29 Mammalian Genomes

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29 Mammalian Genomes

  1. 1. A High-Resolution Map of Evolutionary Constraint In the human genome by Lindblad-Toh & colleagues, Nature 2011 Presented by Nacho Caballero
  2. 2. Constrained Diversity Is the Key to Comparative Genomics
  3. 3. Percentage ofSites that Have 1+ subs Undergone 2+ subs Substitutions 3+ subs 4+ subs 1 - 0.5 - 0 - 0.8 1.25 1.5 3 5 Average # of Subs. per Site (Branch Length)
  4. 4. Percentage of 4 Genomes - 50 bp 0.8 subs/site Sites that HaveUndergone 1.25 subs/site Substitutions 1.5 subs/site 3 subs/site 29 Genomes – 12 bp 5 subs/site 0.5 - 0.3 - 0.1 - 0 1 2 3 4 5 6 Number of Neutral Substitutions per Site
  5. 5. Higher Resolution Uncovers Individual Binding Sites NPAS4 bias 4 genomes 29 genomes
  6. 6. Evolutionary Signatures Help Discover Novel Genes Stop Codons Synonymous Substitution Frame-Preserving Indel Non-Synonymous Substitution Frame-shifting Indel Annotated as an Intron start stop
  7. 7. Evolutionary Signatures Help Identify Stop-Codon Readthrough Stop Codons Synonymous Substitution Frame-Preserving Indel Non-Synonymous Substitution Frame-shifting Indel SACM1L 1st stop codon 2nd stop codon
  8. 8. Evolutionary Signatures Help Identify Stop-Codon Readthrough 2nd stop codon 1st stop codon
  9. 9. A Richer Picture of Conservation: Synonymous Constrained Elements HOXA2 Basewise Conservation Synonymous Constrained Rate Enhancer   Enhancer  
  10. 10. A Richer Picture of Conservation: Codon-Specific Selection dN/dS > 1.5 Positive Selection dN/dS = 1 Neutral Selection dN/dS < 0.5 Purifying Selection
  11. 11. A Richer Picture of Conservation: Codon-Specific Selection dN/dS > 1.5 Positive Selection dN/dS = 1 Neutral Selection dN/dS < 0.5 Purifying Selection
  12. 12. A Richer Picture of Conservation: Codon-Specific Selection dN/dS > 1.5 Positive Selection dN/dS = 1 Neutral Selection dN/dS < 0.5 Purifying Selection
  13. 13. 100-200 Mammalian Genomes Will Allow Single-Nt Resolution 40% of the Constrained Diversity Constrained Genome Is the Key to Is Uncharted territory Comparative Genomics

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