Phylogeny

Hello, everyone, In this lesson, we're going to discuss taxonomy and we're going to begin our discussion on file a genie. Okay, so we've all pretty much heard of taxonomic groups or taxonomy before in general. Basic bio. But let's just go over it one more time. Taxonomy is going to be the science of defining, categorizing, classifying groups of organisms based on shared characteristics that they have and their relatedness. So I want to write and relatedness because that's very important, because a lot of the work that we do now on organisms is that we look at their genetic code. We look at their evolution, and we try to better classify organisms based on how they evolve and how related they are to one another, and not just because of their shared characteristics, because organisms can have very similar looking characteristics and not be related to one another whatsoever. So we're trying mawr to focus on related nous, which is going to tie into our discussion on file a genie. But let's just go over taxonomy because we still do use taxonomy. Ah, lot, just not as much anymore. Basically, it's utilized for naming organisms and naming geniuses and families and species and things like that. So this is gonna be an overview or generalized view of what we call the kind of like Tree of life or the organization off life. So all living things on our planet, you know, us humans. We gotta categorize things. We've got to give everything a name. So we have. And this is going to be the naming system that we use for all the different organisms on our planet. So if you're wondering taxonomy, the word taxonomy comes from the two Greek words. The first word is taxes, which is going to mean the arrangement or organization off something. And then no, Mia is going to mean methods. So the arrangement method off organisms. So that is going to be what we're talking about with taxonomy. Now file a genetics and cledus ticks are going to be how organisms are related, and this is going to tie into this topic a lot. So let's look at these. We have domains, kingdoms, phylum, class, order, family, genus and species. I know you've all probably heard of genus and species before, but all of these other ones are just as important. Now just so you guys know the most inclusive is going to be the domains and the least inclusive is going to be the species. What do I mean by that? Most inclusive means there are mawr organisms in domains than there are in species, because domains are going to be a very wide, overarching group of life. In fact, there are only three domains off life, and this is going to be based on cell type, the type of cell that an organism has. So we're going to have Arcadia bacteria and we're going to have you, Kariya. Now all the organisms that Aaron you carry A are going to be what they're going to be. You carry outs, We belong to this particular domain. But so do millions of other organisms cats, dogs, trees. Anything that is a eukaryotic organism is going to be in this domain. There are going to be so many organisms in domains because they're the largest, overarching, most inclusive group. So these two domains, which are also very, very large RKO and bacteria are both going to be pro Kerasiotes. Bacteria are going to be single celled organisms that we commonly think about that they're going to be found All of our our bodies throughout the environment and soil and dirt and things like that. And they're single celled, pro carry attic organisms just going about their life. Their million different types of them and then RKO are also going to be pro carry attic single celled organisms. But they're generally going to be more extreme environment organisms that live an extremely hot climates. Salty climates, acidic climates there, commonly called extremophiles because they live in very extreme types of environments and they have unique cellular structure to deal with this. So those are the three domains, the largest groups of life. And as you go down and down and down the taxonomic categories, you get smaller and smaller groups of organisms. So you have a domain and then you have a kingdom. Within that domain may be the plant I kingdom inside of the you carry, you carry a domain. So the plant I kingdom inside of the you carry a domain is gonna hold all of the plants and then you go into the phylum and then into the class in order family, genus and species. Now genus and species is what you're normally going to hear when you hear the scientific name often organism. The scientific name of an organism is genus and species. Now you're probably going to need to know this. Well, you're definitely going to need to know this, and I want you all to know how to write the scientific name off an organism. So, like I just said, first it's gonna be genus, and then it's going to be species. Now be careful whenever you do the genus or species of an organism. If you're writing it on the computer, it's always a talus sized, and if you are writing it hand written, most teachers don't really care. But the correct way to write it is you underline it. Okay, so the genus always has to be capitalized. So this is capitalized in this species is lower case. I don't know why that's just the way it ISS, so they're either italicized or underlined, and the geniuses capitalized and the species is lower case. This is very important for all of you who are going thio into research or taxonomy or file a genie or the naming of organisms. It's very important to know. So what's a great example off a a scientific name of something. Well, what about our scientific name? We have homo, that's our genus. And we have SAPIENs. That's our species. And you can see that I have capitalized Homo, lower case SAPIENs and then to be correct, I would underline it. Another great example is Phyllis Caddis. Any idea what this one is? That's a domesticated cat. So all living organisms are going to have scientific name and that's gonna be there genus and their species. Now you guys are probably going to have to know the order off the different tax on the taxonomic groups of life. So there is a saying for this. If you wanted to know so domain Kingdom phylum, class, order, family, genus species You will have to know that order. So the most common one is going to be Dear King Philip, let me write this. Deer King Philip came over four good soup. Now that's the non vulgar version which doesn't stick a swell as the vulgar version. I don't care which one you use, but it could be dear King Philip came over for good soup or, as many people say, dear King Philip came over for good sex. I don't care which one you use, which everyone helps You remember for the test, you go for it. Okay, so now we're going to go down and we're going to talk a little bit about philology. This is just a very short introduction to file a genie. So Systematics is the study of the relationships of organisms. Taxonomy was the study of classifications of organisms and file A genie is the study of the evolutionary relationships between organisms. This is a very important field right now. It is how we are organizing all of the different organisms that we know of on our planet and that we're continuing to discover. And whenever we determine or attempt to determine the evolutionary relationships between organisms, we're going to make a file a genetic tree, which is going to be a branching diagram showing the inferred evolutionary relationships between species inferred Here is a very important word. Please understand that file a genie's file A genetic trees are not set in stone. The more we learn about genetics, the more we learn about cell bio evolutionary biology. The more we learn over time, we realized that we don't actually know how all of these organisms evolved. We're just hypothesizing upon this so file a genetic trees air never set in stone. They are always estimates. They are always hypotheses, but they better help us understand the world around us. This is a great example of a really cool looking circular file. A genie. Not all of them are gonna be circular because these air kind of hard to read this is gonna be I file a genie of just some very big groups in all of the life on our planet. But we will talk more about the more condensed versions, the smaller versions of philology knees, and we'll talk about the different ways you might see file a genetic trees in our coming lessons. Okay, everyone, let's go on to our next topic.

Hello, everyone. In this lesson, we're going to be talking about file a genie, specifically, the difference between ancestral traits, derived traits. HM, ology and analogy. Okay, so whenever we build a file, a genie were specifically going to be looking at certain characters. Generally, you build a fella, Ginny for one character. Maybe it's a particular gene. Maybe it's a morphological character, but these characters could be any genetic morphological, physiological or behavioral characteristic that is being studied. You can pretty much study anything in a file. A genie if you want Thio and whenever you are studying, is going to be called a character. Now, generally, we're going to study different traits. Maybe it's having five fingers versus four fingers. Or maybe it's having two eyes versus one some sort of trait, and you can have different versions of that trait. You can have the ancestral version, and you can have the derived version. So an ancestral trait is a character that existed in an ancestor. It came from an ancestor. A derived trait is a modified form of the ancestral trait, so kind of like a new twist on something. But this twist was not found in the ancestor. Now, whenever we look at these two different file a genies, are they different? Well, they surely look different, don't they? But they're actually not different. The relationships between these organisms are still the same. We can see here that a and b share aim or recent common ancestor at this node. So that is the ancestor to A and B ancestor to A and B so and be are more closely related to one another than they are to species. See. And that is the same thing that is happening in both of these File A genie's Now this particular ancestor here is going to be the ancestor to a be and see, and that is the same over here as well. Okay, everyone. So even though these to file a genie's do look drastically different and A and B are arranged differently, they show us the same information. Now let's talk about the difference between ancestral traits and Dr Traits in the subject of a file a genie. So let's say that we have this particular trait. We're gonna call it Trait A, and it's found in the very first ancestor to all of these organisms trade. A is found in the bottom ancestor down here. And let's say that organism see also has trade a an organism. A also has treat a But then we're going to see that organism B has a new trait called trait be it no longer has trait A. Something is different about this organism. This is the derived trait because it is a trait that is not found in the common ancestor and trait A is the ancestral trait because it is found in the descendants. But it is also found in the ancestor. So trade is the ancestral trait because it is the same trait found in the ancestor and trade. B is the drive trait because it is not found in the ancestor, and it is a modification of the traits found in the ancestor. Now, whenever we're talking about where traits come from, whether they arise on their own or they arise via ancestry, we're gonna be talking about hm ology and analogy. Now, these two topics, these two concepts are very highly tested on and very important for you to understand. So let's go through them and let's make sure that we understand what these two topics are pointing at. Okay, so hm, ology is going to be similarity between organisms due to a shared ancestral trait. Because these organisms share an ancestor because they are closely related, they are similar, and those similarities are homologous. They are a form of hm ology. Now, if the organisms have similarities between each other, but they're not closely related, that means that thes similarities arose due to convergent evolution. Now, do you guys remember exactly what convergent evolution is? Convergent Evolution is a very important topic to understand. It's very highly tested upon topic, and this is going to be when organisms who are not closely related independently create the same tripped so convergent. Evolution is where these two organisms converge on the same idea, the same trait. But this convergence, the similarity is not due to ancestry. In fact, these organisms air not closely related whatsoever. So this is going to be similarity. That's not due to family history, but it's due to some other aspect. Maybe they live in very similar environments, so they created very similar evolutionary adaptations to combat those environments. But but But because it arose due to something else other than ancestry. We call it an analogous structure or an analogy. And this is going to be caused by convergent evolution when organisms become similar, but not because of relatedness, but because of something else. So we also have this topic of home a place e home, a place she is going to be analogous structures that arose independently. So these are gonna be very similar structures like we talked about that arose independently. A great example of home. A place is going to be winged organisms. And you guys can see these organisms right here. In this first example, we're going to have what I believe is a terrorists or some sort of, um, dinosaur, I guess. Let's say this is a pterosaur. If I can spell this terrorists or yeah, So let's say that this is a pterosaur, which would be a flying reptile or a flying dinosaur. And then the number two here is actually a bat, and number three is going to be a bird. Now all of these organisms have powered flight. They have wings that they actively flap to keep themselves in the air. That is a similar structure. Is this similar structure due to related nous. No, it's not. It's due to Homa Place e. It's due to convergent evolution thes to these three organisms. Excuse me are similar, but it's not because they're most closely related. None of the ancestors of these organisms had wings. The ancestors to birds didn't have wings. Birds arose independently to create wings. Bats are mammals. Most mammals don't have wings. So mammals arose. Sorry. Bats arose flight independently of other other other mammals. I'm sorry. I keep tripping over my words there, guys and most reptiles, as we know do not fly. So pterosaurs arose that ability to fly independently as well. So pterosaurs bats and birds arose flight independently of one another via convergent evolution and not via ancestry. So flight is not found in the ancestors of these organisms. All of these organisms evolved flight independently of what? Another via convergent evolution. So this is analogy. Okay, so that is analogy. Now, this particular example, perhaps you recognize it is a very, very famous example. This is going to be a great example of hm ology. You'll probably see this example a lot in class. Whenever your teacher is going over home Ology, This is a very, very famous example. This is going to be the four limbs of vertebrate tetrapods or four legged organisms, and we're actually tetrapods. Even though we're not four legged, we have four limbs. So tetrapods are four limbed organisms and these air all vertebrate organisms these we're gonna be humans, dogs, birds. And this is a whale. I'm covering the word, but it is a whale. Isn't it weird that whales have hands that look like our hands? So this is going to be an example of hm ology. Now, why is this? Because these organisms, all of these organisms, arose from a tetrapod ancestor that had four limbs and bones of those limbs organized in the same fashion. And if you look at the bones in the limbs of all of these organisms, they have all of the same bones. So all of the bones here in this kind of tan orangey color are gonna be the humorous. So we have a humorous and so do dogs and so do birds, and so do Wales. And they're all in the same area, the same general location in the limb. And then we're also going to have the ulna here in red, in all of these organisms. And then we're going to have the radius here in white. In all of these organisms, we're going to have the metacarpals in all of the four limbs of these organisms. That's metatarsals in the hind limbs of these organisms. And then we're gonna have phalanges in brown and all of these bones, even though they are kind of positioned slightly differently in all of these organisms. Or they have different lengths, as you guys could see in Wales. Um, they're all here, and they're all in the same pattern, Same general location, and they all are in the fore limb. All of these structures are due to ancestry because the original ancestor to the tetrapods had these limbs and these bones in this particular order and in this particular fashion. So this is all due to ancestry. They're similar due to a common ancestor. So this is an example of hm ology while flight in all these other organisms is an example of analogy. Okay, everyone All right. So now let's go down and talk about some other interesting topics. We're going to talk about different types of genes. We have or Thala Ghous jeans and parallel parallel August's. You think I know how to say that, but it is hard to say para locus jeans, and these were going to be different types of homologous genes. Remember that is due to ancestry. So an or Thala Ghous gene is going to be a homologous gene. So an ancestral gene that has sequences that are separated by a speciation event. So when a gene or when two genes are or thala Ghous, they diverged. They became different after a speciation event, but the ancestral version created these two new orthe ologists versions. Now, whenever you have a paralysis gene, this is going to be homologous genes as well, so they're gonna be similar due to ancestry. But these genes are gonna be created via a gene duplication event. So when two genes are paralysis, that means that the two genes diverged after a duplication event. So what that's gonna look like is this. You're going to have Gene a let's call it and then you're going to have a duplication event, and then you're going to have to Gina's this. This happens all the time. By the way, genes duplicate themselves via mutations all of the time and a lot of gene families. They're going to be made this way, and then you're going to have an evolutionary change. So we're gonna have evolution here. This is gonna be an evolutionary change to where we still have a gene. A because Gina is important. But that other gene a evolved and changed into a new gene called Jean B. These were going to be or thal or paralysis genes because they diverged. They changed after a gene duplication event that's going to be a paralysis gene. But they are similar because off ancestry. So these two genes are probably very, very similar, but slightly different. But they're similar due to ancestry, so they're homologous now. Horizontal gene transfer is a really interesting topic. Horizontal gene transfer is where genes are transferred from one genome to another, and you may think that doesn't happen. Very often does it actually happens a ton. Just It happens a lot in pro cryonic organisms, so pro chaotic organisms have the ability to pick up genetic material from the environment or transfer genetic material between one another, and that's going to be an example of horizontal gene transfer. So this is transmission of DNA from one genome to another pro Carry. It's very commonly do this. You carry out sometimes. Do this. Now, organelles actually do this a lot. Organelles did this during the development of eukaryotic organisms. Organelles like mitochondria actually moved some of their DNA into the nucleus. Also, transpose ons are going to do this. Plasmas are going to do this and a great example of horizontal gene transfer that happens in human beings is going to be viral horizontal gene transfer. A lot of viruses actually enter yourselves and incorporate their genetic material into your genetic material. So that is an example of horizontal gene transfer. This is different than vertical gene transfer. Vertical gene transfer is when your mother and father gave their genes to you. That is vertical gene transfer. Horizontal gene transfer is going to be two different organisms actually exchanging genetic material. So this actually is not homologous. This should be analogous because this is going to be similar genetic material, but not due to ancestry. It's due to genetic exchange DNA exchange via transpose ons via viruses or via simply too precarious exchanging genetic information. So this is similarity between organisms due to exchange not due to ancestry. So horizontal gene transfer is an analogous transfer of genetic information. Okay, everyone, let's go on to our next topic.

Hello, everyone. In this lesson, we're going to be talking about the different relationships between organisms that you can discover inside of filo genetic trees. Okay, so first off, we're going to go over a generalized term called Cledus Ticks. Claude ist ICS is going to be a field of study inside of biology and inside of genetics and Klytus sticks is going to be a type of classifications based on shared characteristics between common ancestors. And it's going to be utilized for hypothesis, hypothesizing evolutionary relationships between different organisms and it is going to it is now incorporating things like genetics, shared genetic characteristics, shared genetic code and different things like that. And this is one of the main ways that we create file a genie's Klytus sticks and the shared characteristics and genetics between organisms. Now clouded sticks is going to be based off. This word called Played. Ah, played. You are gonna need to know this. I remember being tested on what ACL aid was and what the different types of groups inside of Fila genies were. And the Clague is going to be a group of organisms based on a common ancestor and its descendants, so ACL aid is the ancestor and all of the organisms that evolved from that ancestor. And that is going to be a group. A particular group that you confined within a file, a genie. So, for example, this biology that we have done here, let's say that we're looking at this particular ancestor. Well, this would be a played because it has the ancestor and all of the different organisms that evolved from that ancestor. So that is a played Now there are going to be different types of groups that you confined within a file a genie. And I have seen it many times. Your professor might say, Look at this file a genie and which of these groups is para file, eh, Tik? And you're gonna have to know what that is. Okay, so let's talk about monofilament first, because it is pretty much the easiest to understand. And why is that? Well, it's pretty much the same thing as it played. A monofilament ick group of organisms inside of a file. A genie is the ancestral species and all of its descendants so realize that that is the same thing as it played. They're the exact same thing. A monofilament group and it played are going to be the same thing. Now how do you remember what monofilament means? I'm not sure if this helps everyone, but this usually helps me if I know what the words mean. If I know the basis of the words where the words come from, it usually helps me to remember them. So mono means what? Whenever you're thinking about numbers or you're thinking about groups, mono means Onley or alone. So mono means the Onley ancestor, and it's on Lee descendants. So on Lee, the ancestor and its descendants, so mono means Onley, ancestor and descendant. I'm not sure if that helps everyone, but it does help me. So Onley ancestor plus descendants, not anybody else. Nobody else could be in this group. It's a very closed off special group. You can on Lee be the ancestor or the descendants to be in this group. Nobody else is allowed in. It's like a special club, so that's going to be mono politic Now. There's also pair of politic, a pair of Pillette ick group inside of a file. A genie is going to be the ancestral species, and some but not all of the descendants. So some of the descendants have been left out. For whatever reason, maybe the scientists was only really interested in looking at a certain number of organisms. And those organisms make up a pair of fileting group because all of the descendants were not included. So what does Pere mean? Pera is going to mean near so Pera means near or close to. So it's nearly complete. The group is nearly complete, but not all of the organisms not all of the descendants are within this group. This is why this group is para file a tick and not monofilament IQ. Now which of the groups are going to be para file etiquette? Well, a great example of a para fi led a group is going to be this blue one soap era biologic. And that is because you can see that the common ancestor is down here. And here's a descendant. So lemmerz air A descendant, um lorises, air descendant of that ancestor Tar Sears are a descendant of the ancestor. But all of these guys are descendants as well, but they were not included in this blue group. So this blue group is para file, eh? Tik? Okay, so that is a great example of a parafoil ethic group. Now, I didn't go over it, but just realized that this yellow group is mono file A tick, right? Or a played. Okay. And why is that? Because see that this is the common ancestor, and every single one of its descendants is included in this yellow group. So this is a great example of ACL aid or a monofilament ick group, an ancestor and its descendants. And that's all nobody else on Lee, the ancestor and the descendants, while the para fi led a group is the ancestor and nearly all of the descendants, but not all of them. Okay. All right. So now the last one that we have is not super commonly used, but I have seen it before. Monopolistic and para file, Eric or definitely the mawr important wants to know. But your professor might want you to know Pol if I let it. But it's not as common. Polypill, eh Tik is going to include variously distant related species, but not their common ancestor. So basically what you can think of this as is What does Polly mean? Polly is the opposite of mono. Mono means one or Onley. One Polly means many. So basically, this is going to be many different organisms that aren't really related to each other. So many different organisms, but their ancestor is not included. So a great example of polypill etiquette is going to be right here. Polly, by letting so you can see that the lorises and the tar Sears do have a common in ancestor way back here. But it's not included in the Red Group. The only thing that is included, or the Loris is, and the Tarsus years, which does not include their common ancestor. So this includes distantly related species, because Lorises Antar Sears are pretty distantly related, but not their common ancestor. So basically, polypill Eric means many different organisms without the common ancestor. But again, like I said, polypill, Eric isn't used as often. So you probably don't have to know that one definitely no played monofilament and para file letting those are very important. Okay. All right, so now let's go down, and we're gonna talk about another. We're going to reference another file. A genie. Sorry about that. Okay, So we're going to talk about an out group. What is an out group? Well, an out group is going to be something you use when you are studying the evolutionary relationships between organisms and you need something to compare it to. An out group is going to be a monofilament group. Remember what that means, the ancestor and all of its descendants, and it's going to serve as a reference point for the groups being studied. So the opposite of the out group is the in group, and the in group is going to be your group of interest. Whatever you are studying, maybe you study frogs and your out group is going to be, I don't know, some sort of fish. Okay, so you have an in group that's going to be the one that you are particularly interested in, the one you are studying the evolutionary relationships off, and then you're gonna have an out group which is gonna be a modified leading group of organisms that aren't really related, maybe very distantly related to your group of interest, and you're going to use that group as a reference point. Now we're going to talk about two other things that you can see or you confined inside of file a genetic trees and that's going to be a sin. Apa, morphy and a side sim ply Zo Morphy both very difficult to say. Okay, so a sin apa morphy is going to be a trait shared by taxi and their most common ancestor. This is commonly called a derived treat or a shared drived trait, and this is going to be found in an ancestor and all of its descendants, but not the previous ancestor. So this is going to be basically a trait that evolved within a group. So, for example, let's say if we're looking at, we're looking at the dinosaurs right here. And let's say that the ancestor of the dinosaurs had bird hipped or it had bird hips, which sounds funny, but they reference it right here. So let's say it has bird like hips. The original ancestor of all of the dinosaurs had bird like hips, but then you can see as we go up, lizard like hips evolved. So lizard, I'm sorry I'm in the way. I should probably get out of the picture so you can see so lizard hips evolved over time in the groups of dinosaurs and it evolved in this particular ancestor and all of these species ended up getting lizard hips. So all of these species have lizard like hips and so did their common ancestor, but not the previous ancestor. The previous ancestor did not have that characteristic. So that's going to be a sin. Apa morphy A trait shared by taxi and their most common ancestor, which we can see right here. So we have this common ancestor has lizard hips and all of these ants. All of these descendants have those lizard hips, But this is not shared by the previous ancestor, which is down here. Okay, that is a sin. Apa Morphey Now the simples a more fees are a little bit different. Sim plies a more fees are going to be ancestral traits that are going to be shared by the ancestor and at least two or more of the descendant Taxila. So I'm going to write by two tax or more. Okay, so at least two descendant Taxila now simply Isa Morphy. I want you to know that it's also simply called applies. Oh, Morphey. They both mean the same thing. It just depends on which your professor prefers, applies a more fee or simply is a morphy. They are the same thing. And that is an ancestral trait shared by two or more. Descendant tax. Um So what would that be So like? We said, if the ancestor of the dinosaurs way down here had bird hips and these descendants did not have bird hips, they do not have a simples a morphy. But notice that along this line all of these descendants have bird like hips, which you can see right here they have bird hips. So there are at least two different tax A here that share a traits with their ancestor. Not all of them. Dio This group does not share that particular trait. They do not have bird like hips, but some more than two off. The descendants of the original dinosaur have birdlike hips and work saying that the original dinosaur did have birdlike hips. So this is a simples, a morphine or simply applies a morphy where the ancestral trait from the original ancestor, which is down here, is shared by two or more of its descendant tax A. But not all off its descendant, Taxila. I know that could be kind of confusing. Hopefully, that wasn't too bad. Now I just realized that I did not give you an example of an out group. So let me show you an example of an out group. Okay, so let's say that we were studying are dinosaurs. So are dinosaurs air going to include all of these guys right here? So we have all of these organisms under dinosaurs and say we were studying dinosaurs. What would be our out group for our in group, which is the dinosaur group? Well, a good out group for our dinosaurs would be pterosaurs. Why? Because it's monofilament IQ. Remember? It's one ancestor and all of its descendants. So somewhere up here, we're gonna have an ancestor, and it's going to be the pterosaurs are gonna be a great out group. And scientists might use pterosaurs for comparison for different evolutionary traits with dinosaurs. So that would be a great out group. Now, what if we wanted to study all of the what? I'm not sure how you say this. Ornithology. Dorian's? What if we wanted to study all the ornithology Koreans? Well, that's going to include the dinosaurs and the pterosaurs right. So that means that are out group would be crocks and their relatives. So we would use crocks and their relatives as a out group for the study of the ornithology. Dorian's. I believe that is the correct way to say that. So I hope that was helpful. Just remember that the really important things from this particular lesson are going to be what ACL aid is, What a modify, let it group and what a para fi letting group are inside of a file a genie and how to recognize those different areas or those different groups of organisms inside of a file a genie and be able to identify what a sin APA morphy is. I think knowing what a sin Apple Morpheus is more important than knowing what a Simplicio Morpheus. But again, it depends on what your professor wants. Okay, everyone, let's go on to our next topic