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Molecular Phylogeny in a context of possible Lateral Gene Transfers Eric Bapteste W.F. Doolittle Lab.

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Presentation on theme: "Molecular Phylogeny in a context of possible Lateral Gene Transfers Eric Bapteste W.F. Doolittle Lab."— Presentation transcript:

1 Molecular Phylogeny in a context of possible Lateral Gene Transfers Eric Bapteste W.F. Doolittle Lab

2 The reason(s) why we doubt a strict tree-like representation should be used Biological processes favoring lateral exchanges of DNA... are powerful Phylogenetic evidence for a unique Tree of Life are weak Molecular phylogenies might even suggest that LGT happens … at least in some lineages

3 Biological Processes contribute to lateral exchanges of DNA Internal source of variation Mutator phenotype Baseline replication errors (point mutations) Intragenomic recombination (legitimate and illegitimate) Hypervariable loci Genome of the Organism Deletion of genetic material (Gene loss) Gene duplication Vertical inheritance Genome of the Descendent External source of variation DNA viruses lytic RNA viruses retroviruses Conjugative plasmids and transposons DNA from divergent lineage Transduction Transformation Conjugation Horizontal inheritance Cell fusions membrane vesicle transfer

4 Phylogenetic evidence for a unique Tree of Life are weak “The general lack of conflict observed among the 203 remaining families was not due to the absence of phylogenetic signal in the gene alignments because most genes did conflict with several other topologies (see Figure 3). We interpreted this congruence as a reflection of shared history and a lack of LGT. Therefore, we chose these genes as the basis for inferring the true organismal phylogeny for these 13 species.”Figure 3 Gamma-proteobacteria: an apparent agreement on a tree Lerat E et al., PLoS Biol. 2003 Oct;1(1):E19.

5 Phylogenetic evidence for a unique Tree of Life are weak

6 Testing the congruence/conflict between markers Topologies Genes 1 2 3 4 5 6 7 0 0,1 4,1 0,6 0,1 0,4 0,3 4 5,4 7,8 4,3 4,7 3,1 9,7 13 0,4 17 9 22 47 42 27 0 33 37 29 41 0,2 1,7 3,3 0,1 0 0,4 0,5 ….. R²=0,9 R²=0,05 Principal Component Analysis of p-values for each gene and topology 6 2 1 4 7 5 3

7 genes 1 LGT event Principal Component Analysis of 205 genes of gamma-proteobacteria and simulated markers with transfers

8 genes 1 LGT event 2 LGT events Principal Component Analysis of 205 genes of gamma-proteobacteria and simulated markers with transfers

9 genes 1 LGT event 2 LGT events 3 LGT events Principal Component Analysis of 205 genes of gamma-proteobacteria and simulated markers with transfers

10 genes Random 1 LGT event 2 LGT events 3 LGT events Principal Component Analysis of 205 genes of gamma-proteobacteria and simulated markers with transfers

11 GENE NUMBER i TOPOLOGIES NUMBER i P-value

12 GENES TOPOLOGIES

13 CLUSTER OF GENES CLUSTER OF PLAUSIBLE TOPOLOGIES BLUE: Genes with LGT RED: genes

14 CLUSTER OF GENES CLUSTER OF PLAUSIBLE TOPOLOGIES

15 CLUSTER OF GENES CLUSTER OF PLAUSIBLE TOPOLOGIES

16 1 2 3 4

17

18 genes clearly showing lateral transfer genes showing nothing clearly genes clearly showing vertical descent enthusiastic lateralists committed verticalists INCONGRUENCE OF ORTHOLOGOUS GENES: HOW MUCH IS NOISE, HOW MUCH IS TRANSFER (ORTHOLOGOUS REPLACEMENT)? TRUTH IS, NO ONE REALLY KNOWS

19 What we propose to do A synthesis Vertical partHorizontal part

20 Principles to make a synthesis Reference phylogeny A B C D E F A B C D E F Phylogeny of gene 2 A B C D E F 99 Synthesis Phylogeny of gene 1 F B C D E A 99

21 From a tree …

22 ML Trees BV > 50 strict consensus … to a synthesis

23 Conclusions We need better trees to have better synthesis LGT should be accounted for when reconstructing the evolutionary history Many interesting biological and epistemological avenues to explore in the near future

24 Many thanks to The Doolittle and Roger labs Celine Brochier Yan Boucher Dave MacLeod Robert Charlebois Jessica Leigh Ed Susko Ford Doolittle David Walsh Topology

25 I respect ( and more) Vincent Daubin The reason why my interpretation of the dataset is different : -I believe that these most of these genes do not contain enough phylogenetic signal to tell the whole history of gamma proteobacteria alone This is the very motive for concatenation: genes are too weak alone However, based on biological evidence, transfer could have happened, - so we should not prejudge that these genes with a unknown history have been transmitted only vertically. In context of LGT, concatenation is not safe a priori. In other words, in the possible presence of LGT, « when we do not know, we do not know! » -Test concatenations of markers of entirely simulated data, full of transfers, also gives robust phylogenies (Douady and Doolittle, unpublished) So, even a good support for a tree coming from a concatenation is no garantee that the true history has been recovered. Careful analyses of each marker are required. - During these analyses, if we also see some conflict. We should show it, and then do a synthesis instead of a tree

26 The phylogenetic signal is not robust over the whole Synthesis: basal branches are poorly supported. Distribution of the phylogenetic signal along the synthesis 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1 12345678 distance from the root Total phylogenetic signal Longest consecutive vertical path supported 7 5 6 4 3 2

27 More precisely, many inner nodes are only supported by a minority of the genes (in purple). There are always genes (in dark green) for which we ignore their phylogenetic history.

28 Xfast Xaxo Xcamp Paer Wigg Baphi Vchol Pmult Hinfl YpesCO92 YpesKIM Styphi Ecoli A brief view of the differences between the 16 plausible topologies (AU test, 5%)

29 What are the main evolutionary routes? Genes The road of relationships Are there main routes? Unique routes? Side-issues? Are the genes involved in LGT especially mobile ones?

30 0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 au Average p-value (AU test) for each topology over all the genes The average p-value of the best tree for each gene is: 0.83 The concatenate tree is a good “average”, but for most genes is not the best tree Concatenate tree

31 Electric networkRailway network Maritime network Crystal Web NEW QUESTIONS: Optimisation, functionality, economy, shorter paths ?

32 70 Bacteria Number of Vertical branches visible: 56 Number of Lateral transfers visible: 4 Genes which were Laterally transferred: 0rpl4_1.puz_bip.out, 0efg_1.puz_bip.out, 0rpl18_1.puz_bip.out, 0fmt_1.puz_bip.out Ratio of compatible LGT (single Arrow) versus total LGT: 1.0 * Possibility of Generalizations * |vert + horz| vert| horz links supported by 0 genes|11|11| n/a links supported by 1 gene |6|2| 4 links supported by >1 gene|44|44| 0 * Gene Mobility Summary (how many LGT events are present per gene) * # events| # genes having # events | gene names 1| 4| 0efg_1.puz_bip.out, 0fmt_1.puz_bip.out, 0rpl18_1.puz_bip.out, 0rpl4_1.puz_bip.out

33 Number of Vertical branches visible: 44 Number of Lateral transfers visible: 1 Horizontal/Vertical normalized ratio (HVNR): 1.194494E-1 Genes which were Laterally transferred: a0l37aen.puz_bip.out Ratio of compatible LGT (single Arrow) versus total LGT: 1.0 * Possibility of Generalizations * |vert + horz| vert| horz links supported by 0 genes|9|9| n/a links supported by 1 gene |4|3| 1 links supported by >1 gene|33|33| 0 * Gene Mobility Summary (how many LGT events are present per gene) * # events| # genes having # events | gene names 1| 1| a0l37aen.puz_bip.out Archaea 70

34 Euka 70 Number of Vertical branches visible: 33 Number of Lateral transfers visible: 1 Horizontal/Vertical normalized ratio (HVNR): 1.500456E-1 Genes which were Laterally transferred: 0rps23.puz_bip.out Ratio of compatible LGT (single Arrow) versus total LGT: 1.0 * Possibility of Generalizations * |vert + horz| vert| horz links supported by 0 genes|8|8| n/a links supported by 1 gene |3|2| 1 links supported by >1 gene|24|24| 0 * Gene Mobility Summary (how many LGT events are present per gene) * # events| # genes having # events | gene names 1| 1| 0rps23.puz_bip.out

35 Chloro 70 Number of Vertical branches visible: 23 Number of Lateral transfers visible: 2 Horizontal/Vertical normalized ratio (HVNR): 2.192235E-1 Genes which were Laterally transferred: psbh_0.puz_bip.out, psbk_0.puz_bip.out, psac_0.puz_bip.out, psbc_0.puz_bip.out, psbd_0.puz_bip.out Ratio of compatible LGT (single Arrow) versus total LGT: 1.0 * Possibility of Generalizations * |vert + horz| vert| horz links supported by 0 genes|7|7| n/a links supported by 1 gene |2|1| 1 links supported by >1 gene|17|16| 1 * Gene Mobility Summary (how many LGT events are present per gene) * # events| # genes having # events | gene names 1| 5| psac_0.puz_bip.out, psbc_0.puz_bip.out, psbd_0.puz_bip.out, psbh_0.puz_bip.out, psbk_0.puz_bip.out

36 Strict Consensus BV > 50 % Genes which were Laterally transferred: gp25boocon.txt.out, gp46boocon.txt.out These two events of transfers make a support for two phylogenetic relationships: the last common ancestor of (133, rb69 and T4) would have given two genes to the last common ancestor of 25, 31, and 44RR

37 “A radical departure from conventional thinking” W. Martin/M. Embley Me crazy, but on the shoulders of many philosophers: Leibniz, Whitehead, Deleuze, Parrochia, etc. “A radical departure from thinking?”

38 Rivera and Lake, Nature, 2004 ROOT OF THE RING

39 B H M E P Y1 Y2 E H M B P Y1 Y2 P B H M E Y1 Y2 B H M P E Y1 Y2 E H M P B Y1 Y2 60.5% 16.8% 10% 7.2% 1.8%

40 H M B E P Y1 Y2 Unknown descendent 16.8 10 7.2 1.8 96.3 77.779.189.1 96.3 Y1 Y2 P E B H M Unknown Descendent 96.3 79.177.794.5 96.3 10 16.8 1.8 7.2

41 CLUSTER OF GENES CLUSTER OF PLAUSIBLE TOPOLOGIES

42 We can question: -the choice of the drawing of evolution -if a non-tree like null hypothesis should not be considered to build evolutionary scenarios Heuristic of the synthesis... There are 26 vertical branches and 11 lateral branches The total vertical thickness is about 13 times more important than the total horizontal thickness Yet, 18 genes were laterally transferred 8 lateral branches are mostly compatible with the reference tree 3 lateral branches are mostly incompatible with the reference tree Thus, 72.7% of LGT are mostly compatible with the reference tree


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