1. GENE TREES Abhita Chugh

2. Phylogenetic tree Evolutionary tree showing the relationship among various entities that are believed to have a common ancestor

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

4. Species tree Shows the evolutionary history of a set of species Speciation Nodes

5. 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

6. Gene tree Shows the evolutionary history of a single gene Speciation Nodes Duplication nodes

7. 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

8. Orthologs Genes in different species that evolved from a common ancestral gene by speciation - Retain the same function Primates Human Chimp Speciation

9. Paralogs Genes related by duplication within a genome Evolve new functions Primates Chimp Human Rat Rodents Mouse

10. 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

11. Gene tree can be constructed over a species tree topology PRIMATES INTELLIGENCE

12. No, seriously..

13. 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

14. Macro-evolutionary Problem

16. 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

17. 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

18. 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

19. 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

20. 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

21. out = 1, losses = dups = 0 dups = 1 losses = 0 out = 1, losses = dups = 0 dups = 0 losses = 0 dups = 1 losses = 0

22. 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

24. Hybrid Model