1. Example of bipartition analysis for five genomes of photosynthetic bacteria (188 gene families) total 10 bipartitions R: Rhodobacter capsulatus, H: Heliobacillus mobilis, S: Synechocystis sp., Ct: Chlorobium tepidum, Ca: Chloroflexus aurantiacus Bipartitions supported by genes from chlorophyll biosynthesis pathway Zhaxybayeva, Hamel, Raymond, and Gogarten, Genome Biology 2004, 5: R20 R Ca H S Ct Plurality Ca H R S Ct Chl. Biosynth.

2. Phylogenetic Analyses of Genes from chlorophyll biosynthesis pathway (extended datasets) R: Rhodobacter capsulatus, H: Heliobacillus mobilis, S: Synechocystis sp., Ct: Chlorobium tepidum, Ca: Chloroflexus aurantiacus Xiong et al. Science, 2000 289:1724-30 Zhaxybayeva, Hamel, Raymond, and Gogarten, Genome Biology 2004, 5: R20

3. PROBLEMS WITH BIPARTITIONS No easy way to incorporate gene families that are not represented in all genomes. The more sequences are added, the shorter the internal branches become, and the lower is the bootstrap support for the individual bipartitions. A single misplaced sequence can destroy all bipartitions.

4. Bootstrap support values for embedded quartets + : tree calculated from one pseudo- sample generated by bootstraping from an alignment of one gene family present in 11 genomes Quartet spectral analyses of genomes iterates over three loops:  Repeat for all bootstrap samples.  Repeat for all possible embedded quartets.  Repeat for all gene families. : embedded quartet for genomes 1, 4, 9, and 10. This bootstrap sample supports the topology ((1,4),9,10). 1 4 9 10 1 9 4 1 9 4  Zhaxybayeva et al. 2006, Genome Research, in press

5. This gene family for the quartet of species A, B, C, D Supports the Topology ((A, D), B, C) with 70% bootstrap support Iterating over Bootstrap Samples

6. Bootstrap support values for embedded quartets + : tree calculated from one pseudo- sample generated by bootstraping from an alignment of one gene family present in 11 genomes Quartet spectral analyses of genomes iterates over three loops:  Repeat for all bootstrap samples.  Repeat for all possible embedded quartets.  Repeat for all gene families. : embedded quartet for genomes 1, 4, 9, and 10. This bootstrap sample supports the topology ((1,4),9,10). 1 4 9 10 1 9 4 1 9 4 

7. Total number of gene families containing the species quartet Number of gene families supporting the same topology as the plurality (colored according to bootstrap support level) Number of gene families supporting one of the two alternative quartet topologies Illustration of one component of a quartet spectral analyses Summary of phylogenetic information for one genome quartet for all gene families

8. 330 possible quartets quartets Number of datasets 685 datasets show conflicts with plurality 1128 datasets from relaxed core (core datasets + datasets with one or two taxa missing) Quartet Spectrum of 11 cyanobacterial genomes

9. PLURALITY SIGNAL

10. Conflicts with plurality signal are observed in sets of orthologs across all functional categories, including genes involved in translation and transcription 624/1128 ≈ 55%

11. Genes with orthologs outside the cyanobacterial phylum: Distribution among Functional Categories (using COG db, release of March 2003) Cyanobacteria do not form a coherent group (160) Cyanobacteria do form a coherent group, but conflict with plurality (294) 700 phylogenetically useful extended datasets

12. Example of inter- phylum transfer: threonyl tRNA synthetase

13.  In case of the marine Synecchococcus and Prochlorococcus spp. the plurality consensus is unlikely to reflect organismal history.  This is probably due to frequent gene transfer mediated by phages e.g.:  These conflicting observations are not limited to pro- karyotes. In incipient species of Darwin ’ s finches frequent introgression can make some individuals characterized by morphology and mating behavior as belonging to the same species genetically more similar to a sister species (Grant et al. 2004 “ Convergent evolution of Darwin's finches caused by introgressive hybridization and selection ” Evolution Int J Org Evolution 58, 1588-1599). Species evolution versus plurality consensus

14. The Coral of Life (Darwin)

15. Coalescence – the process of tracing lineages backwards in time to their common ancestors. Every two extant lineages coalesce to their most recent common ancestor. Eventually, all lineages coalesce to the cenancestor. t/2 (Kingman, 1982) Illustration is from J. Felsenstein, “Inferring Phylogenies”, Sinauer, 2003

16. Coalescence of ORGANISMAL and MOLECULAR Lineages 20 lineages One extinction and one speciation event per generation One horizontal transfer event once in 5 generations (I.e., speciation events) RED: organismal lineages (no HGT) BLUE: molecular lineages (with HGT) GRAY: extinct lineages 20 lineages One extinction and one speciation event per generation One horizontal transfer event once in 5 generations (I.e., speciation events) RED: organismal lineages (no HGT) BLUE: molecular lineages (with HGT) GRAY: extinct lineages RESULTS: Most recent common ancestors are different for organismal and molecular phylogenies Different coalescence times Long coalescence time for the last two lineages RESULTS: Most recent common ancestors are different for organismal and molecular phylogenies Different coalescence times Long coalescence time for the last two lineages Time

17. Adam and Eve never met  Albrecht Dürer, The Fall of Man, 1504 Mitochondrial Eve Y chromosome Adam Lived approximately 50,000 years ago Lived 166,000-249,000 years ago Thomson, R. et al. (2000) Proc Natl Acad Sci U S A 97, 7360-5 Underhill, P.A. et al. (2000) Nat Genet 26, 358-61 Cann, R.L. et al. (1987) Nature 325, 31-6 Vigilant, L. et al. (1991) Science 253, 1503-7 The same is true for ancestral rRNAs, EF, ATPases!

18. EXTANT LINEAGES FOR THE SIMULATIONS OF 50 LINEAGES

19. green: organismal lineages ; red: molecular lineages (with gene transfer) Lineages Through Time Plot 10 simulations of organismal evolution assuming a constant number of species (200) throughout the simulation; 1 speciation and 1 extinction per time step. (green O) 25 gene histories simulated for each organismal history assuming 1 HGT per 10 speciation events (red x) log (number of surviving lineages)

20. Bacterial 16SrRNA based phylogeny (from P. D. Schloss and J. Handelsman, Microbiology and Molecular Biology Reviews, December 2004.) The deviation from the “long branches at the base” pattern could be due to under sampling an actual radiation due to an invention that was not transferred following a mass extinction