Cladis'c method of phylogene'c reconstruc'on This method classifies species of organisms into hierarchical monophyle6c groups focuses on shared derived characters (Synapomorphies) How to produce a phylogene6c tree? Establish which characters are primi6ve and which ones are derived How: - Designate an out group Outgroup: an organism or taxon that is known to be related to the taxonomic group in ques6on but is not contained within that group (usually, an outgroup is a member of the next higher taxonomic group that includes the group under study) - Characters of interest that are shared with the outgroup are then classified as primi6ve, while those not shared with the outgroup are considered derived Organisms are ranked on a con6nuum of how many derived character states they share. Organisms sharing similar numbers of derived character traits will be grouped together on the Cladogram.
Derived traits table Complete a derived traits table. Put the taxa and traits in the table and score the table by using the symbols + (indicating the trait is present) and (indicating the trait is absent) Derived trait Taxon Jaws Lungs Claws or Nails Feathers Fur Mammary glands Hagfish (OG) - - - - - - Perch Salamander Lizard Pigeon Mouse Chimpanzee + - - - - - + + - - - - + + + - - - + + + + - - + + + - + + + + + - + +
Similarity matrix Completing a similarity matrix will allow you to determine which organisms are most closely related to each other Simply count up the number of derive characteristics a given pair of species or taxa share. Taxa sharing the same number of derived characters should be sister groups and organisms sharing the least amount of characters with other organisms should branch off the tree first Taxon Taxon Hagfish (OG) Perch Salamander Lizard Pigeon Mouse Chimpanzee Hagfish (OG) X 0 0 0 0 0 0 Perch X 1 1 1 1 1 Salamander X 2 2 2 2 Lizard X 3 3 3 Pigeon X 3 3 Mouse X 5 Chimpanzee X
Cladogram The last task is to place the morphological characteristics on the Cladogram in the order in which they evolved Finally use the principle of parsimony to construct your tree. Parsimony states that the tree representing the least amount of evolutionary steps is most likely correct Hagfish Perch Salamander Pigeon Lizard Mouse Chimpanzee Feathers Fur Mammary glands Lungs Claws or nails Jaws
Summary: making a Cladogram 1. Find the traits that the outgroup does not present 2. Score the traits table 3. Make a similarity matrix 4. Remember that those organisms sharing less number of traits branch off first and those sharing many traits branch off last 5. Map the traits using the principle of parsimony
Animals that we are going to see Snail Horseshoe crab Sponge Urchin Crab Sea star Hermit crab Coral Polychaete Anemone
Some characters that can be used Skeletal structure (- no obvious skeletal structure; + exoskeleton obvious; other skeletal structures?) Eyes (- no evident optical ability; + optical ability) Radial symmetry (- no symmetry or other symmetry; + radial symmetry) Bilateral symmetry (- no symmetry or radial symmetry; + bilateral symmetry) Cephalization/specialized sensory structures (- no evident cephalic structures; + cephalic structures present) Movable mouthparts (- oral area (cavity) unable to move or masticate; + oral area able to move or masticate) Means of movement (- inability to move in coordinated purposeful fashion; + able to move in coordinated and purposeful fashion) Eyes stalks (- no eyes or eyes not on stalks; + eyes present on stalks) Jointed appendages (- appendages lacking or not jointed; + appendages jointed) Usage of a non-self-secreted structure (- not living in a structure or living in a selfsecreted structure; + living in a non-self-secreted structure)
In the style of a scientific paper Report #1 Sections that should be included: 1) Introduction 2) Materials and Methods 3) Results 4) Discussion Refer to the Thorne and Carpenter (1992) paper for useful tips on content and style This report will be graded for clarity, content in each section, strength with which you support your tree using the evidence we have, and the substance of your discussion on alternative parsimonious trees and on the comparison between your tree and the accepted cladogram. You will not be graded on the particular structure of your own tree, so use this as an opportunity to make a case for your tree being the accepted tree. The report should be around 3 pages long (not including figures) Due date: October 28 th at the beginning of lab (penalization for tardiness)
Report #1 (Cont d) Introduction: This section should include a brief background to phylogenetic analysis: i.e. what is it and what can it be used to do, and a short discussion of the different phylogenetic techniques and their strengths/weaknesses. Talk about the goal of the lab as it relates to your discussion of phylogenetic techniques. Materials and Methods: This section should include the organisms studied, the character state definitions you used, and why you chose these characters. You should discuss how one determines what is primitive and derived, and how you scored your cladistic table. Consult Thorne and Carpenter (1992) for help on this, and notice the similarities between their binary coding system (0 s and 1 s) and our polar coding system (- s and + s). Be sure to include the methodology for building your cladogram, mention why the principle of parsimony is important when one constructs a cladogram. Results and Discussion: In this section you should present the tree you came up with. You should also include your derived traits table and similarity matrix but these should be at the end of the paper and if needed referenced in the text (see Thorne and Carpenter, 1992). Note that the tree can also be at the end of the paper but remember to reference it adequately in the text. Figures should have a descriptive title and/or a caption explaining what is going on in them. Tables should also have a title and any comments that will help to clarify the reading of the table. It is here where you should discuss the relationships between the organisms on your cladogram. You should make a case for your conclusions using character states and the principle of parsimony as evidence. You should also consider whether there may be more than one most parsimonious cladogram, and briefly discuss the alternatives. Comment on characters you might use in the future to improve your tree. Finally, discuss the implications of your cladogram as it compares to the accepted cladograms (RNA and morphology based) for all animals. References: If you want you can add references but make sure that they are all in the same format and properly cited in the text.