DNA Phylogeny. Signals and Systems in Biology Kushal EE, IIT Delhi

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1 DNA Phylogeny Signals and Systems in Biology Kushal EE, IIT Delhi

2 Phylogenetics Grouping and Division of organisms Keeps changing with time Splitting, hybridization and termination Cladistics : Methods to determine phylogeny

3 Phylogenetics Grouping and Division of organisms Keeps changing with time Splitting, hybridization and termination Cladistics : Methods to determine phylogeny

4 Phylogenetics Grouping and Division of organisms Keeps changing with time Splitting, hybridization and termination Cladistics : Methods to determine phylogeny

5 Phylogenetics Grouping and Division of organisms Keeps changing with time Splitting, hybridization and termination Cladistics : Methods to determine phylogeny

6 Phylogenetics Grouping and Division of organisms Keeps changing with time Splitting, hybridization and termination Cladistics : Methods to determine phylogeny

7 Tree showing evolutionary relationships between various species Taxa joined if they are believed to have a common ancestor

8 Phylogenetic Tree : Rooted and Unrooted

9 Methods of Phylogenetic Analysis Morphological Analysis Average body size Lengths or sizes of specific physical features Certain kinds of behaviour Comparison of RNA sequences : 18S ribosomal RNA Computational Analysis Compute distance matrix Alignment based and Alignment-Free Methods Generate phylogenetic tree based on this matrix Neighbor joining Fitch-Margoliash method Using independent information Maximum Parsimony

10 Methods of Phylogenetic Analysis Morphological Analysis Average body size Lengths or sizes of specific physical features Certain kinds of behaviour Comparison of RNA sequences : 18S ribosomal RNA Computational Analysis Compute distance matrix Alignment based and Alignment-Free Methods Generate phylogenetic tree based on this matrix Neighbor joining Fitch-Margoliash method Using independent information Maximum Parsimony

11 Methods of Phylogenetic Analysis Morphological Analysis Average body size Lengths or sizes of specific physical features Certain kinds of behaviour Comparison of RNA sequences : 18S ribosomal RNA Computational Analysis Compute distance matrix Alignment based and Alignment-Free Methods Generate phylogenetic tree based on this matrix Neighbor joining Fitch-Margoliash method Using independent information Maximum Parsimony

12 Methods of Phylogenetic Analysis Morphological Analysis Average body size Lengths or sizes of specific physical features Certain kinds of behaviour Comparison of RNA sequences : 18S ribosomal RNA Computational Analysis Compute distance matrix Alignment based and Alignment-Free Methods Generate phylogenetic tree based on this matrix Neighbor joining Fitch-Margoliash method Using independent information Maximum Parsimony

13 Methods of Phylogenetic Analysis Morphological Analysis Average body size Lengths or sizes of specific physical features Certain kinds of behaviour Comparison of RNA sequences : 18S ribosomal RNA Computational Analysis Compute distance matrix Alignment based and Alignment-Free Methods Generate phylogenetic tree based on this matrix Neighbor joining Fitch-Margoliash method Using independent information Maximum Parsimony

14 Methods of Phylogenetic Analysis Morphological Analysis Average body size Lengths or sizes of specific physical features Certain kinds of behaviour Comparison of RNA sequences : 18S ribosomal RNA Computational Analysis Compute distance matrix Alignment based and Alignment-Free Methods Generate phylogenetic tree based on this matrix Neighbor joining Fitch-Margoliash method Using independent information Maximum Parsimony

15 Methods of Phylogenetic Analysis Morphological Analysis Average body size Lengths or sizes of specific physical features Certain kinds of behaviour Comparison of RNA sequences : 18S ribosomal RNA Computational Analysis Compute distance matrix Alignment based and Alignment-Free Methods Generate phylogenetic tree based on this matrix Neighbor joining Fitch-Margoliash method Using independent information Maximum Parsimony

16 Methods of Phylogenetic Analysis Morphological Analysis Average body size Lengths or sizes of specific physical features Certain kinds of behaviour Comparison of RNA sequences : 18S ribosomal RNA Computational Analysis Compute distance matrix Alignment based and Alignment-Free Methods Generate phylogenetic tree based on this matrix Neighbor joining Fitch-Margoliash method Using independent information Maximum Parsimony

17 Methods of Phylogenetic Analysis Morphological Analysis Average body size Lengths or sizes of specific physical features Certain kinds of behaviour Comparison of RNA sequences : 18S ribosomal RNA Computational Analysis Compute distance matrix Alignment based and Alignment-Free Methods Generate phylogenetic tree based on this matrix Neighbor joining Fitch-Margoliash method Using independent information Maximum Parsimony

18 Methods of Phylogenetic Analysis Morphological Analysis Average body size Lengths or sizes of specific physical features Certain kinds of behaviour Comparison of RNA sequences : 18S ribosomal RNA Computational Analysis Compute distance matrix Alignment based and Alignment-Free Methods Generate phylogenetic tree based on this matrix Neighbor joining Fitch-Margoliash method Using independent information Maximum Parsimony

19 Methods of Phylogenetic Analysis Morphological Analysis Average body size Lengths or sizes of specific physical features Certain kinds of behaviour Comparison of RNA sequences : 18S ribosomal RNA Computational Analysis Compute distance matrix Alignment based and Alignment-Free Methods Generate phylogenetic tree based on this matrix Neighbor joining Fitch-Margoliash method Using independent information Maximum Parsimony

20 Methods of Phylogenetic Analysis Morphological Analysis Average body size Lengths or sizes of specific physical features Certain kinds of behaviour Comparison of RNA sequences : 18S ribosomal RNA Computational Analysis Compute distance matrix Alignment based and Alignment-Free Methods Generate phylogenetic tree based on this matrix Neighbor joining Fitch-Margoliash method Using independent information Maximum Parsimony

21 Methods of Phylogenetic Analysis Morphological Analysis Average body size Lengths or sizes of specific physical features Certain kinds of behaviour Comparison of RNA sequences : 18S ribosomal RNA Computational Analysis Compute distance matrix Alignment based and Alignment-Free Methods Generate phylogenetic tree based on this matrix Neighbor joining Fitch-Margoliash method Using independent information Maximum Parsimony

22 Neighbor Joining (NJ)

23 Maximum Parsimony Number of evolutionary events necessary to explain the observed differences Every evolutionary event has an associated cost Locate a tree with the minimum cost Not every event is equally likely NP-hard problem!! Heuristic search methods for the cheapest tree

24 Maximum Parsimony Number of evolutionary events necessary to explain the observed differences Every evolutionary event has an associated cost Locate a tree with the minimum cost Not every event is equally likely NP-hard problem!! Heuristic search methods for the cheapest tree

25 Maximum Parsimony Number of evolutionary events necessary to explain the observed differences Every evolutionary event has an associated cost Locate a tree with the minimum cost Not every event is equally likely NP-hard problem!! Heuristic search methods for the cheapest tree

26 Maximum Parsimony Number of evolutionary events necessary to explain the observed differences Every evolutionary event has an associated cost Locate a tree with the minimum cost Not every event is equally likely NP-hard problem!! Heuristic search methods for the cheapest tree

27 Maximum Parsimony Number of evolutionary events necessary to explain the observed differences Every evolutionary event has an associated cost Locate a tree with the minimum cost Not every event is equally likely NP-hard problem!! Heuristic search methods for the cheapest tree

28 Maximum Parsimony Number of evolutionary events necessary to explain the observed differences Every evolutionary event has an associated cost Locate a tree with the minimum cost Not every event is equally likely NP-hard problem!! Heuristic search methods for the cheapest tree

29 Maximum Parsimony Number of evolutionary events necessary to explain the observed differences Every evolutionary event has an associated cost Locate a tree with the minimum cost Not every event is equally likely NP-hard problem!! Heuristic search methods for the cheapest tree

30 Genetic Distance X,Y : Two populations for which L loci have been sampled X u,y u : Frequency of uth allele at the lth location Nei s method : D a = l u X u Y u ln ( l u X 2 u )( l u Y 2 u ) ( Cavalli-Sforza chord measure : D CH = 2 2 π L l ) X u Y u u

31 Genetic Distance X,Y : Two populations for which L loci have been sampled X u,y u : Frequency of uth allele at the lth location Nei s method : D a = l u X u Y u ln ( l u X 2 u )( l u Y 2 u ) Cavalli-Sforza chord measure : ( D CH = 2 2 π L l ) X u Y u u

32 Genetic Distance X,Y : Two populations for which L loci have been sampled X u,y u : Frequency of uth allele at the lth location Nei s method : D a = l u X u Y u ln ( l u X 2 u )( l u Y 2 u ) ( Cavalli-Sforza chord measure : D CH = 2 2 π L l ) X u Y u u

33 Genetic Distance : Information ( ) K (x) K x y d (x,y) = 1 K (xy) K ( ) : Kolmogorov Complexity d (x,y) satisfies triangle inequality d (x,y) d (y,x) : non-trivial proof M. Li et. al., Bioinformatics 2001

34 Genetic Distance : Information ( ) K (x) K x y d (x,y) = 1 K (xy) K ( ) : Kolmogorov Complexity d (x,y) satisfies triangle inequality d (x,y) d (y,x) : non-trivial proof M. Li et. al., Bioinformatics 2001

35 Genetic Distance : Information ( ) K (x) K x y d (x,y) = 1 K (xy) K ( ) : Kolmogorov Complexity d (x,y) satisfies triangle inequality d (x,y) d (y,x) : non-trivial proof M. Li et. al., Bioinformatics 2001

36 Genetic Distance : Correlation Based I (k) = p (k) p (k) (i,j) (i,j) log 4 p (i)p (j) i,j S S = {A,T,G,C} M. Dehnert et. al., J. Computational Biology 2005

Phylogenetic trees 07/10/13

Phylogenetic trees 07/10/13 A tree is the only figure to occur in On the Origin of Species by Charles Darwin. It is a graphical representation of the evolutionary relationships among entities that share