Gene trees
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GENE TREES. Abhita Chugh. Phylogenetic tree. Evolutionary tree showing the relationship among various entities that are believed to have a common ancestor. Species tree. A phylogenetic tree showing the relationship among various species that are believed to have a common ancestor.

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Gene trees l.jpg

GENE TREES

Abhita Chugh


Phylogenetic tree l.jpg
Phylogenetic tree

Evolutionary tree showing the relationship among various entities that

are believed to have a common ancestor


Species tree l.jpg
Species tree

  • A phylogenetic tree showing the relationship among various species that are believed to have a common ancestor


Species tree4 l.jpg
Species tree

Speciation Nodes

Shows the evolutionary history of a set of species


Gene tree l.jpg
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


Gene tree6 l.jpg
Gene tree

Speciation Nodes

Duplication

nodes

Shows the evolutionary history of a single gene


Some definitions homologs l.jpg
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


Orthologs l.jpg
Orthologs

  • Genes in different species that evolved from a common ancestral gene by speciation - Retain the same function

Speciation

Primates

Human

Chimp


Paralogs l.jpg
Paralogs

  • Genes related by duplication within a genome

  • Evolve new functions

Primates

Rodents

Chimp

Human

Rat

Mouse


Why are gene trees interesting l.jpg
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




Gene tree reconstruction l.jpg
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




Reconstruction algorithm l.jpg
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


Reconstruction algorithm17 l.jpg
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


Step 1 annotates minimum cost tables for all nodes l.jpg
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


Slide19 l.jpg

cost[1, 1] = 0 + 1 + 1 = 2

cost[1, 2] = 1 + 0 + 1 = 2

cost[1] = 2

cost[1, 1] = 0 + 0 + 1 = 1

cost[1, 2] = 1 + 1 + 0 = 2

cost[1] = 1

cost[2, 1] = 1 + 0 + 1 = 2

cost[2] = 1

cost[1] = 1

cost[2, 2] = 0 + 1 + 0 = 1

cost[2] = 0

cost[1] = 0

cost[1] = 1

cost[2] = 1

cost[2] = 0

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


Step 2 enumerate all histories from the cost tables l.jpg
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


Slide21 l.jpg

out = 1, losses = dups = 0

out = 1 , losses = dups = 0

dups = 1

losses = 0

dups = 0

losses = 0

dups = 1

losses = 0


Step 3 build a gene tree to represent the history l.jpg
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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