1. The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer By Fan Ge, Li-San Wang, Junhyong Kim Published: August 30, 2005 Presented By: Vishal S. Doshi Course: CS 502 15 th April 2014

2. Fact of the day "Biology is the only science in which multiplication means the same thing as division."

3. Agenda Terminologies Motivation Overview Experiment Conclusion

4. Terminologies Phylogeny: History of the Evolution of a species or group, especially lines of descent and relationships among broad groups.

5. Tree of Life Terminologies

6. Horizontal Gene Transfer (HGT): Horizontal gene transfer occurs when genes jump between unrelated organisms.

7. Terminologies Horizontal Gene Transfer (HGT): Horizontal gene transfer occurs when genes jump between unrelated organisms. E.g. Think of it as acquiring genes from your neighbor instead of your parents.

8. Terminologies Horizontal Gene Transfer (HGT)

9. Pun Intended Why is the mushroom always asked to a party?

10. Pun Intended Why is the mushroom always asked to a party? Because he’s a fungi (fun guy).

11. Agenda Terminologies Motivation Overview Experiment Conclusion

12. Motivation There are 10 types of people in the world:

13. Motivation There are 10 types of people in the world: 01. Those who understand binary, and

14. Motivation There are 10 types of people in the world: 01. Those who understand binary, and 10. those who don't.

15. Motivation Similarly, there are 2 types of people in the world:

16. Motivation Similarly, there are 2 types of people in the world: 1.Who believe HGT constitutes only minor interference when inferring phylogeny. Tree of Life

17. Motivation Similarly, there are 2 types of people in the world: 2.And others who believe HGT has an impact on Phylogeny ( the tree-like structure of life) and the old structure should be replaced with a new net-like structure.

18. Motivation Similarly, there are 2 types of people in the world: 2.And others who believe HGT has an impact on Phylogeny ( the tree-like structure of life) and the old structure should be replaced with a new net-like structure.

19. Motivation This established the aim of this experiment. The results would be breakthrough.

20. Agenda Terminologies Motivation Overview Experiment Conclusion

21. Overview Horizontal Gene Transfer (HGT): – Its role in speciation, adaptation and evolution is studied intensively –Growing evidence of lateral transfer of genes among species.

22. Overview Debate: Whole-Genome analysis of different prokaryotes indicate rampant HGTs. Suggesting role of HGT to be: ⁻ Pivotal in prokaryotic evolution. ⁻ To be considered essence of Phylogeny. Therefore life history cannot be well represented by tree-like form, but rather a network-like form.

23. Overview Debate : Therefore life history cannot be well represented by tree-like form, but rather a network-like form.

24. Overview Debate : Therefore life history cannot be well represented by tree-like form, but rather a network-like form.

25. Overview Unresolved issues in the debate : Estimation of HGT Frequency. Thus, inferring its impact on phylogeny. And the experiment conducted by our authors is to deal with them.

26. Overview Suggested HGT frequency: –At 24% in Thermatoga –A range up to 17% among different prokaryotes Led some researchers to believe absence of tree-like structure.

27. Overview Other researchers propose: –HGT constitutes only minor interference when inferring phylogeny.

28. Overview Other researchers propose: –HGT constitutes only minor interference when inferring phylogeny. –Methods for inferring HGT have various problems leading to Over-estimation E.g. : Different methods of estimation gave different HGT candidates applied to same genome.

29. Overview Other researchers propose: –HGT constitutes only minor interference when inferring phylogeny. –Methods for inferring HGT have various problems leading to Over-estimation E.g. : Different methods of estimation gave different HGT candidates applied to same genome. –Phylogeny can be sufficiently retrieved via a core of genes that may be resistant to HGT

30. Overview Inference of HGT can be done by tree comparisons. But it should be done under a proper statistical framework. Even though, if HGT events are randomly distributed across lineage: there still exist a backbone tree structure.

31. Agenda Terminologies Motivation Overview Experiment Conclusion

32. Experiment Specific questions asked in this paper are: 1.What is the fundamental structure of the whole-genome (W-G) tree?

33. Experiment Specific questions asked in this paper are: 1.What is the fundamental structure of the whole- genome (W-G) tree? 2.How do individual gene trees differ from this tree, especially in terms of general HGT events? 3.How do individual gene trees differ from one another in terms of HGT? 4.What is the rate of HGT events per genome? 5.What kind of genome-specific patterns or gene- specific patterns are evident for HGT events?

34. Experiment Specific questions asked in this paper are: 1.What is the fundamental structure of the whole-genome (W-G) tree? 2.How do individual gene trees differ from this tree, especially in terms of general HGT events?

35. Experiment Specific questions asked in this paper are: 1.What is the fundamental structure of the whole-genome (W-G) tree? 2.How do individual gene trees differ from this tree, especially in terms of general HGT events? 3.How do individual gene trees differ from one another in terms of HGT?

36. Experiment Specific questions asked in this paper are: 1.What is the fundamental structure of the whole-genome (W-G) tree? 2.How do individual gene trees differ from this tree, especially in terms of general HGT events? 3.How do individual gene trees differ from one another in terms of HGT? 4.What is the rate of HGT events per genome?

37. Experiment Specific questions asked in this paper are: 1.What is the fundamental structure of the whole- genome (W-G) tree? 2.How do individual gene trees differ from this tree, especially in terms of general HGT events? 3.How do individual gene trees differ from one another in terms of HGT? 4.What is the rate of HGT events per genome? 5.What kind of genome-specific patterns or gene- specific patterns are evident for HGT events?

38. Experiment Figure 1. Flowchart of the HGT Inference Procedure Ge F, Wang L-S, Kim J (2005) The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer. PLoS Biol 3(10): e316. doi:10.1371/journal.pbio.0030316

39. Experiment: Step 1 High Quality Clusters of Orthologous Groups (COGs)

40. Experiment: Step 1 Figure 1. Flowchart of the HGT Inference Procedure Ge F, Wang L-S, Kim J (2005) The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer. PLoS Biol 3(10): e316. doi:10.1371/journal.pbio.0030316 Use the COG database to assemble a set of high-quality orthologous groups for tree inference.

41. Experiment: Step 1 The COG database used, covered 43 microorganisms. Stringent high-quality COG selection procedure resulted in: –Retention of only 297 out of 3852 COG entries. –These covered 40 genomes and on average ~16 genomes/entry.

42. Step 1: Outcome Table 1. Number of COG Entries That Contain Each of 40 Genomes Ge F, Wang L-S, Kim J (2005) The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer. PLoS Biol 3(10): e316. doi:10.1371/journal.pbio.0030316

43. Experiment: Step 2 High-Quality Gene Groups and the W-G Tree

44. Experiment: Step 2 Figure 1. Flowchart of the HGT Inference Procedure Ge F, Wang L-S, Kim J (2005) The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer. PLoS Biol 3(10): e316. doi:10.1371/journal.pbio.0030316 Construct the W-G tree that represents the best treelike description for the genealogical relationship of the genomes.

45. Experiment: Step 2 Figure 1. Flowchart of the HGT Inference Procedure Ge F, Wang L-S, Kim J (2005) The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer. PLoS Biol 3(10): e316. doi:10.1371/journal.pbio.0030316 Construct the W-G tree that represents the best treelike description for the genealogical relationship of the genomes. We estimate a tree for each orthologous group (gene tree)

46. Experiment: Step 2 Use of median tree estimator designed by Kim and Salisbury to approximate W-G tree. –It is robust –Overcomes major genetic distortions like HGTs

47. Step 2: Outcome Figure 2. The W-G Tree Based on the Median Tree Algorithm Ge F, Wang L-S, Kim J (2005) The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer. PLoS Biol 3(10): e316. doi:10.1371/journal.pbio.0030316

48. Step 2: Outcome Branches with bootstrap scores <50% were collapsed into the polytomous form. Three domains of life are shown as –(A) Archaea, –(B–J) Bacteria, and –(K) Eukaryote. Taxonomy labels are: A.Euryarchaea, B.Proteobacteria, C.Chlamydiae, D.Spirochaetes, E.Thermotogae F.Aquificae, G.Actinobacteria, H.Deinococcus, I.Cyanobacteria, J.Firmicutes, and K.Fungi.

49. Step 2: Outcome Figure 2. The W-G Tree Based on the Median Tree Algorithm Ge F, Wang L-S, Kim J (2005) The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer. PLoS Biol 3(10): e316. doi:10.1371/journal.pbio.0030316 Inferred HGT rates: red, >4%; yellow, 3%–4%; pink, 2%–3%; blue, 1%–2%; green,<1%.

50. Experiment: Step 3 & 4 HGT events for a particular gene or sequence can be detected by comparing the estimated gene tree against: –Other gene trees, or –Some candidate tree that represents the history of the genomes (W-G Tree)

51. Method Statistical Inference of HGT and Power Test

52. Method A.Statistical Inference: Method used for comparison: 1.Maximum Agreement Subtree (MAST) algorithm. 2.Symmetric Difference (SD)  Both process return a MAST score and SD score respectively.  Authors used PAUP* software tool to carry out this process.

53. Maximum Agreement Subtree (MAST) algorithm. Figure 3. Example for MAST

54. Symmetric Difference (SD) The symmetric difference of: The sets {1,2,3} and {3,4} is {1,2,4} Figure 4. Example for SD

55. Method Table 2. HGT inference MAST Score SD Score Explanation Small No HGT Large No easily explained by HGT SmallLargeHGT Event LargeSmallCannot occur

56. MAST= 2, SD= 2 MAST= 2, SD= 8 Figure 5. HGT Inference via Tree Comparison Method Ge F, Wang L-S, Kim J (2005) The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer. PLoS Biol 3(10): e316. doi:10.1371/journal.pbio.0030316

57. MAST= 2, SD= 2 MAST= 2, SD= 8 HGT Event Figure 5. HGT Inference via Tree Comparison Method Ge F, Wang L-S, Kim J (2005) The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer. PLoS Biol 3(10): e316. doi:10.1371/journal.pbio.0030316

58. Method B.Power Test A hypothesis test for HGT, using the difference between the normalized values of the two metrics. i.e SD and MAST

59. Method For a pair of trees T and T′, with m and n splits (i.e., branches), respectively, and with x number of taxa, our statistic γ is defined as: d S is the SD metric d M is the MAST metric

60. Method For a pair of trees T and T′, with m and n splits (i.e., branches), respectively, and with x number of taxa, our statistic γ is defined as: d S is the SD metric d M is the MAST metric Normalized values of the SD and the MAST metrics

61. Method Now, compute the p-Value(Significance) of an observed γ-value by generating a nonparametric null distribution based on randomly bootstrapped gene trees (Subtree Pruning-Regrafting)

62. Experiment Figure 1. Flowchart of the HGT Inference Procedure Ge F, Wang L-S, Kim J (2005) The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer. PLoS Biol 3(10): e316. doi:10.1371/journal.pbio.0030316 Assess the difference between the tree structure of each gene tree and that of the W-G tree.

63. Experiment: Step 3 HGT Estimation via Comparisons between Each Gene Tree and the W-G Tree

64. Experiment: Step 3 Hypothesis test described before was applied to each of the 297 COG gene trees against the W-G tree.

65. Step 3: Outcome Figure 6. Power of the γ Test in Detecting HGT Ge F, Wang L-S, Kim J (2005) The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer. PLoS Biol 3(10): e316. doi:10.1371/journal.pbio.0030316

66. Step 4: Outcome Figure 7. The Relationship between Detecting COG Entries with HGT and the p-Values Ge F, Wang L-S, Kim J (2005) The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer. PLoS Biol 3(10): e316. doi:10.1371/journal.pbio.0030316

67. Step 3: Outcome At the significance level of 0.05, authors inferred that 33 out of 297 COG entries (i.e., 11.1%) contain putative HGT events

68. Experiment: Step 4 HGT Estimation via Comparisons among Gene Trees

69. Experiment Figure 1. Flowchart of the HGT Inference Procedure Ge F, Wang L-S, Kim J (2005) The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer. PLoS Biol 3(10): e316. doi:10.1371/journal.pbio.0030316 Assess the difference between the tree structure of each gene tree vs. every other gene tree.

70. Experiment: Step 4 Same operation was carried out, but this time every gene-tree was compared with every other gene-tree and not W-G Tree. 14,004 pairs were compared. 1,764 pairs were significant. 13% COGs contain HGTs

71. Experiment: Step 5 HGT Frequency in 40 Genomes

72. Step 5: Outcome Table 3. Frequency of HGT in 40 Genomes and List of Transferred Genes Ge F, Wang L-S, Kim J (2005) The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer. PLoS Biol 3(10): e316. doi:10.1371/journal.pbio.0030316

73. Step 5: Outcome The estimated rates of HGT in different genomes are between 0% and 6.7%, with an average of 2.0% among the 40 genomes studied here.

74. Agenda Terminologies Motivation Overview Experiment Conclusion

75. Imagine a very large tree 10,000 taxa. 10, 000 Potential “units” of HGT per genome If each such element had, say, 1,000 actual HGTs across the 10,000 taxa. All the HGTs will appear as extremely thin connections like “cobwebs” when layed over the tree.

76. Conclusion So pictorially:

77. Conclusion So pictorially:

78. Conclusion So pictorially:

79. Questions

80. I have one for you..

81. How do you tell the sex of chromosome?

82. I have one for you.. How do you tell the sex of chromosome? Pull down it's genes!