1. RECONSTRUCTING A “UNIVERSAL TREE” Classical view Prokaryotes Eukaryotes 1977: C. Woese 3 “primordial kingdoms” (or domains) - based on ribosomal RNA sequence comparisons All living things share same common ancestor Bacteria Archaea Eucarya Aside: Archaea are not just extremophiles “...the large numbers of environmental rRNA gene sequences...show that [archaea] are present in almost all environments examined...” Robertson Curr Opin Microbiol 2006

2. 1989: Iwabe - rooting the universal tree - if set of duplicated genes is present in all 3 lineages, - can use one gene (eg. Gene A2) as an outgroup when comparing the other one (Gene A1) in all 3 lineages Fig. 5.40 then duplication must have occurred in their common ancestor

3. Fig. 5.41 - Translational elongation factors EF-G and EF-Tu are homologous and both genes are present in all life forms … so ancient duplication prior to divergence of 3 superkingdoms Bacterial lineage diverged prior to archaeal & eukaryotic ones

4. Plant-animal-fungal trichotomy Fig. 5.39 Where would you place the root on this tree? Bacteria Archaea Eucarya

5. Maximum parsimony analysis of  – tubulin sequences “Bootstrap values above 50% are indicated above the nodes … and decay values (additional steps needed to collapse a node) below.” “…all parsimony and distance-based analyses of four large and diverse data sets support a sister-group relationship between animals and fungi.” Baldauf & Palmer PNAS 90:11558, 1993

6. ENDOSYMBIOTIC ORIGIN OF ORGANELLES 1910 - Mereschkowsky – morphological similarities between chloroplasts/mitochondria and bacteria 1960’s - DNA and ribosomes discovered in chloroplasts/mitochondria 1970 - Margulis – physiological, biochemical similarities… late 1970’s - Gray, Doolittle (Halifax) - molecular evidence for endosymbiotic origin, from ribosomal RNA data eg. chloroplast & cyanobacterial sequences are more similar than either is to nuclear homologue….

7. Fig. 5.45

8. Gray PNAS 86: 2267, 1989 Phylogenetic tree based on SSU ribosomal RNA data chloroplast mitochondrial How do you interpret the data in this figure? Dot = divergence point of  -proteobacterial and mitochondrial lineages

9. Certain protists (a few? lineages) lack mitochondria Fig. 5.39 Protists are very diverse grouping Tree based on ribosomal RNA data

10. Did such protist lineages diverge before time of mitochondrial endosymbiotic event? … or did they lose their mitochondria later on? 1997- 98 Mitochondrial-type genes for heat shock proteins, etc … found in nucleus of Microsporidia, Giardia… 1999 - additional sequence data places Microsporidia within fungal clade 2003 – Giardia actually has remnant mitochondria mitosome Nature 426: 172, 2003

11. Brown Nat Rev Genet 4:121, 2003

12. Alberts Fig. 14-56 Evolutionary pathway for origin of eukaryotic cell Many genes transferred to nucleus & others lost … a few retained in organelle

13. Fig. 5.43 Certain genes for DNA replication/repair, transcription/translation… shared by archaea & eukaryotes (but absent in bacteria) Chimeric nature of eukaryotic nuclear genomes Possible explanations: 1. Eukaryotic ancestor - archaeal, but bacterial-type genes acquired through horizontal transfer - from organelles (bacterial endosymbiotic origin) - more recent direct transfer from bacteria 2. Eukaryotic ancestor - chimeric fusion of bacterial & archaeal-type genomes Eukaryotic genomes have bacterial-type and archaeal-type genes

14. Martin & Koonin Nature 44:41, 2006 Model for origin of nucleus-cytosol compartmentalization “in the wake of mitochondrial origin”

15. HORIZONTAL GENE TRANSFER (p. 359-366) - lateral transfer of genetic information from one genome to another (eg. between two species) Mechanisms: 1.Transformation - via free DNA (vector not essential) 2. Transduction - via bacteriophage or virus 3. Conjugation in bacteria - via conjugative plasmid Estimated that ~ 10-18% of E.coli genome due to LGT eg. lactose operon (milk sugar lactose used as carbon source in mammalian colon)

16. Detecting lateral gene transfer 1. Odd distribution patterns or unexpectedly high similarity to homologues in distant species 2. Unusual nucleotide composition (eg. codon usage bias, GC content) 3. Incongruent phylogenetic trees A B CAB C True treeInferred tree Fig. 7.22

17. Implications of lateral gene transfer? 1. Acquisition of new function 2. Replacement of “native” gene with “captured” one 3. In bacteria, acquired genes for particular function may be co-ordinately regulated (operon) 4. Acquisition may re-define ecological niche of microbe

18. and Doolittle Science 284: 2124, 1999 “Web-of-life” How rampant was (is) lateral gene transfer - especially among microbes? Was early cellular life communal? “Highways of gene sharing” among prokaryotes? Transposable elements carry along “foreign genes?” www.whoi.edu/cms/images/oceanus/2005/4/v43n 2-teske_edwards1en_8591.gif Doolittle “Uprooting the tree of life” Sci.Amer. 282:90, 2000

19. Operational genes: “housekeeping genes” for cellular processes (biosynthesis of amino acids, fatty acids, nucleotides, cell envelope proteins...) Informational genes: machinery for transcription, translation, DNA replication... Doolittle Cold Spring Harbor Symp. 2009

20. Bapteste et al. Biol. Direct 4:34, 2009 Pace “Mapping the Tree of Life: Progress and Prospects” Microbiol.Mol. Biol. Rev. 73:565, 2009 “Prokaryotic evolution and the tree of life are two different things” “A molecular tree-of-life based on ribosomal RNA sequence comparisons”