as evidence. Birds and turtles simply inherited those traits as a legacy of their common vertebrate ancestors. Now let's look at this on a tree. I'll add a frog as a second outgroup. Now here are some primitive traits for both outgroups. oviparate, cloaca, interclavicle, coracoid, nucleated red blood cells, single middle irosicle, double aortic arch. All of these are found in amphibians as well as in amniotes. Epidermal scales and an amnion are shared and derived in the amniotes, but we are using the turtle as an out-group. So relative to the in-group, the platypus, the camel, dog, crow and chicken, these are still primitive characters. Now let's look for some synapomorphies. Here are some new characters shared by all birds, including the two in our tree. This is evidence for the birds being acclaid. Here is another group of synapomorphies for the mammals. They are derived relative to the out group. and shared in the mammal clade and therefore provide evidence for this clade. For the placental mammals, represented by the camel and the dog, synapomorphies, not shared by the platypus or anything else in the tree. So let's see what happened to the primitive traits. Oviparine, egg laying, we find it in the frog, which is an amphibian, and in the turtle, and it's also primitive within the fish. Within the N group, it's retained in the platypus and in the birds, but lost in the placental mammals, where the flashing hash mark is. And it's retained in the frog, turtle, platypus, crow, and chicken, because it was a character state. found in the common ancestor of those organisms, but then lost in the ancestor of the placental mammals. I should say that it's also lost independently in some other vertebrates not shown on the tree. Some group of snakes, lizards, fish, and others also give live birth. But oviparate egg laying is primitive. Turtles and platypuses and chickens lay eggs because that's the primitive trait for vertebrates. Placental mammals all give live birth because they share, by descent, a common trait. It's a synapomorphy for them. Now, rattlesnakes and placental mammals and some sharks and other vertebrates all give live birth. And that is a shared derived trait because remember oviparie, laying eggs, is primitive. However, the strongly supported phylogeny indicates that it is a trait that arose independently in, say, rattlesnakes and placental mammals and sharks. And so in that accepted phylogenetic tree, it would be a homoplasy, a character that arose separately. in mammals, rattlesnakes, and sharks. Now, which organisms have a cloaca? Again, everything except for the placental mammals. And again, all these clades retain the cloaca because they inherited it from the earliest vertebrate ancestors. And it's only lost in the placental mammals who develop separate openings for each system. What about these primitive traits? Which organisms retain them? Here it's just the outgroup and the birds. The ancestor of the mammals, including the platypus, has added two bones to the middle ear and lost the nucleated red blood cells and everybody else retains the primitive state. So you need to be able to explain Why evidence for clades is based only on shared derived character states determined by outgroup analysis. You need to understand why things will go awry if you use primitive character states, or if you simply look at shared traits by themselves without considering their history. If you look at organisms and simply say they all have the same number of legs, or they're all the same color, or they all are warm-blooded, you're probably going to come to the wrong conclusion as to phylogeny. You need to start with an out-group and then see what shared differences have arisen from there.

You can see here that feathers are a synapomorphy, a shared derived trait of the ostrich, the eagle, and the crow, and in fact all birds. The amnion, as we've said, is a synapomorphy, a shared derived trait of the amniotes, the reptiles, the mammals, and the birds. Tetrapod means four legs and the tetrapods include the amphibians as well as the amniotes.

So the tetrapod limb is a synapomorphy for the tetrapods. But notice that the trait can be later lost in some groups. So do you see any organisms among the tetrapods that have lost the tetrapod limb that was found in the in the ancestor? Well, you know, of course the front limb is modified in the birds into a wing, and in the bats it's modified into a wing. The limbs have been completely lost in the snakes and in some other organisms that aren't shown here, but the ancestors had it, so the tetrapod limb is a synapomorphy.

for the tetrapods, that is the amphibians, reptiles, mammals, and birds. Now, I want to discuss the importance of inferring phylogeny with shared derived characters rather than with primitive characters. You need to be able to understand and explain why we need to look for shared derived characters instead of just looking for shared characters. We'd have to look for primitive states to see what's new, what is derived.

So consider these four organisms. Now we know we have two birds and three mammals. But what evidence leads us to say that we have here these two clades that are indicated with the blue and the yellow?

We can look at the characteristics. of these organisms. We can say that birds have feathers, they have the right aortic arch that comes out of the heart towards the right side, they have air-filled bones, they have lungs that have air sacs, mammals of course have hair, they have a left aortic arch, mammals have mammary glands, they have red blood cells.

that are non-nucleated. They have three middle ear bones, the hammer, anvil, and stirrup. Now, all of these happen to be good synapomorphies for these clades, but we might have chosen different characters that would lead us to different taxa.

For example, we might have chosen these groupings, and we might have chosen characters that would lead us to these groups. So, for example, the chicken, the... crow, and the platypus share some important traits.

The platypus and these birds, and in fact all birds, are oviparous, that is they are egg-laying. They have a cloaca. Cloaca is the Latin word for sewer.

Cloaca is a single opening for the digestive, the urinary, and the reproductive systems. All three of these organisms have The interclavicle bone and the coracoid bone and exactly what those are. If you look at a bird the interclavicle is fused with the furcula or the wishbone and the coracoid is this bone that connects the sternum with the shoulder joint. So look for this the next time you eat a chicken breast. You don't have one but platypuses and birds do.

Now all placental mammals such as humans, dogs, camels, and every other placenta A placental mammal has lost those two bones and there's no cloaca. Instead of a single opening in placental mammals, in the females at least, there are separate openings for the digestive, urinary, and reproductive system. Placental mammals are viviparous, that is, they nourish the young inside the body until birth.

So what exactly is the problem with... these traits that we have chosen that lead us to this erroneous conclusion? Well, the problem is that we have chosen here primitive traits to define what we wanted to be a clade. Every one of these characters is something that was inherited from the ancestors of the birds and the mammals rather than something new that was derived in the hypothetical ancestor of the chicken, the crow, and the platypus. So, what do we do?

Well, as you know, we need an outgroup to determine primitive states. In this case, the outgroup will need to be outside the common ancestor of the birds and the mammals. A turtle will do.

So let's look at some of the primitive traits of a turtle. A turtle... is oviparous, it lays eggs. It has a cloaca, a single opening for all three of those systems.

It has epidermal scales. It has both an interclavicle and a coracoid bone. It has, like most vertebrates, it has nucleated red blood cells. It has a single bone in the middle ear.

It has a double aortic arch, both left and right, coming out of the heart. And of course it has an amnion. Now that we know what's primitive for our in-group, we can look for what's shared and derived.

For birds, feathers instead of epidermal scales. Well, really it's in addition to epidermal scales. Some of the scales have been modified into feathers.

Birds do have scales on their legs. Birds have a right aortic arch. They've really just lost the left aortic arch.

out group had both left and right. We didn't say anything about the out group about the the bones or the lungs but the lungs with air sacs are new. For mammals, hair instead of the epidermal scales, red blood cells have lost their nuclei, the middle ear has added two middle ear bones instead of just one, and the right aortic arch has been lost from what was the double aortic arch, and a new characteristic, the mammary glands, has been developed in the mammals.

Within the mammals, the placental mammals, represented here by the dog and the camel, have separate openings for the various systems instead of a common cloaca, and are viviparous, or bare-life young. and have lost those bones in the pectoral girdle. What about the other primitive traits? Simply retained in the descendants, unless they have acquired a derived state. The amnion, well, it's retained in everything.

Mammals and birds. Oviparie, retained in the birds, and... in the monotremes, in the platypus. But placental mammals have something new.

The cloaca, the cloaca retained in the birds and in the platypus, but lost in the placental mammals. What about the nucleated red blood cell, the single middle ear bone? All those are lost in the mammal, but birds retained them from their ancestors. So the loss of those characters are synapomorphies supporting the mammal clade.

But, and this is very important, we can't suggest a turtle and bird clade and point to nucleated red blood cells, interclavicles, a coracoid bone, or a single middle ear bone as evidence. Birds and turtles simply inherited those traits as a legacy of their common vertebrate ancestors. Now let's look at this on a tree. I'll add a frog as a second outgroup.

Now here are some primitive traits for both outgroups. oviparate, cloaca, interclavicle, coracoid, nucleated red blood cells, single middle irosicle, double aortic arch. All of these are found in amphibians as well as in amniotes.

Epidermal scales and an amnion are shared and derived in the amniotes, but we are using the turtle as an out-group. So relative to the in-group, the platypus, the camel, dog, crow and chicken, these are still primitive characters. Now let's look for some synapomorphies.

Here are some new characters shared by all birds, including the two in our tree. This is evidence for the birds being acclaid. Here is another group of synapomorphies for the mammals. They are derived relative to the out group. and shared in the mammal clade and therefore provide evidence for this clade.

For the placental mammals, represented by the camel and the dog, synapomorphies, not shared by the platypus or anything else in the tree. So let's see what happened to the primitive traits. Oviparine, egg laying, we find it in the frog, which is an amphibian, and in the turtle, and it's also primitive within the fish. Within the N group, it's retained in the platypus and in the birds, but lost in the placental mammals, where the flashing hash mark is. And it's retained in the frog, turtle, platypus, crow, and chicken, because it was a character state.

found in the common ancestor of those organisms, but then lost in the ancestor of the placental mammals. I should say that it's also lost independently in some other vertebrates not shown on the tree. Some group of snakes, lizards, fish, and others also give live birth.

But oviparate egg laying is primitive. Turtles and platypuses and chickens lay eggs because that's the primitive trait for vertebrates. Placental mammals all give live birth because they share, by descent, a common trait.

It's a synapomorphy for them. Now, rattlesnakes and placental mammals and some sharks and other vertebrates all give live birth. And that is a shared derived trait because remember oviparie, laying eggs, is primitive.

However, the strongly supported phylogeny indicates that it is a trait that arose independently in, say, rattlesnakes and placental mammals and sharks. And so in that accepted phylogenetic tree, it would be a homoplasy, a character that arose separately. in mammals, rattlesnakes, and sharks. Now, which organisms have a cloaca? Again, everything except for the placental mammals.

And again, all these clades retain the cloaca because they inherited it from the earliest vertebrate ancestors. And it's only lost in the placental mammals who develop separate openings for each system. What about these primitive traits? Which organisms retain them?

Here it's just the outgroup and the birds. The ancestor of the mammals, including the platypus, has added two bones to the middle ear and lost the nucleated red blood cells and everybody else retains the primitive state. So you need to be able to explain Why evidence for clades is based only on shared derived character states determined by outgroup analysis.

You need to understand why things will go awry if you use primitive character states, or if you simply look at shared traits by themselves without considering their history. If you look at organisms and simply say they all have the same number of legs, or they're all the same color, or they all are warm-blooded, you're probably going to come to the wrong conclusion as to phylogeny. You need to start with an out-group and then see what shared differences have arisen from there.

Transcript for:Understanding Phylogeny and Traits

Transcript for:
Understanding Phylogeny and Traits