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GENE TREES Abhita Chugh
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Phylogenetic tree Evolutionary tree showing the relationship among various entities that are believed to have a common ancestor
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Species tree A phylogenetic tree showing the relationship among various species that are believed to have a common ancestor
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Species tree Shows the evolutionary history of a set of species Speciation Nodes
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Gene tree A phylogenetic tree that depicts how a single gene has evolved in a group of related species For this talk, evolve = duplication or loss Can be constructed over the topology of a species tree
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Gene tree Shows the evolutionary history of a single gene Speciation Nodes Duplication nodes
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Some definitions: Homologs Homolog: A gene related to a second gene by descent from a common ancestral DNA sequence Two types: (i) Orthologs (ii) Paralogs
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Orthologs Genes in different species that evolved from a common ancestral gene by speciation - Retain the same function Primates Human Chimp Speciation
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Paralogs Genes related by duplication within a genome Evolve new functions Primates Chimp Human Rat Rodents Mouse
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Why are Gene Trees interesting? Determine the evolutionary history of a gene family Infer gene duplications and losses Estimate bounds on times these events occurred Determine whether a given pair of homologs is orthologous or paralogous
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Gene tree can be constructed over a species tree topology PRIMATES INTELLIGENCE
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No, seriously..
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Gene Tree Reconstruction Problem: Given a set of sequences from a gene family, find the tree that best explains the data 2 models: –Micro-evolutionary: considers sequence evolution only –Macro-evolutionary: considers duplication and losses only; useful but rarely used
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Macro-evolutionary Problem
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Reconstruction algorithm Only macroevolutionary events are considered i – number of gene copies a node inherits from its parent j – number of gene copies a node sends to its children Range from 1 to m, where m is the maximum multiplicity of the gene in any species
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Reconstruction algorithm The entering number of genes in root should be one For each node, v, the dynamic program calculates the minimum D/L Score of the subtree rooted at v, for all possible values of i and j
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Step 1: Annotates minimum cost tables for all nodes cost [ i, j ] = cost at a node if it inherits i genes and sends j genes cost [ i ] = minimum cost at a node if it inherits i genes = minimum { cost [ i, j ] }, for all j
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cost[1] = 1 cost[2] = 0 cost[1] = 1 cost[2] = 0 cost[1] = 0 cost[2] = 1 Cost of an internal node = cost of duplication/loss at the node + optimal cost of left subtree + optimal cost of right subtree, if they inherit j copies cost[1, 1] = 0 + 0 + 1 = 1 cost[1, 2] = 1 + 1 + 0 = 2 cost[2, 1] = 1 + 0 + 1 = 2 cost[2, 2] = 0 + 1 + 0 = 1 cost[1] = 1 cost[2] = 1 cost[1, 1] = 0 + 1 + 1 = 2 cost[1, 2] = 1 + 0 + 1 = 2 cost[1] = 2
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Step 2: Enumerate all histories from the cost tables Maintain 3 variables for each node dups = optimal number of duplicated genes losses = optimal number of lost genes out = optimal number of genes to pass to its children
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out = 1, losses = dups = 0 dups = 1 losses = 0 out = 1, losses = dups = 0 dups = 0 losses = 0 dups = 1 losses = 0
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Step 3: Build a gene tree to represent the history From step 2: 1 duplication in humans & 1 duplication in frogs Build the gene tree with this information & the topology of the species tree
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Hybrid Model
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