W4L1 Inferring phylogeny.pdf

2 steps 2 steps 2 steps 1 2 3 4 5 outgroup 1 a 1 1 1

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2 steps 2 steps 2 steps 1 2 3 4 5 Outgroup 0 0 0 1 0 A 1 0 1 0 1 B 1 0 1 0 0 C 0 1 1 0 1 On every tree, find the character reconstruction that requires the fewest character state changes Trait 1 on Tree 1 0 1 1 0 1 0 0 1 1 0 0 0 1 1 0 287 1 2 3 4 5 Outgroup 0 0 0 1 0 A 1 0 1 0 1 B 1 0 1 0 0 C 0 1 1 0 1 1 step 2 steps 2 steps Trait 1 - A parsimonious reconstruction of trait 1 onto every tree is shown - What matters is not the reconstruction, but the number of steps - Find the reconstruction with the smallest number of steps (there are algorithms for this, but we’ll do it manually) 0 0 1 0 1 0 0 1 0 1 0 0 1
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1 step 1 2 3 4 5 Outgroup 0 0 0 1 0 A 1 0 1 0 1 B 1 0 1 0 0 C 0 1 1 0 1 1 step 1 step 1 step 1 step 1 step Trait 2 Trait 3 0 1 0 0 0 0 0 1 0 1 0 1 0 1 0 1 0 0 288 2 steps 1 2 3 4 5 Outgroup 0 0 0 1 0 A 1 0 1 0 1 B 1 0 1 0 0 C 0 1 1 0 1 2 steps 1 step Trait 4 Trait 5 1 step p 1 step 1 step 0 1 1 0 0 0 1 0 0 1 0 0 0 1 0 1 0 0 1 0 0 1 289 290 1 2 3 4 5 Outgroup 0 0 0 1 0 A 1 0 1 0 1 B 1 0 1 0 0 C 0 1 1 0 1 2+1+1+1+2 = 7 1+1+1+1+2 = 6 2+1+1+1+1 = 6 Tree Length Trees 2 & 3 are the most parsimonious
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# taxa # of trees 4 3 5 15 6 105 7 945 8 10,395 9 135,135 10 2,027,025 11 34,459,425 20 ~221,643,095,476,699,771,875 --- 62 6.664 x 10 98 63 >10 100 How many rooted trees? 291 # of atoms in the universe: 10 78 – 10 81 ! ! = ( 2 ! 5 ) ! ! ! ! Heuristic algorithms search tree space Heuristic search: a search that is designed to find optimal trees in tree space without considering all possible trees 292 Tree space can have low & high peaks 293 Solution : multiple heuristic searches, in an attempt to find the highest peak (= best tree)
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294 Parsimony chooses the shortest tree as the best hypothesis of relationships Parsimony using DNA ...ACAGGAT... ...ACACGCT... ...GTAAGGT... ...GCACGAC... Same methodology as we did with morphology 1. Consider every tree possible 2. On every tree, find the character reconstruction that requires the fewest character state changes 3. Add up these character state changes for every tree 4. The tree with the smallest sum is the most parsimonious 295 - Why are characters 162, 166, & 167 parsimony informative?
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  • Spring '18
  • MORRIS
  • outgroup, tree making

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