>> Fellow students, this is plants and animals in Southern California, and today I want to talk about the taxonomic classification, in particular about ranks, and then how that relates to phylogenetics. Phylogenetics is, like, the study of the tree of life. So about 300 years ago there was this Swede named Carl Linnaeus. You probably know about this a little bit. Of course, for time out of mind, people have been classifying things, but Linnaeus was, he was kind of ambitious guy, and he wanted to classify all of the organisms that were known, and, of course, that was during a time when Europeans were starting to explore the world and bring back organisms from around the world, and he set up a system whereby that classification was strictly nested. Species were inside of genera, and a species could be only inside of one genus. In fact, he set up the convention of having the species name be the name of the genus, which is a noun, followed by an adjective, of course, in Latin. So, for instance, Homo sapiens, homo is the genus and sapiens is an adjective that always belongs with the noun. You would never just refer to humans as sapiens. Alright. You would always refer to them as Homo sapiens, or at h. sapiens. So each species is named as the genus and the epithet, and that's a binomial. And species have to be in only one genus. And then genera are grouped together into families, and a genus can only be in one family. It can't be in another family, and you can't have genera inside of other genera, and you can't have families inside of other families. Families are grouped together into orders, orders are grouped together into classes, classes are grouped together into phyla, phyla are grouped into kingdoms, and that's sort of how Linnaeus did it. So it was species, genus, family, order, class, phylum, kingdom, but then, of course, people want extra ranks. So like when it was discovered that bacteria are way different, then we had to invent this thing called a domain that's even bigger than a kingdom, and then it's useful to sometimes have a family but break that family up into subfamilies. And then you might also, if you want to break the subfamilies up, you could break them up into tribes, and then you can break the tribes up into subtribes. That's kind of a common thing to do. Also within a genus, you might want to break the genus up into subgenera like see, you know, this is break, broken up into a couple subgenera, and then you could break the, a subgenus up into sections, and you could have different subsections within a section, you know. So it keeps on going, and then, of course, somebody had to invent subspecies, right, because, you know, there was some species that existed, and somebody wanted to recognize some variation within the subspecies. So intraspecific taxonomy had to be invented. Usually that's for geographic races or something, you know, something like that. Now, when evolution was discovered, it didn't revolutionize the classification. Because evolution just reflects the classification that already existed. Like, some of those things that were recognized before Darwin, they were, they existed because they were branches on the tree of life or twigs within branches on the tree of life. And actually we didn't really have very good methods for figuring out what the tree of life was until pretty recently. For 250 years after Linnaeus, people just, you know, they made the system better and better and better and better, but not really more and more phylogenetic. And that was true really, you know, like, up to the time I was a student. By the time I was a student, we were starting to figure out how to figure out the tree of life, but we hadn't quite done it yet, and then now where there's this huge cottage industry that's figuring out the tree of life, and we're getting better and better at knowing the tree of life, and, of course, people want to name the branches and name the twigs and name the twiglets within the tree of life. And the way this works is if you really want to name things in a phylogenetic way, that really reflects the evolutionary relationships, then you have to name whole and complete branches. In other words, it has to be all the descendants of a common ancestor that belong in a group, not just some of them, but all of the descendants of a common ancestor. That's called a monophyletic group. A group that contains all of the descendants of a common ancestor is a monophyletic group, and that's in contrast to a paraphyletic group. A paraphyletic group is a group that excludes some of the, a paraphyletic group is a group that excludes some of the descendants of a common ancestor. So, for instance, if we recognized a group that was the great apes without the humans, that would be a paraphyletic group. The great apes without the humans, like gorillas and chimpanzees and bonobos and orangutans. Because the common ancestor of orangutan and a chimpanzee is also the ancestor of a human. So you couldn't recognize, you couldn't say, OK, let's make a family that's the great apes, and then we'll have another family that's the humans. If you wanted to put humans in a separate family from the great apes and put them in a family, then you would be making that great ape family a paraphyletic group. What this means is that the taxonomy is very unstable. Right now, as we're figuring out the tree of life, every time people figure this out, they figure out, you know, that something is, like, a family inside of a family, then they're forced to change the name. They got to either change the [inaudible], you know, they've got to somehow change the name because Linnaeus' system doesn't allow families within a families, and it doesn't allow genera within genera. And, yet, the received taxonomy, the taxonomy that's built up ever since Linnaeus, it has a ton of paraphyletic groups in it. There's all sorts of groups that are paraphyletic. Like you might know the difference between monocots and dicots, right. Well, it turns out to monocots are a group that was derived from within dicots. So that blows apart the dicot group. Like, it's not a monophyletic group. Or you might think of [inaudible], mosses, liverworts, and whatever. That's not a monophyletic group because out of that arose the vascular plants. And, you know, similarly, there's just any number of cases where at the same rank, at exactly the same rank, you had one taxon that evolved out of another taxon of the same rank. And so if you really want to be naming branches on the tree of life, you're going to have to change the ranks. And it turns out that since Linnaeus' time, these rules for giving names have been codified into nomenclatural codes. Like, there's a botanical nomenclatural code, and there's a zoological nomenclatural code. There's also one for microorganisms, for bacteria. And these codes enforce these rules. Now, what's been happening in the last few years is people have proposed that we set aside the old system of naming and invent a new system of naming that would be rank free. Be phylogenetic and rank free, and it's called the phylocode. By the phylocode, we would not have the rank of family. We would not have the rank of genus. We would not have the rank of suborder. You would just have name groups, and then groups would be inside of groups. If you did this, you would still have to change the names occasionally, you know, because of new understanding of how things are related, but you wouldn't have to change the name just because of a rank conflict. And I don't know if it'll ever catch on, but I think it's a cool idea. Like it illustrates just how kind of arbitrary these ranks are, and how kind of unfortunate the codes of nomenclature are. Like, for instance, the family of roses, which [inaudible] is in and [inaudible] is in, that's the rose ACE, and the ACE part denotes that it's a family. So you kind of want to tear off that ACE part and put something else on the end just to, you know, so to not call it a family, but you've got some other problems. Like within the family rose ACE, rosea is in a subfamily called the [inaudible], which, you know, starts out with rose, and then it has [inaudible] at the end, which means that it's a subfamily, and then there's a larger group that includes the rose AC, and it's the group of, that's the order of roses, and it's called rose [inaudible]. So you'd have to rip the [inaudible] part off the end of that, and you'd want to name these, you know, you want to come up with a whole new system of names. It actually might be just great in about two generations. It would be really painful for people like me who know the old names and want to keep on using them. It would be a little bit painful for you, but then by the time you're teaching plants and animals at Southern California, those students, they would never even remember the rose ACE. They would just name it whatever. The, it would be called the rose [inaudible] or something like that, and that would be the end of it. OK. Well, that's all that I have to say about that.