hi and welcome to your first podcast for bisque 162. the reason that we're having videos outside of lecture is to prepare you for the material that we will work with in the lecture so sometimes presenting you with definitions right in the middle of lecture and then expecting you to work with them can be really challenging the goal here in this particular the first podcast is to review the parts of phylogeny really get a good grip on the definitions of the different terms identify the parts of the diagram that are represented with these terms and the processes that they represent and then also to identify the things that are synonyms so there are quite a few terms that are used in phylogenetic trees that mean the same thing and so i want to give you an sort of a boost to understand this when we get to it in lecture you'll have several podcasts throughout this semester and for each of them we will try to put together an activity or a quiz to give your faculty your professors information on where you are with the material that we presented and also get this information to you before the start of class so you can learn more in the classroom this particular set of iclicker questions that we will have will be fairly simple uh they will give me the idea of one are you able to use iclicker two have you watched the podcast and three what more do i need to put in the lecture for you so that you're getting the the concepts we want you to get when you go to iclicker you can still this particular assignment you can do um via the web or for the app on your phone or tablet okay so this is where we'll get started let's first get to talking about phylogenetic trees you were first introduced to phylogenetic trees in bisque 160 and we gave you some very basics about phylogenetic trees but they're going to be some more terms that we have to use to be able to talk about them the way we want to in this particular course they're going to be a lot of terms as you can see some of them are listed along the right side of the slide but there are also a lot of synonyms the first one is that some people refer to these diagrams the colorful diagram as the phylogenetic tree some will just call them a phylogeny or phylogenys other people just call them trees so right at the beginning you can use the term phylogenetic tree phylogeny or tree just to talk about this diagram if you remember from bisque 160 the phylogenetic tree represents the evolutionary history of the organisms shown on the right all right so we are going to talk about just the parts here then we'll follow up with the process and then we get to lecture we'll talk about the uses and more about what they are representing in terms of disc 162 and biodiversity so first when you look at a phylogenetic tree you need to recognize that this is a diagram that shows relationships among organisms based on the characters or characteristics that organisms share with each other the assumption is that if two organisms share a trait they share an evolutionary history and we represent the fact that they share an evolutionary history using these diagrams so let's first start out by talking about the parts of the tree we'll just name the parts of the drawing and you can see up at the top right you have the tip or the taxon so the tip really refers to the end of that yellow line or the end of the red or green or blue line so it's a part of the tree and then at that tip we have the organism or taxon that we're interested in so the taxon in this case is shown by an image in these in this example here there are four different tips of this tree at each of the tips there is a taxon but there are four taxa so in this case we use the word taxon to represent an individual organism taxa is when you uh use the plural of the word taxon all right so remember that what we're trying to do is look at how each of these four organisms have evolved or share traits together sometimes instead of an image you'll see words there so the name of the organism so you could switch out the mountain lion picture for just the word mountain lion the horizontal lines are called branches and they represent an evolutionary lineage so anything that moves along a branch has shared changes in it or shared characteristics in it we also there's a little bit more information in each of the branches so they really represent two two things first when we move from left to right in a phylogeny there's an assumption that time has passed and time moves from the left to right in this diagram so older is on the left current or present day or more recent is on the right so we assume that along a branch time has passed since the lineage actually broke apart from any other group and it's also the second thing it represents is that the lineage is separated from other taxa so the yellow branch at the top of this diagram is separate from the red green or blue branches that means a couple things it means one that they are not interchanging genes they're not the same thing and it also means that they've acquired new characteristics so they're unique and different from the other lineages or other branches so it's easy to think about that when we look at the yellow branch alone but let's take a look at the branches that are labeled in red so there are two different red horizontal lines here there's the one that leads to a tip but then there's also the one that's a little bit further back behind that dotted line this indicates that any of the taxa that come off of this branch later so the red the green the blue or the archaea bacteria the archaea prokaryotes the tulips or the mountain lions have some shared characteristics so these branches excuse me these branches where the red line is here the short red line indicates that the taxes that come after it all have some shared characteristics for example if you look at the blue line here we would know that all of the organisms after that blue line have a nucleus and membrane-bound organelles because they're eukaryotes so they share that trait okay the next part of the tree is the node or the speciation event the node is where the actual vertical and horizontal lines intersect these nodes represent a common ancestor of the group so where the arrow is pointing that represents the common ancestor of archaea plants and animals it also can represent a speciation event now in this diagram it's kind of hard to envision that how that speciation event would happen but the nodes can represent that as well you might also notice now if the definition of a node is where the horizontal and vertical lines intersect there are several nodes on the phylogeny that means there are several common ancestors on the phylogeny and the common ancestor we're talking about is often relative to the organisms you've chosen to talk about if you talk about the where the green the node where the green dot just appeared this is the common ancestor of all of the organisms in the phylogeny right so that's everybody's common ancestor you can also look at this next node where the green dot has appeared and that is the common ancestor of archaea tulips and mountain lions then if you add this other node you can see there's also a common ancestor of tulips and mountain lions now if you talk about the ancestor of tulips and mountain lions for a second i might ask a question like what is the most recent common ancestor of tulips and mountain lions so the most recent common ancestor of these guys is where the yellow dot has just appeared what it means what the common ancestor really represents is not an actual organism it's a hypothetical species or hypothetical group of organisms that had the same shared characteristics so we assume if we start at the origin of life that all living things there was an ancestor to all living things that shared a set of characteristics similarly at the ancestor that's shared between archaea tulips and mountain lions they all had a set of that common ancestor had a set of shared characteristics that led to the differences in um archaea and eukaryotes now the most recent common ancestor is often used and we'll see how in a couple slides from now but when we talk about the most recent common ancestor of tulips and mountain lions it's where the yellow dot is but if i ask you what the most recent common ancestor of archaea tulips and mountain lions are we might actually go back to where the arrow is pointing at the node or speciation event right that would be the most recent common ancestor of um archaea tulips and mountain lions so what you know now about common ancestors is one there are a lot of common ancestors in a phylogeny right in this case there are three for the four taxes that you see two there's also a most recent common ancestor of a set of organisms and that will depend again this is going to be relative it'll depend on which organisms you're talking about when we talk about what is the most recent common ancestor now that most recent common ancestor or any common ancestor for that matter is not really a living thing it's something that maybe never even really existed but it's a concept of there was something there that shared all of these traits now the node often is called a splitting event and when we talk about that splitting event what we're talking about is there was a population of organisms at the node that acquired some differences so they might have acquired differences that lead up the red line or lead down the blue line so that splitting event is typically at the node and then we show a vertical line to help us actually visualize that changes are happening and lineages or branches are becoming isolated okay the last thing that we want to talk about is the fact that sometimes we use phylogenetic trees to talk about how traits evolve so right now all the horizontal lines are indicating shared traits right so all of the things within the yellow lineage they have shared characteristics that lead up to that yellow image of bacteria and then everything within red they have shared characteristics but then things become slightly different okay so if you want to show a new trait show up like for example let's talk about um in mountain lions let's say their fur evolved right there's a new trait that appeared within the lineage that led to mountain lions where the animals had fur all right so this new trait doesn't tell us anything about how mountain lions are related to tulips it can't it's a unique characteristic to mountain lions but it does in fact tell us that oh this new trait evolved here at the point where the red dot is and not behind the yellow dot all right so sometimes when we look at these new this new terminology it's a little hard to kind of take it all in without having some idea of what you're trying to represent so what i'm going to do is walk through how a tree is made in terms of the process of evolution so remember if we're trying to talk about describing relationships through common ancestry or the evolutionary history of organisms or the evolutionary relationships of organisms we can use this tree to represent that so what you're looking at now is basically just those dotted lines left behind after the drawing we just looked at and we're going to walk through this tree talking about the process that would have happened so we know at the origin of life that there were characteristics that organisms had so the first organism in order for it to be called alive had to have a set of characteristics if you remember from bisque 160 these are things like um having a cell membrane extracting energy from the environment things like that so things that all um all living things have ability to reproduce presence of dna that sort of things so this horizontal branch represents the fact that there's a lineage that has all those characteristics what happens next is at that node we have a splitting event or speciation where there's no longer just one set of shared characteristics we have a split where some organisms have some traits and others have different traits and we represent this by drawing this vertical line we're still kind of moving through time right because these aren't straight vertical lines are kind of curved but they are splitting so that we're showing that these this node that former black lineage now has split into two different lineages now part of the reason we draw these vertical lines the way that we do is to make them easier to represent in our diagram so the height is sort of non-specific and it doesn't really have meaning meaning the meaning is coming from the left to right part of the diagram so now what we know is we had a splitting event and then these two lineages are independent the red and yellow lines don't intermix right so they're acquiring differences they're changing over time and they're becoming more and more isolated from one another so this can go on for one lineage where they're accumulating changes but they're not also then having more splitting events but if you have something happen where suddenly within the red lineage they had all the same characteristics and then all of a sudden a splitting event occurs where the red lineage actually becomes very different than what is now the blue lineage again they are isolated lineages or isolated branches and they're evolving over time okay they're still independent lines independent lineages they don't intermix with one another and they're acquiring new differences and they're evolving over time this process can repeat itself so either there are no new splitting events like you see in the yellow and you end up with this taxon at the end of the tip of the branch and similarly in the red lineage you don't get another splitting event and so we can just label that with archaea and then again you get another splitting event and a node where the blue lineage splits into two and you have a new green lineage evolve and the blue lineage becomes a separate isolated lineage from the green the green has tulips the blue becomes the mountain lion and if you wanted to point out the most recent common ancestor then most recent common ancestor that contained traits that are shared by both mountain lions and tulips is shown at the yellow dot all right and again when we talk about this process we're not just talking about a diagram yes we're reading a diagram to represent something but there's this process we just walked through that's happening okay so you have a process associated with the labels that we had to use and practice using but now there's another part of the tree we need to talk about and those are probably the most important parts of the phylogeny and these are called monophyletic groups so i'm going to provide you the definition of this a couple times the monophyletic group is an ancestor and all of the descendants from that ancestor so if we focus on tulips and mountain lions and this yellow dot we know that the yellow dot is the most recent common ancestor of tulips and mountain lions and that at some point because they share a common ancestor or there was an organism that shared a bunch of traits that both tulips and mountain lions have we can call this a monophyletic group if we include the yellow dot and the terminal the taxa at the tips of the tree so what you see now is a purple box that includes the ancestor the yellow dot that represents a shared set of traits and then also the taxa at the tips of the trees the tulips and the mountain lions this group is a monophyletic group a monophyletic group is the ancestor and all of the descendants that you see on the phylogeny now you may also hear the term clade and that is a synonym of monophyletic group it's much easier to say than monophyletic group but we use monophyletic group more accurately than clade so both the clade terminology and the monophyletic group are terms that represent that these organisms have a shared evolutionary history they have a common ancestor that has characteristics that are shared by both tulips and mountain lions and remember again that ancestor doesn't have to have been an existing organism now it also includes that there are differences between tulips and mountain lions of course those lineages are independent and there's this implication that they are different from one another but when we define it we're actually mostly interested in all of the descendants from a single ancestor and the traits that they shared so in this case this is very meaningful because it tells us that mountain lions and tulips have a shared evolutionary history and you actually know this because these are both eukaryotes you know that they have a nucleus and membrane-bound organelles and a whole series of other traits of eukaryotic organisms that we'll talk about in a week or so that represent that shared evolutionary history even though the all the eukaryotes are very different than one another we also know that the traits that they evolved this nucleus and membrane bound organelles happened a long time ago it doesn't what we like to have is these these representatives of uh the shared evolutionary history before this yellow dot includes when those traits evolved like the nucleus or the membrane-bound organelles so not only does identifying monolithic groups help us understand the evolutionary history of living things it also helps us talk about parts of the tree so i can say what is the monophyletic group that includes mountain lions and tulips and you would show this box around the ancestor and all of its descendants now one thing about phylogenys you will learn is that they're all relative right so you might be interested in these relationships or you the relationship between tulips and mountain lions for example or you might be interested in relationships even before that so there are more monophyletic groups within a phylogeny for example if i ask you what the most recent or excuse me what the monophyletic group is that includes archaea and mountain lions you could actually circle this one you'd have the ancestor with the green dot and then all of the descendants including archaea tulips and mountain lions okay now this is an interesting concept because we have two monophthetic groups that we've highlighted one is nested inside of the other so tulips and mountain lions are within the clade that includes archaea it'll be really handy if there's a way to talk about that sort of relationship other than using all that mouthful of words i just said and there is so in this case archaea is the sister taxon to the eukaryotes all right so it's an individual representative so it's sister a sister taxon is one that shares an evolutionary history to another one so archaea is the sister taxon to eukaryotes or you could say that the eukaryote group so mountain lions and tulips are the sister group to archaea what you're saying when you use that term sister is that they share a common ancestor and so it makes it really easy to talk about parts of the tree you could also say that bacteria are the sister taxon to archaea tulips and mountain lions all right so this is all about monophyle it's all about shared evolutionary history okay so here's the term clade showing up with the arrows so when we talk about phylogeny so the last thing i kind of want to talk to you about is really that phylogenys are relative we've talked about it in terms of which node we're talking about which common ancestor we're talking about which monophyletic group we're talking about there's a little bit more flexibility as well so anytime you build a phylogeny among taxi it's really only the ones that you've included that are in your tree so in our case we talked about eukaryotes in representing tulips and mountain lions you know there are more eukaryotes than this including yourself right so phylogenys can be expanded um and each tip even if it's just a representative that you threw in your tree for convenience so i chose mountain lion to do this um we could also look at what else is in this tree all right so what do i mean by that well i think all of us know um that there are more than one cat in the world right you probably think lions you might think tigers you might think panthers you might think um leopards they're a whole bunch of different cats so even if we talk about this in terms of cats we know that really what's at this tip are all the cats that belong in its group if you wanted to expand this phylogeny we also could actually split it out and assume that at that tip is a monophletic group and in that monophyletic group would be say domestic cats and the mountain lion right that assumption is that at the tip of that tree even if it's a representative taxa it's also a monophyletic group okay so it's relative right now when you think about domestic cats many of you are probably thinking of your own pet and you realize that domestic cats aren't even just one individual right they're many individuals so you could expand this even further if you get down to the species level we assume that all members of the species form a monolith phyletic group so here are two cats these are my cats this is vinnie in black on the top and matilda at the bottom she has stripes um these two cats are representative of domestic cats right they're pets they have a common ancestor that led to domestic cats so they have some shared traits but they each have their own branch because they're different individuals okay now before we go into more details i want to tell you that normally with phylogenesis we have this representative of time and when you see that phylogenys are all shifted to the left side all the attacks are at the or sorry all attacks are at the right it implies that they're all living at the same time right or the same time period so if you want to pretty this phylogeny up after you expand it you would just expand these branches okay and what this tells you is that mountain lions and vinnie and matilda form a monophyletic group that had a common ancestor in the back here right and that cat 1 and cat 2 share a common ancestor vinnie and matilda share a common ancestor and the other thing you will know is that these two are the same species so that we know a single species is typically a monophyletic group okay so when we talk about phylogenys they show relative things but there is also some expansion that can be done when we look at phylogenys all right so as somebody who studies phylogenys i look at a group of frogs um and so there are some assumptions that i know about frogs right so if i work on one species of frog in north america it's going to belong within a monophyletic group of frogs from south america as well so there's a lot of relative data in these trees so the reason i'm telling you this is that in your textbook there is a an appendix it's on both the ebook and um in the text itself it's appendix a you may find this useful to deal with your lab material and organizing what you learn in labs but we also recognize that all of these different taxa that are shown here are representatives of those tips so even though you see quite a few organisms here you also recognize they can be expanded just like the cat was this resource is really cool if you go on to achieve you can actually if you're interested in a particular group of organisms you can expand it and look at what else is in there it tells you a whole bunch about living things but this is uh a collective project by many many different scientists across the world building what we call the tree of life okay and we'll talk more about this when you come into lecture