when we do biological systematics what we're trying to do is to reconstruct or elucidate or infer the phylogeny of organisms now remember the phylogeny is the actual relationships among the organisms when we make a tree such as this one what we what we are doing is making our best estimate of the tree based on the evidence that we have so this is a tree that shows phylogeny at the highest level it shows the the three domains of life the archaeobacteria the eu bacteria and the eukaryotes and you can see within the eukaryotes the multicellular organisms that we're most familiar with the plants the animals and the fungi are just three branches on that tree and any phylogenetic tree what we're looking at is the branching pattern we're trying to find out which organisms are most closely related to which other organisms and what we mean by that is who most recently shared a common ancestor this is a figure from your textbook if you look at the the trees in the top row you'll see that these are different ways of drawing the same tree we can draw it with rectangular branches or forked branches we can have the root of the tree at the top at the bottom or left or right it doesn't matter it just depends on what we're trying to show but the important thing is that there is a a recent common ancestor between b and c here or here or here here that is more recent than the common ancestor of a b and c and so we would say that b and c are each other's nearest relatives this is analogous to uh for example your relatives in your own family your closest relatives would be your brothers and sisters and you share a near common ancestor your parents with your brothers and sisters your first cousins you share a more distant common ancestor and that would be your grandparents second cousins you would share great grandparents third cousins you would sure great great grandparents as you get more distantly related common ancestors your relatives become more distantly related and as we go forward in the tree as we go from the root of the tree forward in time for example in this tree this direction shows uh time moving forward now very often we don't put any scale on this we don't show it in millions of years but we can do that if we wish or we can show the geological time scale but the most important aspect of a phylogenetic tree is to show the sequence of the branching now if you look at the bottom row which i will enlarge here you'll see three different trees here and these trees look very different but really they're not these trees all have what we call the same topology all of these show that b and c whatever b and c are share a more recent common ancestor with each other than they do with a so no matter how we draw that all of these are showing exactly the same thing and these trees are exactly equivalent they're not different at all all we're really doing here is rotating the branches along an axis and if you look at those trees carefully you'll see that the branching pattern is is exactly identical now if i go back to the previous tree you'll see some other examples of trees that are not equivalent here a and c share a more recent common ancestor than they do with b here a and b share a more recent common ancestor than they do with c so systematics is the inference of phylogeny and we base that on a study of characters and these characters or traits can be morphological characters physical characters what the organisms look like it can be genetic characters in the dna can be biochemical something in the proteins it could even be a behavioral character now there's an important distinction in systematics between a character and a character state a character is a given trait a character state is a form of a character so for example if character is the color of the wings character states would be blue or red if the character is height the character state might be tall medium and short if the character is a nucleotide in a particular sequence in the dna the character states would be g a t or c now character states can either be primitive or derived and again whether the character state is primitive or derived is very important in the process of elucidating phylogeny a primitive state is ancestral this is the character state of the ancestor of the group that we're trying to understand a derived character state is something new something after some evolutionary change and so it's very important when we do systematics that we distinguish between primitive and derived character states because it's derived character states that will help us understand phylogeny so as an example character is the skin covering that is produced from the epidermis we have two different states here we have scales and we have feathers uh hair might be a third state but the organisms that we're looking at have these two character states which one of these is primitive do you think the scales or the feathers now what what we mean by primitive is in the ancestor of these two organisms did that ancestor have scales or feathers as their epidermal skin covering and if you said scales you are correct the primitive character state in the common ancestor of these two organisms was scales scales is the primitive character state feathers was something new something that was derived in the ancestor of the birds this is a new uh evolutionary novelty within that group and so when we see that these organisms have this shared derived character state something new and something that's different from the ancestor that is evidence that they share a common ancestor now there's some important terminology in systematics plesiomorphic or a plesiomorphy is a primitive character state so the word plesiomorphic simply means per uh primitive apomorphic means derived something new a derived character state is called an apomorphy or it's called an apomorphic character and further a synapomorphy is a shared derived state and an ought apomorphy is a unique derived state something that's only found in one organism or one group of organisms that we're looking at and it's the shared derived character states the synapomorphies that are going to be very important when we begin to elucidate phylogeny another term that you need to be familiar with is a clade and a clade is all of the organisms that are descended from a common ancestor and clades by definition are monophyletic groups a monophyletic taxon includes the common ancestor in all of its descendants so it is a clade now here we're talking about a taxon and remember a taxon is something that humans do this is this is classification humans have come along and decided that organisms b c and d are going to be in a taxon we're going to classify them together so regardless of what the phylogeny might be if we say that b c and d are part of a named taxon a family or an order or whatever with a particular name if this taxon includes the common ancestor and all of its descendants then we could call that monophyletic and it represents a clade a paraphyletic taxon includes the common ancestor which would be right here and some but not all of the descendants so if our taxon includes b and c but not d this is a paraphyletic taxon it includes only some of the descendants of the common ancestor and this is problematic in modern taxonomy because we want all of our taxa to represent clades to represent monophyletic groups in other words to reflect the actual phylogeny the actual relationships among the organisms and there are a number of examples of taxa that we traditionally recognize that are not monophyletic that are not clades that are rather paraphyletic for example reptiles as we commonly understand the the term traditionally understood reptiles includes turtles lizards snakes crocodilians but birds which are part of the same clade are traditionally not included in the class reptilia and so the reptilia as commonly understood is paraphyletic there are two ways we can solve that problem one is that we can include the birds within the class reptilia or we can simply not recognize a class reptilian another term is a polyphyletic taxon and a polyphyletic taxon includes organisms really that are completely unrelated and does not include the common ancestors so if our taxon in this case includes a c and d but not b and not the common ancestor of a c and d we would say that this taxon represented in green is polyphyletic and that also is not a clade