Outline Review of trees. Coun4ng features. Characterbased - PDF document

1/27/09 CSCI1950‐Z Computa4onal Methods for Biology Lecture 2 Ben Raphael January 26, 2009 hHp://cs.brown.edu/courses/csci1950‐z/ Outline • Review of trees. Coun4ng features. • Character‐based phylogeny – Maximum parsimony – Maximum likelihood 1

1/27/09 Tree Defini4ons tree : A connected acyclic graph G = (V, E). graph : A set V of vertices ( nodes ) and a set E of edges , where each edge ( v i , v j ) connects a pair of vertices. A path in G is a sequence ( v 1 , v 2 , …, v n ) of vertices in V such that ( v i , v i+1 ) are edges in E. A graph is connected provided for every pair v i v j of vertices, there is a path between v i and v j . A cycle is a path with the same starting and ending vertices. A graph is acyclic provided it has no cycles. Tree Defini4ons degree of vertex v is the number of edges incident to v . A phylogenetic tree is a tree with a label for each leaf (vertex of degree one). A binary phylogenetic tree is a phylogenetic tree where every interior (non-leaf) vertex has degree 3; (one parent and two children ). A rooted (*binary) phylogenetic tree is phylogenetic tree with a single designated vertex r (* of degree 2). w is a parent (ancestor) of v provided (v,w) is on path to root. In this case v is a child ( descendant ) of w . 2

1/27/09 Tree Defini4ons tree : A connected acyclic graph G = (V, E). degree of vertex v is the number of edges incident to v . A phylogenetic tree is a tree with a label for each leaf (vertex of degree one). • Leaves represent existing species • Other vertices represent most recent common ancestor. • Length of branches represent evolutionary time. • Root (if present) represents the oldest evolutionary ancestor. Coun4ng and Trees • A tree with n ver4ces has n ‐1 edges. (Proof?) • A rooted binary phylogene4c tree with n leaves has n ‐1 internal ver4ces; and thus 2 n ‐1 total ver4ces. • How many rooted binary phylogene4c trees with n leaves? 3

1/27/09 Character‐based Phylogene4c Tree Reconstruc4on Output Input Op6mal phylogene4c Characters tree Molecular Algorithm Morphological 1. What is character data? 2. What is the criteria for evalua6ng a tree? 3. How do we op6mize this criteria: 1. Over all possible trees? 2. Over a restricted class of trees? Character‐Based Tree Reconstruc4on • Characters may be morphological features # of eyes or legs or the shape of a beak or a fin. • Characters may be nucleo4des of DNA (A, G, C, T) or amino acids (20 leHer alphabet). • Values are called states of character. 2‐state character Gorilla: CCTGTGACGTAACAAACGA Chimpanzee: CCTGTGACGTAGCAAACGA CCTGTGACGTAGCAAACGA Human: Non‐informa4ve character 4

1/27/09 Character‐Based Tree Reconstruc4on GOAL : determine what character strings at internal nodes would best explain the character strings for the n observed species An Example Value1 Value2 Mouth Smile Frown Eyebrows Normal Pointed 5

1/27/09 Character‐Based Tree Reconstruc4on Which tree is beAer? Character‐Based Tree Reconstruc4on Count changes on tree 6

1/27/09 Character‐Based Tree Reconstruc4on Maximum Parsimony : minimize number of changes on edges of tree Maximum Parsimony • Ockham’s razor: “simplest” explana4on for the data • Assumes that observed character differences resulted from the fewest possible muta4ons • Seeks tree with the lowest possible parsimony score , defined sum of cost of all muta4ons found in the tree 7

1/27/09 Character Matrix Given n species, each labeled by m characters. Each character has k possible states . Gorilla: CCTGTGACGTAACAAACGA Chimpanzee: CCTGTGACGTAGCAAACGA Human: CCTGTGACGTAGCAAACGA n x m character matrix Assume that characters in character string are independent. Parsimony Score Gorilla: CCTGTGACGTAACAAACGA Chimpanzee: CCTGTGACGTAGCAAACGA Human: CCTGTGACGTAGCAAACGA Assume that characters in character string are independent. Given character strings S=s 1 …s m and T=t 1 …t m : #changes (S  T) = Σ i d H ( s i , t i ) where d H = Hamming distance d H ( v , w ) = 0 if v=w d H ( v , w ) = 1 otherwise parsimony score of the tree as the sum of the lengths (weights) of the edges 8

1/27/09 Parsimony and Tree Reconstruc4on Maximum Parsimony Two computa4onal sub‐problems: 1. Find the parsimony score for a fixed tree. – Small Parsimony Problem (easy) 2. Find the lowest parsimony score over all trees with n leaves. – Large parsimony problem (hard) 9

1/27/09 Small Parsimony Problem Input: Tree T with each leaf labeled by an m ‐ character string. Output: Labeling of internal ver4ces of the tree T minimizing the parsimony score. Since characters are independent, every leaf is labeled by a single character. Small Parsimony Large Parsimony Problem Problem Input: Input: T : tree with each leaf M : an n x m character labeled by an m ‐character matrix . string. Output: A tree T with: Output: • n leaves labeled by the n Labeling of internal ver4ces rows of matrix M of the tree T minimizing • labeling of the internal the parsimony score. ver4ces of T minimizing the parsimony score over all possible trees and all possible labelings of internal ver4ces 10

1/27/09 Small Parsimony Problem Input: Binary tree T with each leaf labeled by an m ‐character string. Output: Labeling of internal ver4ces of the tree T minimizing the parsimony score. Since characters are independent, every leaf is labeled by a single character. Weighted Small Parsimony Problem More general version of Small Parsimony Problem • Input includes a k x k scoring matrix δ describing the cost of transforming each of k states into another state. • Small Parsimony Problem is special case: δ ij = 0, if i = j , 1, otherwise. 11

1/27/09 Scoring Matrices Weighted Small Small Parsimony Problem Parsimony Problem A T G C A T G C A 0 1 1 1 A 0 3 4 9 T 1 0 1 1 T 3 0 2 4 G 1 1 0 1 G 4 2 0 4 C 1 1 1 0 C 9 4 4 0 Unweighted vs. Weighted Small Parsimony Scoring Matrix: A T G C A 0 1 1 1 T 1 0 1 1 G 1 1 0 1 C 1 1 1 0 Small Parsimony Score: 5 12

1/27/09 Unweighted vs. Weighted Weighted Parsimony Scoring Matrix: A T G C A 0 3 4 9 T 3 0 2 4 G 4 2 0 4 C 9 4 4 0 Weighted Parsimony Score: 22 Weighted Small Parsimony Problem Input: T: tree with each leaf labeled by an m ‐character string from a k ‐leHer alphabet. δ : k x k scoring matrix Output: Labeling of internal ver4ces of the tree T minimizing the weighted parsimony score. 13

1/27/09 Sankoff Algorithm Calculate and keep track of a score for every possible label at each vertex: s t ( v ) = minimum parsimony score of the subtree rooted at vertex v if v has character t s t ( v ) t …. …. Sankoff Algorithm s t ( v ) = minimum parsimony score of the subtree rooted at vertex v if v has character t The score s t ( v ) is based only on scores of its children: s t (parent) = min i { s i ( leo child ) + δ i, t } + min j { s j ( right child ) + δ j, t } t δ i, t δ j, t s i (leo child) s j (right child) 14

1/27/09 Sankoff Algorithm (cont.) • Begin at leaves: – If leaf has the character in ques4on, score is 0 – Else, score is ∞ Sankoff Algorithm (cont.) s t ( v ) = min i { s i ( u ) + δ i, t } + min j { s j ( w ) + δ j, t } s i ( u ) sum δ i, A A 0 0 0 s A ( v ) = 0 s A ( v ) = min i { s i ( u ) + δ i, A } + min j { s j ( w ) + δ j, A } T ∞ 3 ∞ G ∞ 4 ∞ C ∞ 9 ∞ 15

1/27/09 Sankoff Algorithm (cont.) s t ( v ) = min i { s i ( u ) + δ i, t } + min j { s j ( w ) + δ j, t } s j ( u ) sum δ j, A A ∞ 0 ∞ s A ( v ) = min i { s i ( u ) + δ i, A } + s A ( v ) = 0 min j { s j ( w ) + δ j, A } + 9 = 9 T ∞ 3 ∞ G ∞ 4 ∞ C 0 9 9 Sankoff Algorithm (cont.) s t ( v ) = min i { s i ( u ) + δ i, t } + min j { s j ( w ) + δ j, t } Repeat for T, G, and C 16

1/27/09 Sankoff Algorithm (cont.) Repeat for right subtree Sankoff Algorithm (cont.) Repeat for root 17

1/27/09 Sankoff Algorithm (cont.) Smallest score at root is minimum weighted parsimony score In this case, 9 – so label with T Sankoff Algorithm: Traveling down the Tree • The scores at the root vertex have been computed by going up the tree • Aoer the scores at root vertex are computed the Sankoff algorithm moves down the tree and assign each vertex with op4mal character. 18

1/27/09 Sankoff Algorithm (cont.) 9 is derived from 7 + 2 So left child is T, And right child is T Sankoff Algorithm (cont.) And the tree is thus labeled… 19

1/27/09 Analysis of Sankoff’s Algorithm A dynamic programming problem algorithm: Op>mal substructure : solu4on obtained by solving smaller problem of same type. s t (parent) = min i { s i ( leo child ) + δ i, t } + min j { s j ( right child ) + δ j, t } t Recurrence terminates at δ i, t δ j, t leaves, where solu4on is s i (leo child) s j (right child) known. Analysis of Sankoff’s Algorithm How many computa6ons do we perform for n species, m characters, and k states per character? Forward step: • At each internal node of tree: s t (parent) = min i { s i ( leo child ) + δ i, t } + min j { s j ( right child ) + δ j, t } • 2k sums and 2 (k‐1) comparisons = 4k ‐2 • n‐1 internal nodes. • (4k – 2)(n ‐1) sums. Traceback: one “lookup” per internal node. (n‐1) opera4ons For each character (4k – 2)(n‐1) + (n‐1) opera4ons ≤ C n k • Above calcula4on performed once for each character: ≤ C m n k opera4ons • O( m n k) 4me. [“big‐O”] • Increases linearly w/ # of species or # of characters. 20