okay so now we're going to look at the diversity of life so first some disclaimers or information the trees we're going to use are a combination of those on the tree of life web project which is a website that's contributed to by researchers who are doing systematics and phylogenetics and a paper in science from 2001 which is the phylogeny of the mammals so in truth phylogenies are constantly being tweaked and refined and so some of the details the following trees may be in dispute they may change there may actually be two different phylogenies that different groups of researchers argue with each other about which is the accurate one so the phylogen you get in other courses May therefore differ in some of the details that's just what happens when you're in the process of figuring out what Nature has done okay so first up when we took ribosomal RNA so this is RNA that everything uses right all living things have ribosomes when you sequence the ribosomal RNA sequences and from basically everything 600 different species you get a relationship that looks like this where bacteria are mostly in one big group kind of surprisingly archaebacteria were in their own separate group and then eukaryotes are in a third group so we're kind of surprised we sort of didn't really expect archebacteria to not be right in there with all the other bacteria it's not really a surprise that eukaryotes are different from bacteria but if we look at this really this tree is just bacteria archaebacteria and eukaryotes being different from each other we don't really know what the root of that tree is right so is it the common ancestor this last Universal communist Ester here then there's a Divergence where archebacteria is the out group of bacteria and eukaryotes or are bacteria the out group of eukaryotes narcobacteria or eukaryotic out group of bacteria and archaeobacteria just from this ribosomal RNA all we have is this pattern we don't know which of these three trees is the more accurate one so using duplicated genes that duplicated before the Divergence of all three of these tags are from one another and this is a technique I talk about a little bit in the molecular Evolution course that I teach using this data we can actually put the root of the tree right here and so the actual shape of the tree is bacteria as the out group for archebacteria and eukaryotes and that was actually kind of a surprise right we didn't really expect archaebacteria to be more closely related to eukaryotes than they were to bacteria so of course follow-up Studies have shown that there are also other biochemical aspects of metabolism that are more similar in these two groups than either as to bacteria so we have the root of the Tree of Life occurring right here we have archaebacteria and eukaryotes as sister taxa and bacteria as the out group you can also represent a phylogeny with a circular diagram like this where the root of the phylogeny is at the very middle and we can see the branching pattern spiraling outwards this is one for bacteria and archaebacteria this is one for animals one of the nice things about this phylogeny is it indicates that basically everything has been around the same amount of time you don't have anything on the edge of a phylogeny versus in the middle so you should be aware that sometimes phylogenes especially phylogenes for very very large numbers of species are depicted with these sort of circular diagrams for these diagrams here they're a little easier to learn with so this phylogeny here is the phylogeny we'll be looking at we'll look at examples of all these different texts on the tips of this phylogenic tree there's a separate PDF that has just this image it's available for download that you'll want to use to study you can read all these with great detail but this tree is also incomplete there are lots of groups that are not shown in this tree either because they're extinct or they're alive and they're not major groups also these Branch links are not necessarily to scale so the fact that this length here is less than this length here is meaningless right I've just made this in a way of kind of organizing it all so this phylogeny here is a really nice outline of Life as we know it you're responsible for knowing this phylogeny for exams and assignments and one of the reasons that I have this phylogeny in this course was a couple reasons first of all it's nice to see how life is related all in one figure and second I actually remember when I was an undergrad I never actually got a tree like this right so I learned all this stuff all about all these different organisms learned about Evolution learned about ecology but I never really had this so I decided to give it to you so you guys can have the experience that I missed out on um for example the things like well we're a dinosaurs right dinosaurs were a big deal when you're a kid and then you know you grow up and everybody starts talking about them well dinosaurs are here right there this little group here that went extinct but they're in the middle of reptiles in the middle of amphibians and and mammals although this is kind of a daunting phylogeny and it's a lot of information as you're studying this and thinking about it you do also want to take a little bit of time to kind of step back look at it and take it all in with the realization that this is some of that Wonder of life life laid out in one diagram in a way where we can understand the history all right so the first section of this phylogeny we'll look at is you have bacteria and archebacteria Eubacteria is the out group to RQ bacteria and eukaryotes so Eubacteria these are true bacteria their cells have cell walls they don't have nuclei and we can also really consider mitochondria and chloroplasts to be descendants of Eubacteria because these organelles are the results of a symbiotic relationship between a eubacterial organism and the eukaryotic organism that it infected and then became a symbiote with so we can often understand mitochondria and chloroplasts better by thinking about them as being bacteria and then archibacteria they look a lot like the Eubacteria microscopically they're all single celled they tend to live in unusual places geothermal Springs and the intestines of animals they look just like bacteria but when you start analyzing the biochemistry and metabolism and genetics then you can actually see they have more in common with eukaryotes than they do with Eubacteria despite their kind of superficial physical appearance moving on now to eukaryotes so eukaryotes have nucleated cells and this is where we get true multicellularity right there are some examples here where sets of cells will kind of stick together but all the cells are exactly the same there's no division of tasks within eukaryotes we have true multicellularity where there will be an organism made up of more than one cell and the cells do different things So within eukaryotes we have three major groups we have green plants as the out group two fungi and animals which are monofletic clade there and this was actually another one of the big surprises from phylogenetics I mentioned earlier we were kind of surprised that Eubacteria and archibacteria weren't more closely related to each other than they were to eukaryotes a second surprise was when we started making phylogenies we totally expected fungi and plants to be more closer related maybe animals to be the different one but that's not in fact what we see right we see plants branching off earlier and then this common ancestor here branching one set of descendants becoming animals another set of descendants becoming fungi and again when you analyze some of the details of metabolism you can see that there are more similarities between fungi and animals than there are between fungi and green plants all right so what do these guys look like so fungi are mushrooms and yeast so toads tools and mushrooms and also yeast so one of the reasons why we study yeast so much in biology is because it's a eukaryotic organism that's more closely related to us than any plant that we could grow would be and it's single cell so it grows quickly so there's actually a lot of research using yeast because again they're more similar to us than arabidopsis or E coli or anything like that and then they also do useful things like make beer so what do plants look like you live in LA so you don't get to see too many plants but there are plants all over the world green plants includes algaes mosses Ferns and seed plants of gymnosperms which don't have flowers and angiosperms which do I'm a little bit of an animal biased person so we're not going to great detail about the diversity within plants but there is in fact a huge diversity within green plants and we could easily have another phylogeny for plants as big as the one that you have in this class for animals