Lab+5.+Phylogeny 2

Biology 106: Your Name:

Biology 106 Lab 5 Because ancestral traits are shared by all organisms in the tree, they provide little information about closest relatives within the tree. On the other hand, derived traits possessed by all members of a group provide a lot of information about closest relatives because they reflect a shared common ancestry in which those characters first evolved. Members of no other group will have this shared derived character. Therefore, during the process of making cladograms, we search for shared-derived characters that can be used to hypothesize shared ancestral relationships and designate monophyletic groups, and particularly sister clades. Here is another example of a group of organisms organized into a cladogram. In this cladogram shared traits are shown in between nodes. For example, turtles, leopards and frogs all have 4 walking legs but none of the other organisms do, therefore the label for that trait is at the point where this taxon separated from the common ancestry with the other taxa. Notice also that the frog, turtle and leopard all share the hinged jaw characteristic, along with the bass. All taxa appearing after that trait first evolved in the common ancestor, will have inherited that characteristic. In order to determine which character state is ancestral (arising first) and which are derived (appearing later) during the evolutionary journey of a group, you can use an outgroup. An outgroup is a group that

Biology 106 Lab 5 Q. Looking at the character matrix, what is the character state for four walking legs for the Lamprey? Highlight one: No legs (ancestral) / 4 legs (derived) Part 2: Practicing constructing phylogenetic trees, and ultimately answering evolutionary questions using them. Open the following website – the link is also in your lab folder for today. ● Each tree building exercise is a puzzle in logic. https://www.pbs.org/wgbh/nova/labs/lab/evolution/ Instructions: ● Read the opening statement. ● Click “Play Game” (you can use the Guest Access) and get started. ● Complete Missions 1 and 2 (you can do the next missions if you’d like!). Use the magnifying glass to get insight into who has which traits. ● For each tree you build, you will know you got it right when ... o ... all of the circles above the species are filled in. o ... a sidebar appears with a question for you to answer. ● When you are finished, take a screenshot of your screen indicating successful completion of all missions! Attach it below Enjoy! Add your screenshot here:

Biology 106 Lab 5

Biology 106 Lab 5 Keep going for Part 3

Biology 106 Lab 5 Part 3: Making Cladograms Using Character Matrices Making cladograms and character matrices Now that you have had lots of practice, your next task is to make a cladogram for a group of invented but evolutionarily related organisms called caminalcules. To make a cladogram you must first construct a character matrix similar to the example above. But the example above is very simple because the organisms used are very different. In the real world of phylogenetics, things are more complicated. Choosing characters It is important to understand how to choose useful taxonomic characters to construct a character matrix. The definition of a character for taxonomic purposes is “a feature of an organism that is divisible into at least 2 conditions”. Once you start to look at the organisms you will notice that some have “feet”, but others have rear appendages that look more like flippers, and the types of “feet” are different. So the presence of a rear appendage could be one character, and the two options for the state would either be 0- for absence or 1- presence. But you have to decide how to further subdivide all the various rear appendages so that each taxon can be classified as either a 0 or 1 for any particular character. Homology and homoplasy When examining a group of organisms, if there is a character state that two taxa share, then the most logical assumption of phylogenetics is that that state evolved before the separation of the two taxa. For example, we have hair and dogs have hair. Thus, the inference about the evolutionary relationship between humans and dogs is that we share a common ancestor that had hair. This example - hair in humans and dogs - is called homology . However; this is not always the case. Sometimes an adaptation to the environment can arise independently, more than once. For example, insects, bats and birds all have wings, but this character state has arisen independently in these three different lineages. This is called homoplasy . This type of homoplasy is known as parallel or convergent evolution. Occasionally another type of homoplasy arises in which a particular trait reverses back to a more ancestral state, this is simply know as reversa l. Exercise 1: Observe the Caminalcules and create a character matrix. ● Find the separate document with the fictional caminalcules. Print it out and be prepared to cut the organisms out to make moveable cards. ● There are many different characters in this group of organisms. Take a few minutes to observe the variety, before you start to make your character matrix. ● Keep the outgroup taxon to one side. This represents the most ancestral state of these organisms and it will be the first branch of your cladogram.

Biology 106 Lab 5 Before moving on, show your work to your TA. TA check-in 3 _________ Exercise 2: Construct your Caminalcule cladogram Use your character matrix to construct a cladogram of the Caminalcules. Remember : When you construct your cladogram of the Caminalcules, it may take some time to organize the organisms into the most logical arrangement. It will look more complex than the examples earlier on in this lab, and you may observe an example of homoplasy. In the space below, draw a draft of your cladogram – you can use the draw tool in Word, sketch on a piece of paper and then paste a picture in below, etc . ● Include tickmarks at each point a character is used to divide the lineages (in a similar way to the lancelet-leopard cladogram earlier). ● At each split/ node of the cladogram there can only be 2 options. Outgroup

Biology 106 Lab 5

Biology 106 Lab 5 ● Indicate a different paraphyletic group by positioning the GREEN box and label to include all members belonging to this type of group on the diagram above. ● Name the animals included in the paraphyletic group you drew: Another possible way to group organisms is to group organisms together who do not share a common ancestry. These groupings use non-evolutionary traits to define them. There is a polyphyletic group shown on the tree. You can see they share traits in common which have evolved independently. In this case the cetaceans and seals are both mammals that live in water and have reduced limbs, but who did not inherit these shared traits from a common ancestor – instead they evolved them independently of each other. ● Indicate this polyphyletic group by positioning the BLUE box and label to better this type of group on the diagram above. Research using modern phylogenetic tools, such as DNA sequencing, is revealing that many traditionally recognized taxonomic groups are either para- or polyphyletic. This has led to extensive reorganization and renaming of taxa in order to standardize the practice of only recognizing “natural” groups, i.e. monophyletic groups.

Biology 106 Lab 5 LAB 6: Phylogeny EXIT QUESTIONS Online Phylogeny Interactive [10 pts] _____ Use this phylogenetic tree to answer the questions below: 1. Interpret the phylogenetic tree shown below to answer the following questions: [½ pt each = 3½ pts total] a. Which node represents the most recent common ancestor of B and C ? Highlight the one: Node 1 / Node 2 / Node 3 / Node 4 / Node 5 / Node 6 b. Which node represents the most recent common ancestor of A and B ? Highlight the one: Node 1 / Node 2 / Node 3 / Node 4 / Node 5 / Node 6 c. Which species is the outgroup? Highlight the one: A B C D E F G d. Which species have trait 1? Highlight all who do: A B C D E F G e. Which species have trait 2? Highlight all who do: A B C D E F G f. Which species is/are most closely related to E? ______________ g. Which species is/are most closely related to F? ______________ 2. Impose a taxonomy on the tree above. Position boxes and labels below to indicate different possible groupings on this tree. Any correct answer will earn you points. [1½ pts] Trait 2 Trait 1 Node 1 Node 5 Node 4 Node 3 Node 2 Node 6 You are now ready for the Exit Questions. Monophyletic group Polyphyletic group Paraphyletic group