Microbial Diversity Part 5: Rooting the Tree of Life
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The document discusses ways to root the universal tree of life using gene duplication events. Specifically, it describes using elongation factor genes EF-Tu and EF-G, which duplicated early in evolution before the last universal common ancestor. By constructing gene trees of these factors and identifying the duplication point, the tree can be rooted between the two forms, placing the root before the divergence of Archaea, Bacteria, and Eukarya. This rooted tree matches the canonical three domain tree of life.
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Microbial Diversity Part 5: Rooting the Tree of Life
- 1. Rooting the tree of life Dr. Rachel Mackelprang
- 2. Rooting the Universal Tree From this To this
- 3. Simplified Three Domain Unrooted Tree of Life Eukaryotes Archaea Bacteria What are the possible ways in which this tree could be rooted?
- 4. Let’s go to a more familiar tree Humans Gorillas Chimps How can we root this tree?
- 5. Let’s go to a more familiar tree Humans Gorillas Chimps How can we root this tree? Use an outgroup: one or more taxa (usually closely related to the ingroup) that are not members of the ingroup
- 6. Let’s go to a more familiar tree Humans Gorillas Chimps Use an outgroup: one or more taxa (usually closely related to the ingroup) that are not members of the ingroup Orangutans
- 7. Back to the Tree of Life Eukaryotes Archaea Bacteria Is there an outgroup for the tree of life?
- 8. Back to the Tree of Life Eukaryotes Archaea Bacteria Is there an outgroup for the tree of life?
- 9. Can’t root the tree of life with rRNA genes • Take 9 species –3 archaea –3 eukaryotes –3 bacteria • Take their rRNA genes • Align them and create your data matrix • Build tree
- 10. Tree Generated Using rRNA Sequences
- 11. For Simplicity There are multiple ways you can root this tree
- 12. For Simplicity There are multiple ways you can root this tree
- 13. For Simplicity There are multiple ways you can root this tree
- 14. For Simplicity There are multiple ways you can root this tree
- 15. Can Root the Tree Using Gene Duplications
- 16. Are there genes that duplicated before the MRCA to all life?
- 17. Yes. Elongation factors Elongation factors are proteins that assist in translation. They increase the speed and accuracy of the translation mechanism. There are two types we will consider. EF-Tu and EF-G
- 18. Rooting the Tree of Life • Take 9 species –3 archaea –3 eukaryotes –3 bacteria • Take their elonga=on factor TU genes • And their elonga=on factor G genes • Align them • Build and unrooted tree
- 19. What Might the Tree Look Like?
- 20. What Might the Tree Look Like? E1 E2 E3 B3 B1 B2 A1 A3 A2 E1 E2 E3 B3 B1 B2 A1 A3 A2
- 21. What Might the Tree Look Like? E1 E2 E3 B3 B1 B2 A1 A3 A2 E1 E2 E3 B3 B1 B2 A1 A3 A2 EF-Tu EF-G
- 22. Root the Tree Between the Two Forms
- 23. Root the Tree Between the Two Forms E1 E2 E3 B3 B1 B2 A1 A3 A2 E1 E2 E3 B3 B1 B2 A1 A3 A2 EF-Tu EF-G
- 24. Draw the Rooted Tree
- 26. Identify Possible Duplication Events
- 28. Merge Gene Tree with Species Tree by Overlaying the Forms
- 29. Merge Gene Tree with Species Tree by Overlaying the Forms E1 E2 E3 A1 A2 A3 B1 B3 B2 E1 E2 E3 A1 A2 A3 B1 B3 B2 E1 E2 E3 A1 A2 A3 B1 B3 B2
- 30. Canonical Three Domain Tree of Life Very ancient prokaryotes EUKARYA BACTERIA ARCHAEA Ancient Present Time Origin of life