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Fixations along phylogenetic lineages

Fixations along phylogenetic lineages. Phylogenetic reconstruction: a simplification of the evolutionary process. Cladists and pheneticists. Anatomy of a phylogenetic tree. Edges and nodes. Depictions of phylogenetic trees. Slanted Cladogram. Rectangular Cladogram. Phylogram. Circle tree.

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Fixations along phylogenetic lineages

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  1. Fixations along phylogenetic lineages

  2. Phylogenetic reconstruction: a simplification of the evolutionary process

  3. Cladists and pheneticists

  4. Anatomy of a phylogenetic tree

  5. Edges and nodes

  6. Depictions of phylogenetic trees Slanted Cladogram Rectangular Cladogram Phylogram

  7. Circle tree Unrooted cladogram Unrooted phylogram

  8. Depicting trees with branch lengths Ultrametric tree Unconstrained tree Time Time Present

  9. Branch lengths and phylogenetic trees Unequal branch lengths Ultrametric trees

  10. Trees with and without branch lengths

  11. A character matrix

  12. Counting the number of steps on a phylogenetic tree

  13. Sites 4 and 6 on the same tree

  14. Rooted and unrooted trees

  15. Convergence and homoplasy in mantids

  16. “One should not increase, beyond what is necessary, the number of entities required to explain anything.” Parsimony, Hennig and Occam’s razor William of Ockham (ca. 1285-1349) Synapomorphies designate clades… But what if synapomorphies are reversed? Willi Hennig

  17. The number of rooted, labelled, bifurcating trees

  18. Informative and uninformative site patterns

  19. Long-branch attraction p, q probability of observing a change between nodes or From node to tip

  20. Parsimony is consistent when p2 < q(1-q) The “Felsenstein zone”

  21. Parsimony: pros and cons Pros: Simple and fast (sometimes) Cons: Depends on a very simple ‘model’ of substitution Does not estimate branch lengths well Susceptible to long-branch attraction

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