Whenthisstateisalsopresentinamemberoftheingroupthegrou

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Unformatted text preview: tion of mouth Position of eyes on the head Teeth Caudal fin Species (1) (2) (3) (4) (5) (6) (7) (8) (9) SG* Slits Eggs Absent 1 No Dorsal Dorsal Present Round A Operculum Viviparous Present 1 Yes Terminal Dorsal Present Pointed B Operculum Viviparous Present 1 Yes Terminal Dorsal Present Square C Operculum Eggs Present 2 No Terminal Lateral Absent Pointed D Operculum Eggs Present 1 No Terminal Lateral Absent Pointed E Operculum Eggs Absent 1 No Ventral Dorsal Present Round F Operculum Eggs Present 1 No Ventral Dorsal Present Pointed G Operculum Viviparous Present 2 Yes Terminal Dorsal Present Square *Sister group I‐ Polarization Using the Outgroup Comparison In this example, the sister group (SG) will be used for the outgroup comparison. This comparison will enable you to polarize the state of each of the characters that you have found. When a character state is present in the sister group, it is coded "0". When this state is also present in a member of the ingroup (the group studied), it is also coded "0". If a state is different from that observed within the ingroup, it is apomorphic and must be coded "1" (when that character is binary: 0, 1) or "1" or "2" when that character displays three states (0, 1, 2). At the end of your analysis, your matrix should be the following. Table2: Polarized Matrix Characters (1) Species SG A B C D E F G 0 1 1 1 1 1 1 1 (2) (3) (4) (5) (6) (7) (8) (9) 0 1 1 0 0 0 0 1 0 1 1 1 1 0 1 1 0 0 0 1 0 0 0 1 0 1 1 0 0 0 0 1 0 1 1 1 1 2 2 1 0 0 0 1 1 0 0 0 0 0 0 1 1 0 0 0 0 1 2 1 1 0 1 2 65 Lab3 ‐ Vertebrate phylogeny Each new character must be added up to the cladogram from the previous step. This way, the cladogram increases in complexity at each step as well as the resolution of your phylogenetic analysis. II‐ Construction of the Phylogenetic Tree General principle: you will progressively add each character on your cladogram while following three fundamental rules: 1‐ The cladogram must present the distribution of derived character states. 2‐ Species that share the same derived character states must be grouped together (=you create monophyletic groups). 3‐ When several solutions are possible, you must choose the one that implies the fewer number of steps or transformations (=use the principle of parsimony). Step 1. The first hypothetical cladogram (with no resolution) is the following: SG A B C D E F G Cladogram 1: No resolution. Step 2. Then, we start refining the cladogram by progressively adding more characters to it. The choice of the first character to start with is somehow subjective, but as a general rule you should always start with binary characters (those with only 0 or 1 as a value) and characters that appear derived in a large number of species (coded ”1” in the matrix). Such characters define large monophyletic groups. In our example, character #1 indicates that all fish species of the ingroup have an operculum (bone that covers the branchial chamber) w...
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