1 / 94

Phylogenetic Reconstruction: Parsimony

Phylogenetic Reconstruction: Parsimony. Anders Gorm Pedersen gorm@cbs.dtu.dk. Trees: terminology. Trees: terminology. Trees: terminology. “Reptilia” is a non-monophyletic group. Trees: representations. Three different representations of the same tree-topology. Trees: rooted vs. unrooted.

metta
Download Presentation

Phylogenetic Reconstruction: Parsimony

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Phylogenetic Reconstruction: Parsimony Anders Gorm Pedersen gorm@cbs.dtu.dk

  2. Trees: terminology

  3. Trees: terminology

  4. Trees: terminology “Reptilia” is a non-monophyletic group

  5. Trees: representations Three different representations of the same tree-topology

  6. Trees: rooted vs. unrooted • A rooted tree has a single node (the root) that represents a point in time that is earlier than any other node in the tree. • A rooted tree has directionality (nodes can be ordered in terms of “earlier” or “later”). • In the rooted tree, distance between two nodes is represented along the time-axis only (the second axis just helps spread out the leafs) Early Late

  7. Trees: rooted vs. unrooted • A rooted tree has a single node (the root) that represents a point in time that is earlier than any other node in the tree. • A rooted tree has directionality (nodes can be ordered in terms of “earlier” or “later”). • In the rooted tree, distance between two nodes is represented along the time-axis only (the second axis just helps spread out the leafs) Early Late

  8. Trees: rooted vs. unrooted • A rooted tree has a single node (the root) that represents a point in time that is earlier than any other node in the tree. • A rooted tree has directionality (nodes can be ordered in terms of “earlier” or “later”). • In the rooted tree, distance between two nodes is represented along the time-axis only (the second axis just helps spread out the leafs) Early Late

  9. Trees: rooted vs. unrooted • In unrooted trees there is no directionality: we do not know if a node is earlier or later than another node • Distance along branches directly represents node distance

  10. Trees: rooted vs. unrooted • In unrooted trees there is no directionality: we do not know if a node is earlier or later than another node • Distance along branches directly represents node distance

  11. Reconstructing a tree using non-contemporaneous data

  12. Cladistics: group organisms based on shared, derived characters (“synapomorphies”)

  13. Homology: limb structure Homology: any similarity between characters that is due to their shared ancestry

  14. Homology vs. Homoplasy X X X X Homology: similar traits inherited from a common ancestor Homoplasy: similar traits are not directly caused by common ancestry (convergent evolution).

  15. Homoplasy: wings

  16. A A G C G T T G G G C A A B A G C G T T T G G C A A C A G C T T T G T G C A A D A G C T T T T T G C A A 1 2 3 DNA and protein sequences Homologous characters inferred from alignment. Other molecular data: absence/presence of restriction sites, DNA hybridization data, antibody cross-reactivity, etc. (but losing importance due to cheap, efficient sequencing). Molecular phylogeny

  17. Morphology vs. molecular data African white-backed vulture (old world vulture) Andean condor (new world vulture) New and old world vultures seem to be closely related based on morphology. Molecular data indicates that old world vultures are related to birds of prey (falcons, hawks, etc.) while new world vultures are more closely related to storks Similar features presumably the result of convergent evolution

  18. Phylogenetic reconstruction

  19. Phylogenetic reconstruction

  20. Parsimony criterion: choose simplest hypothesis

  21. Parsimonious reconstruction A G.. B G.. C T.. D T..

  22. Parsimonious reconstruction A G.. B G.. C T.. D T.. G.. T.. T..

  23. Parsimonious reconstruction A G.. B G.. C T.. D T.. G.. T.. T..

  24. Alternative tree: homoplasy A G.. B G.. C T.. D T.. G.. T.. T.. A G.. C T.. D T.. B G..

  25. Alternative tree: homoplasy A G.. B G.. C T.. D T.. G.. T.. T.. A G.. C T.. D T.. B G.. T.. T.. T..

  26. Alternative tree: homoplasy A G.. B G.. C T.. D T.. G.. T.. T.. A G.. D T.. C T.. B G.. T.. T.. T..

  27. One character: Assumption of no homoplasy is equivalent to finding shortest tree A G... B G... C T... D T... G.. T.. T.. A G.. C T.. D T.. B G.. T.. T.. T..

  28. Phylogenetic reconstruction A ..G B ..G C ..T D ..T ..G ..T ..T

  29. Phylogenetic reconstruction A G.G B G.G C T.T D T.T G.G T.T T.T

  30. Phylogenetic reconstruction: conflicts A B C D A .G. C .G. B .T. D .T. .G. .T. .T.

  31. Phylogenetic reconstruction: conflicts A .G. B .T. C .G. D .T. .T. .T. .T. A C B D

  32. Phylogenetic reconstruction: conflicts A B C D A G.G C T.T B G.G D T.T T.T T.T T.T

  33. Several characters: choose shortest tree(equivalent to fewer assumptions of homoplasy) A GGG B GTG C TGT D TTT GTG Total length of tree: 4 Total length of tree: 5 TTT TTT A GGG C TGT B GTG D TTT TGT TTT TTT

  34. Maximum Parsimony • Maximum parsimony: the best tree is the shortest tree (the tree requiring the smallest number of mutational events) • This corresponds to the tree that implies the least amount of homoplasy (convergent evolution, reversals) • How do we find the best tree for a given data set?

  35. Maximum Parsimony: first approach • Construct list of all possible trees for data set • For each tree: determine length, add to list of lengths • When finished: select shortest tree from list • If several trees have the same length, then they are equally good (equally parsimonious)

  36. Maximum Parsimony: problems • We need algorithm for constructing list of all possible trees • We need algorithm for determining length of given tree • Should all mutational events have same cost?

  37. Constructing list of all possible unrooted trees • Construct unrooted tree from first three taxa. There is only one way of doing this • Starting from (1), construct the three possible derived trees by adding taxon 4 to each internal branch • From each of the trees constructed in step (2), construct the five possible derived trees by adding taxon 5 to each internal branch. • Continue until all taxa have been added in all possible locations

  38. Maximum Parsimony: problems • We need algorithm for constructing list of all possible trees  • We need algorithm for determining length of given tree • Should all mutational events have same cost?

  39. Algorithm for determining length of given tree: Fitch C A A G C What is the length of this tree? (How many mutational steps are required?)

  40. Algorithm for determining length of given tree: Fitch • Root the tree at an arbitrary internal node (or internal branch) • Visit an internal node x for which no state set has been defined, but where the state sets of x’s immediate descendants (y,z) have been defined. • If the state sets of y,z have common states, then assign these to x. If there are no common states, then assign the union of y,z to x, and increase tree length by one. • Repeat until all internal nodes have been visited. Note length of current tree.

  41. Algorithm for determining length of given tree: Fitch C A A G C

  42. Algorithm for determining length of given tree: Fitch C A A  G C

  43. Algorithm for determining length of given tree: Fitch A C C A G 

  44. Algorithm for determining length of given tree: Fitch C A C A G

  45. Algorithm for determining length of given tree: Fitch C A C A G Length so far = 0

  46. Algorithm for determining length of given tree: Fitch C A C A G {C, A} Length so far = 1

  47. Algorithm for determining length of given tree: Fitch C A C A G {A, G} {C, A} Length so far = 2

  48. Algorithm for determining length of given tree: Fitch C A C A G {A, G} {A, C} {A, C, G} Length so far = 3

  49. Algorithm for determining length of given tree: Fitch C A C A G {A, G} {A, C} {A, C, G} Length so far = 3 {A, C}

  50. Algorithm for determining length of given tree: Fitch C A C A G {A, G} {A, C} {A, C, G} Length of tree = 3 {A, C}

More Related