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Phylogenetics Phylogenetics Phylogenetics Phylogenetics Phylogenetics Phylogenetics Phylogenetics is the estimation of the Phylogenetics is the estimation of the “tree” through “time” “tree” through “time” knowing only the “leaves” Phylogenetics Phylogenetics However, the “leaves” are scattered over “space”. Some Additionally, many related “leaves” diverge in “form”, areas have related “leaves”, others have unrelated “leaves”. while other unrelated “leaves” converge in “form”. Thus, Thus, phylogenetics is compounded by issues of both “time” phylogenetics is compounded by issues of “time” and and “space”. “space” and “form”. 1 Phylogenetics Phylogenetics In natural and phylogenetic systems of classification, characters What characters are selected or even considered, has been very are selected a posteriori for their value in correlating with other subjective. Consider Cronquist and Dalghren with mustard oil characters to form hierarchical structure of groups families . Phylogenetics Phylogenetics These first phylogenetic classifications were “phyletic” - In the 1960s, two main groups of systematists became involving a subjective selection of characters for classification dissatisfied with the phyletic approach and developed more objective methods: phenetic and cladistic 2 Phylogenetics Phenetics vs. Cladistics With the rise of molecular phylogenetics in the 1980s, additional approaches are now invoked (ML, Bayesian) - a continuum of models are now seen • Phenetics uses “overall • Cladistics uses only similarity” - all characters “phylogenetically used (“distance” approaches) informative” characters • species similarity (or • derived state is shared differences) often scaled by at least 2 but not all from 0 to 1 taxa - “shared derived character states” Phenetics Phenetics UPGMA cluster analysis Data Matrix Data Matrix taxa • convert data matrix into characters pair-wise matrix based on sympetaly bicarpellate apocarpy epipetaly trees epigyny poll. beetle tepals heterostyly states vessels overall similarity 1. Magnolia + + - - + - + + - - 1. Magnolia + + - - + - + + - - 2. Nymphaea - + - - - - + + - - 2. Nymphaea - + - - - - + + - - 3. Rosa + + - - - - - - - - 3. Rosa + + - - - - - - - - 4. Primula + - + + - - - - - + 4. Primula + - + + - - - - - + 5. Gentiana + - + + - - - - + - 5. Gentiana + - + + - - - - + - 6. Aster + - + + - + - - + - 6. Aster + - + + - + - - + - 3 Phenetics Phenetics UPGMA cluster analysis UPGMA cluster analysis • convert data matrix into • reduce overall similarity pair-wise matrix based on matrix by clustering together overall similarity Gentiana and Aster and recalculate similarity values • identify most similar pair of taxa and cluster them • identify most similar pair of taxa and cluster them Magnolia Nymphaea Aster Gentiana 90% 80% Phenetics Phenetics UPGMA cluster analysis UPGMA cluster analysis • reduce overall similarity • cluster together Gentiana, matrix by clustering together Aster, and Primula and Magnolia and Nymphaea and recalculate values recalculate similarity values • identify most similar pair of • identify most similar pair of taxa and cluster them taxa and cluster them Nymphaea Aster Magnolia Gentiana Rosa Primula 75% 70% 4 Phenetics Phenetics UPGMA cluster analysis • many different methods based on similarity or differences (including multiple components, ordination, etc.) • cluster together Magnolia, Nymphaea, and Rosa and • in lab you will be using UPGMA & Neighbor-joining recalculate values using a computer program PAUP • cluster the two remaining larger groups at 42.5% to make final phenogram Cladistics Cladistics How do you analyze this same data based on cladistics - “shared Issue #1- How do you determine what is derived? derived character states”? vessels apocarpy sympetaly epipetaly trees epigyny poll. beetle tepals bicarpellate heterostyly vessels apocarpy sympetaly epipetaly trees epigyny poll. beetle tepals bicarpellate heterostyly 1. Magnolia + + - - + - + + - - 1. Magnolia + + - - + - + + - - 2. Nymphaea - + - - - - + + - - 2. Nymphaea - + - - - - + + - - 3. Rosa + + - - - - - - - - 3. Rosa + + - - - - - - - - 4. Primula + - + + - - - - - + 4. Primula + - + + - - - - - + 5. Gentiana + - + + - - - - + - 5. Gentiana + - + + - - - - + - 6. Aster + - + + - + - - + - 6. Aster + - + + - + - - + - 5 Cladistics Cladistics Issue #1- ordering or polarizing character states (primitive or derived) Issue #1- ordering or polarizing character states (primitive or derived) vessels (+) → no vessels (-) OR eterostyly vessels noapocarpy vesselssympetaly (epipetaly -) → trees vesselsepigyny (+)poll. beetle tepals bicarpellate 1. Magnolia + + - - + - + + - - 2. Nymphaea - + • -can be- subjective- - + + - - 3. Rosa + + • -fossil- record- - - - - - 4. Primula + - • +development,+ - ontogeny- - - - + 5. Gentiana + - • +look +at groups- most- closely- - related+ - 6. Aster + - to+ your+ group- of +interest- (outgroup- + ) - Cladistics Cladistics Issue #1- ordering or polarizing character states (primitive or derived) Issue #1- ordering or polarizing character states (primitive or derived) plesiomorph - primitive state apomorph - derived state Blue flowers = synapomorph - shared derived state sister group - use outgroups ? ? ? 6 Cladistics Cladistics Add in Amborella as sister outgroup to rest of angiosperms Convert data matrix to “0” “ ” & 1 sympetaly bicarpellate heterostyly apocarpy epipetaly trees epigyny poll. beetle tepals vessels Amborella - + - - + - + + - - vessels apocarpy sympetaly epipetaly trees epigyny poll. beetle tepals bicarpellate heterostyly 1. Magnolia + + - - + - + + - - 1. Magnolia + + - - + - + + - - 2. Nymphaea - + - - - - + + - - 2. Nymphaea - + - - - - + + - - 3. Rosa + + - - - - - - - - 3. Rosa + + - - - - - - - - 4. Primula + - + + - - - - - + 4. Primula + - + + - - - - - + 5. Gentiana + - + + - - - - + - 5. Gentiana + - + + - - - - + - 6. Aster + - + + - + - - + - 6. Aster + - + + - + - - + - e.g., “-” to “0” and “+” to “1” Cladistics Cladistics Convert data Convert data matrix to “0” matrix to “0” “ ” “ ” & 1 sympetaly bicarpellate heterostyly & 1 sympetaly bicarpellate heterostyly apocarpy epipetaly trees epigyny poll. beetle tepals apocarpy epipetaly trees epigyny poll. beetle tepals vessels vessels Amborella 0 1 0 0 1 0 1 1 0 0 Amborella - + - - + - + + - - 1. Magnolia 1 1 0 0 1 0 1 1 0 0 1. Magnolia + + - - + - + + - - 2. Nymphaea 0 1 0 0 0 0 1 1 0 0 2. Nymphaea - + - - - - + + - - 3. Rosa 1 1 0 0 0 0 0 0 0 0 3. Rosa + + - - - - - - - - 4. Primula 1 0 1 1 0 0 0 0 0 1 4. Primula + - + + - - - - - + 5. Gentiana 1 0 1 1 0 0 0 0 1 0 5. Gentiana + - + + - - - - + - 6. Aster 1 0 1 1 0 1 0 0 1 0 6. Aster + - + + - + - - + - e.g., “-” to “0” and “+” to “1” e.g., Amborella state (either “-” or “+”) to “0” 7 Cladistics - Cladistics - - - other other - - - - - - - - - - - - Primitive 0 Primitive 0 - - - - Derived 1 Derived 1 Tepals Tepals sepals peals + Tepals sepals peals + No vessels vessels Polypetaly sympetaly Free stamens epipetaly Trees herbs Hypogyny epigyny beetle poll. poll. carpels Various bicarpellate Homostyly heterostyly No vessels vessels Polypetaly sympetaly Free stamens epipetaly Trees herbs Hypogyny epigyny beetle poll. poll. carpels Various bicarpellate Homostyly heterostyly Apocarpy syncarpy Apocarpy syncarpy Amborella 0 0 0 0 0 0 0 0 0 0 Amborella 0 0 0 0 0 0 0 0 0 0 1. Magnolia 1 0 0 0 0 0 0 0 0 0 1. Magnolia 1 0 0 0 0 0 0 0 0 0 2. Nymphaea 0 0 0 0 1 0 0 0 0 0 2. Nymphaea 0 0 0 0 1 0 0 0 0 0 3. Rosa 1 0 0 0 1 0 1 1 0 0 3. Rosa 1 0 0 0 1 0 1 1 0 0 4. Primula 1 1 1 1 1 0 1 1 0 1 4. Primula 1 1 1 1 1 0 1 1 0 1 5. Gentiana 1 1 1 1 1 0 1 1 1 0 5. Gentiana 1 1 1 1 1 0 1 1 1 0 6. Aster 1 1 1 1 1 1 1 1 1 0 6. Aster 1 1 1 1 1 1 1 1 1 0 e.g., Amborella state (either “-” or “+”) to “0” “shared derived” character states Cladistics - Cladistics - other - - - - - - Issue #2 - how do you select the “best” tree? Note: 2 - uniformative - • with 3 ingroup species and one outgroup (*), there are characters Tepals Tepals sepals peals + No vessels vessels Polypetaly sympetaly Free stamens epipetaly Trees herbs Hypogyny epigyny beetle poll. poll. carpels Various bicarpellate Homostyly heterostyly Apocarpy syncarpy 3 trees possible Amborella 0 0 0 0 0 0 0 0 0 0 1. Magnolia 1 0 0 0 0 0 0 0 0 0 * 1 2 3 * 2 1 3 * 3 1 2 2. Nymphaea 0 0 0 0 1 0 0 0 0 0 3. Rosa 1 0 0 0 1 0 1 1 0 0 4. Primula 1 1 1 1 1 0 1 1 0 1 5. Gentiana 1 1 1 1 1 0 1 1 1 0 6. Aster 1 1 1 1 1 1 1 1 1 0 not “shared derived” character states 8 Cladistics Cladistics Issue #2 - how do you select the “best” tree? Issue #2 - how do you select the “best” tree? • estimation procedure, however, usually involves vast • estimation procedure, however, usually involves vast number of possible “trees” number of possible “trees” • this study with 7 taxa - there are 10,395 possible tree topologies • for a study with 50 taxa - there are 3 X 10 74 possible 79 • examining all trees is possible here, but with larger trees or approaching number of atoms in universe (10 )! numbers of taxa (as the 14 taxa used in lab this week – • landmark paper in 1993 for angiosperms had 499 taxa - 7.9 trillion trees!) a heuristic approach is required astronomical number of possible trees! >> 10 1000 • for a study of the Tree of Life - 10 70,000,000 Cladistics Cladistics Issue #2 - how do you select the “best” tree? Issue #2 - how do you select the “best” tree? • the “best” tree is dependent on assumption of an • in the context of evolution, maximum parsimony = optimality criterion: e.g., likelihood, parsimony choosing the tree that requires the fewest number of evolutionary changes (apomorphies) •
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