Phylogeny - Online Tutor, Practice Problems & Exam Prep

Taxonomy is the science of classifying organisms based on shared characteristics and evolutionary relationships. It includes hierarchical categories: domain, kingdom, phylum, class, order, family, genus, and species. Phylogeny studies evolutionary relationships, using traits like ancestral and derived characteristics. Homology indicates similarity due to shared ancestry, while analogy arises from convergent evolution. Cladistics classifies organisms into clades, with monophyletic groups containing an ancestor and all descendants, paraphyletic groups missing some descendants, and polyphyletic groups lacking a common ancestor. Understanding these concepts is crucial for studying biodiversity and evolutionary biology.

Taxonomy and Phylogeny

Hello, everyone. In this lesson, we are going to discuss taxonomy, and we are going to begin our discussion on phylogeny. Okay. So, we've all pretty much heard of taxonomic groups or taxonomy before in general basic biology. But let's just go over it one more time. Taxonomy is going to be the science of defining, categorizing, and classifying groups of organisms based on shared characteristics that they have, and their relatedness. 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 more to focus on relatedness, which is going to tie into our discussion on phylogeny. But let's just go over taxonomy because we still do use taxonomy a lot, just not as much anymore. Basically, it's utilized for naming organisms, and naming genera, and families, and species, and things like that. So, this is going to be an overview or a generalized view of what we call the kind of like tree of life, or the organization of life. So all living things on our planet, you know, us humans, we gotta categorize things, we gotta 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 2 Greek words. The first word is taxis, which is going to mean the arrangement or organization of something. And then, nomia is going to mean method. So the arrangement method of organisms. So that is going to be what we're talking about with taxonomy. Now, phylogenetics and cladistics 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, phyla, classes, orders, families, genera, 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 more 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 3 domains of 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 Archaea, Bacteria, and we're going to have Eukarya. Now, all the organisms that are in Eukarya are going to be what? They're gonna be Eukaryotes. We belong to this organism is going to be in 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, Archaea and Bacteria are both going to be prokaryotes. Bacteria are going to be single-celled organisms that we commonly think about are gonna be found all over our bodies throughout the environment, in soil, and dirt, and things like that. And there are single-celled prokaryotic organisms just going about their life. There are a million different types of them. And then Archaea are also going to be prokaryotic single-celled organisms, but they're generally going to be more extreme environment organisms that live in extremely hot climates, salty climates, acidic climates. They're 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 3 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. Maybe the Plantae Kingdom inside of the Eukarya domain. So, the Plantae Kingdom inside of the Eukarya domain is going to hold all of the plants. And then you go into the phylum, and then into the class, and order family, genus, and species. Now, genus and species are what you're normally going to hear when you hear the scientific name of an 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 of an organism. So, like I just said, first it's going to 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 italicized. And if you are writing it handwritten, 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. And the species is lowercase. I don't know why, that's just the way it is. So, they're either italicized or underlined. And the genus is capitalized, and the species is lowercase. This is very important for all of you who are going into research, or taxonomy, or phylogeny, or the naming of organisms. It's very important to know. So, what's a great example of 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, lowercase sapiens, and then, to be correct I would underline it. Another great example is Felis catus. Any idea what this one is? It's a domesticated cat. So, all living organisms are going to have a scientific name, and that's going to be their genus and their species. Now, you guys are probably going to have to know the order of the different 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. Dear King Philip came over for good soup. Okay. So, now, we're going to go down and we are going to talk a little bit about phylogeny. This is just a very short introduction to phylogeny. So, Systematics is the study of the relationships of organisms. Taxonomy was the study of classification of organisms. And phylogeny 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 are continuing to discover. And whenever we determine or attempt to determine the evolutionary relationships between organisms, we're going to make a phylogenetic 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 phylogenies, phylogenetic trees, are not set in stone. The more we learn about genetics, the more we learn about cell biology, evolutionary biology, the more we learn over time, we realize that we don't actually know how all of these organisms evolved. We are just hypothesizing upon this. So phylogenetic trees are 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 phylogeny. Not all of them are going to be circular because these are kind of hard to read. This is going to be a phylogeny 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 phylogenies. And we'll talk about the different ways you might see phylogenetic trees in our coming lessons. Okay, everyone. Let's go on to our next.

Homology and Homoplasy

Hello, everyone. In this lesson, we are going to be talking about phylogeny. Specifically, the difference between ancestral traits, derived traits, Homology, and Analogy. Okay. So, whenever we build a phylogeny, we're specifically going to be looking at certain characters. Generally, you build a phylogeny for one character. Maybe it's a particular gene, maybe it's a morphological character. But these characters can be any genetic, morphological, physiological, or behavioral characteristic that is being studied. You can pretty much study anything in a phylogeny if you want to. And whenever you are studying it is going to be called a character. Now, generally, we're going to study different traits. Maybe it's having 5 fingers versus 4 fingers. Or maybe it's having 2 eyes versus 1. 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 phylogenies, 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 a more recent common ancestor at this node. So that is the ancestor to a and b. Ancestor to a and b. So a and b are more closely related to one another than they are to species c. And that is the same thing that is happening in both of these phylogenies. Now, this particular ancestor here is going to be the ancestor to a, b, and c. And that is the same over here as well. Okay, everyone? So even though these two phylogenies 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 derived traits in the subject of a phylogeny. So, let's say that we have this particular trait. We're going to call it trait a. And it's found in the very first ancestor to all of these organisms. Trait a is found in the bottom ancestor down here. And let's say that organism c also has trait a, and organism a also has trait a. But then we're going to see that organism b has a new trait called trait b. 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, trait A is the ancestral trait because it is the same trait found in the ancestor. And trait B is the derived 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 going to be talking about homology 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, homology 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 homology. Now, if the organisms have similarities between each other, but they are not closely related, that means that these 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 a very highly tested upon topic. And this is going to be when organisms who are not closely related, independently create the same trait. So convergent evolution is where these two organisms converge on the same idea, the same trait. But this convergence, this similarity, is not due to ancestry. In fact, these organisms are 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 because it arose due to something else other than ancestry, we call it an analogous structure or an analogy. 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 homoplasy. Homoplasy is going to be analogous structures that arose independently. So these are going to be very similar structures like we talked about that arose independently. A great example of Homoplasy 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 pterosaur, some sort of dinosaur, I guess. Let's say this is a pterosaur. Yeah. So, let's say that this is a pterosaur, which would be a flying reptile, or a flying dinosaur. And then the number 2 here is actually a bat, and number 3 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 relatedness? No. It's not. It's due to homoplasy. It's due to convergent evolution. 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 or, sorry. Bats arose flight independently of other mammals. 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 one another via convergent evolution. So this is analogy. Okay? So that is analogy. Now, this particular example, perhaps you recognize it as a very, very famous example. This is going to be a great example of homology. You'll probably see this example a lot in class whenever your teacher is going over homology. This is a very, very famous example. This is going to be the forelimbs of vertebrate tetrapods, or 4-legged organisms. And we are actually tetrapods. Even though we're not 4-legged, we have 4 limbs. So, tetrapods are 4-limbed organisms, and these are all vertebrate organisms. These are going to 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 homology. Now, why is this? Because these organisms, all of these organisms arose from a Tetrapod ancestor that had 4 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 going to be the Humerus. So, we have a Humerus, and so do dogs, and so do birds, and so do whales. 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 forelimbs of these organisms, it's metatarsals in the hindlimbs of these organisms. And then, we're going to 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 can see in whales. They're all here. And they're all in the same pattern, same general location, and they all are in the forelimb. 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 are similar due to a common ancestor, so this is an example of homology. While flight and all these other organisms is an example of analogy. Okay, everyone? Alright. 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 orthologous genes and par paralogous? You'd think I'd know how to say that, but it is hard to say. Paralogous genes. And these are going to be different types of homologous genes. Remember, that is due to ancestry. So an orthologous gene is going to be a homologous gene, so an ancestral gene that has sequences that are separated by speciation event. So when a gene, or when 2 genes are orthologous, they diverged, they became different after a speciation event. But the ancestral version created these 2 new orthologous versions. Now, whenever you have a paralogous gene, this is going to be homologous genes as well. So, they're going to be similar due to ancestry. But these genes are going to be created via a gene duplication event. So, when 2 genes are paralogous, that means that the 2 genes diverged after a duplication event. So, what that's going to 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 2 gene A's. This happens all the time, by the way. Genes duplicate themselves via mutations all of the time, and a lot of gene families are going to be made this way. And then you're going to have an evolutionary change. So we're going to have evolution here. This is going to be an evolutionary change to where we still have a gene a, because gene a is important, but that other gene a evolved and changed into a new gene called gene b. These are going to be ortho or paralogous genes because they diverged, they changed after a gene duplication event. That's going to be a parallogous gene. But they are similar because of 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? It actually happens a ton, just it happens a lot in prokaryotic organisms. So prokaryotic 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 1 genome to another. Prokaryotes very commonly do this. Eukaryotes 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, transposons are going to do this, plasmids 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 your cells 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 2 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 transposons, via viruses, or via simply 2 prokaryotes 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.

Cladistics

Hello, everyone. In this lesson, we are going to be talking about the different relationships between organisms that you can discover inside of phylogenetic trees. Okay. So, first off, we're going to go over a generalized term called cladistics. Cladistics is going to be a field of study inside of Biology and inside of Genetics. And Cladistics is going to be a type of classification based on shared characteristics between common ancestors. And it's going to be utilized for hypothesizing evolutionary relationships between different organisms. And it is going to incorporate 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 phylogenies. Cladistics and the shared characteristics and genetics between organisms. Now, cladistics is going to be based on this word called clade. A clade, you are going to need to know this. I remember being tested on what a clade was, and what the different types of groups inside of phylogenies were. And the clade is going to be a group of organisms based on a common ancestor and its descendants. So a clade 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 can find within a phylogeny. So, for example, this phylogeny that we have down here, let's say that we're looking at this particular ancestor. Well, this would be a clade because it has the ancestor and all of the different organisms that evolved from that ancestor. So that is a clade. Now, there are going to be different types of groups that you can find within a phylogeny. And I have seen it many times, your professor might say look at this phylogeny and which of these groups is paraphyletic. And you're going to have to know what that is. Okay?

So, let's talk about monophyletic first because it is pretty much the easiest to understand. And why is that? Well, it's pretty much the same thing as a clade. A monophyletic group of organisms inside of a phylogeny is the ancestral species and all of its descendants. So, realize that that is the same thing as a clade. They are the exact same thing. A monophyletic group and a clade are going to be the same thing. Now, how do you remember what monophyletic 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 only or alone. So mono means only the ancestor and its descendants. So, only the ancestor and its descendants. I'm not sure if that helps everyone, but it does help me. So, only ancestor, plus descendants. Not anybody else, nobody else can be in this group. It's a very closed off, special group. You can only 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 monophyletic. Now, there's also paraphyletic. A paraphyletic group inside of a phylogeny 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 scientist was only really interested in looking at a certain number of organisms, and those organisms make up a paraphyletic group because all of the descendants were not included. So, what does para mean? Para is going to mean near. So, 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 paraphyletic and not monophyletic. Now, which of the groups are going to be paraphyletic? Well, a great example of a paraphyletic group is going to be this blue one. So, paraphyletic. And that is because you can see that the common ancestor is down here, and here is a descendant. So lemurs are a descendant, lorises are a descendant of that ancestor, Tarsiers are a descendant of that ancestor, but all of these guys are descendants as well, they were not included in this blue group. So this blue group is paraphyletic. Okay?

So that is a great example of a paraphyletic group. Now, I didn't go over it, but just realize that this yellow group is monophyletic. Right? Or a Clade. Okay? And why is that? Because you can 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 a clade or a monophyletic group, an ancestor, and its descendants, and that's all. Nobody else, only the ancestor and the descendants. While the paraphyletic group is the ancestor and nearly all of the descendants, but not all of them. Okay? Alright. So now the last one that we have is not super commonly used, but I have seen it before. Monophyletic and paraphyletic are definitely the more important ones to know, but your professor might want you to know polyphyletic, but it's not as common. Polyphyletic is going to include variously distant related species, but not their common ancestor.

Here’s what students ask on this topic:

What is the difference between taxonomy and phylogeny?

Taxonomy is the science of classifying organisms based on shared characteristics and hierarchical categories such as domain, kingdom, phylum, class, order, family, genus, and species. It focuses on naming and organizing organisms. Phylogeny, on the other hand, studies the evolutionary relationships between organisms. It uses traits like ancestral and derived characteristics to infer these relationships, often represented in phylogenetic trees. While taxonomy provides a structured way to name and categorize organisms, phylogeny aims to understand their evolutionary history and relatedness. Both fields are crucial for understanding biodiversity and the evolutionary processes that shape life on Earth.

How do you write the scientific name of an organism correctly?

The scientific name of an organism is written using binomial nomenclature, which includes the genus and species names. The genus name is always capitalized, while the species name is lowercase. When typed, both names should be italicized, e.g., Homo sapiens. When handwritten, they should be underlined, e.g., Homo sapiens. This format ensures consistency and clarity in scientific communication. For example, the scientific name for humans is Homo sapiens, and for domestic cats, it is Felis catus.

What is the significance of homology and analogy in phylogeny?

In phylogeny, homology refers to similarities between organisms due to shared ancestry. These homologous traits indicate evolutionary relationships and help construct phylogenetic trees. For example, the forelimbs of humans, dogs, birds, and whales are homologous, sharing a common tetrapod ancestor. Analogy, however, refers to similarities that arise from convergent evolution, not shared ancestry. These analogous traits result from similar environmental pressures leading to similar adaptations in unrelated organisms. An example is the wings of bats, birds, and pterosaurs, which evolved independently. Understanding homology and analogy is crucial for accurately interpreting evolutionary relationships.

What are monophyletic, paraphyletic, and polyphyletic groups?

In phylogenetics, a monophyletic group, or clade, includes an ancestor and all its descendants, representing a complete branch on the tree of life. A paraphyletic group includes an ancestor and some, but not all, of its descendants, leaving out certain lineages. A polyphyletic group consists of various organisms without including their common ancestor, often grouped based on similar traits rather than evolutionary history. Understanding these groupings helps in accurately classifying organisms and understanding their evolutionary relationships. For example, reptiles excluding birds form a paraphyletic group, while flying animals like bats and birds form a polyphyletic group.

What is a phylogenetic tree and how is it used?

A phylogenetic tree is a branching diagram that represents the inferred evolutionary relationships among various species based on their genetic, morphological, or other traits. Each branch point, or node, represents a common ancestor, and the branches represent the descendants. Phylogenetic trees are used to hypothesize the evolutionary pathways and relatedness of organisms. They are essential tools in evolutionary biology, helping scientists understand how species have evolved over time and how they are related. These trees are not set in stone and are continually refined as new data becomes available.