1. The Last Common Ancestor and the Three Domains of Life or….

2. A Case History of the only current example of life that we have..
Trees, domains, and ancestry..
Where does the whole idea come from?

9. 16S rRNA
Chop into pieces with enzymes
Separate pieces with 2D electrophoresis gel
Creates fingerprint
Sequence and catalogue each spot
Phylogenetic structure of the prokaryotic domain: the primary kingdoms, PNAS November 1, 1977 vol. 74 no

12. These observations gave rise to…
The root of the tree
The idea of a last common ancestor
The role of horizontal gene transfer vs lateral transfer

13. Tree Structure
Bifurcating – sex vs clonal
Rooting

14. Time
Now
Then
Gogarten et al and Miyata et al in 1989, used ancient duplication event to root the tree that separated the bacteria from the archaea/eukaryotes

15. Mosaic nature of genomes once we started sequencing them
Mosaic nature of genomes once we started sequencing them. We can now sequence a genome in a week… if you have the money… even that’s getting cheaper..

16. Complex -> Simple, Forterre et al
All attempts to reconcile various nucleic acid datasets
Ring of Life, Lakes et al

17. Last Common Ancestor LUCA – last universal common ancestor
LUA – last universal ancestor
Cenancestor (number one)
MRCA – most reacent common ancestor

19. Properties shared by all living organisms
Genetic code based on 4 nucleotides
3 letter codons, 20 AA,
DNA repair
DNA polymerase, double stranded DNA maintained
single stranded RNA intermediate
genetic code expressed in proteins
Ribosomes
ATP as energy currency
lipid bilayers as cellular membrane
intracellular sodium is lower, phosphorus is higher and mainatined by ion pumps
cell division
COMPLEX
COMPLEX

20. LUCA Not a simple, primitive, hyperthermophilic prokaryote
a complex community of protoeukaryotes with a RNA genome, adapted to a broad range of moderate temperatures, genetically redundant, morphologically and metabolically diverse.
LUCA's genetic redundancy predicts loss of paralogous gene copies in divergent lineages to be a significant source of phylogenetic anomalies, i.e. instances where a protein tree departs from the SSU-rRNA genealogy
horizontal gene transfer may not have the rampant character assumed by many.
Examining membrane lipids suggest LUCA had sn1,2 ester fatty acid lipids from which Archaea emerged from the outset as thermophilic by "thermoreduction," with a new type of membrane, composed of sn2,3 ether isoprenoid lipids; this occurred without major enzymatic reconversion.
Bacteria emerged by reductive evolution from LUCA and some lineages further acquired extreme thermophily by convergent evolution.
This scenario is compatible with the hypothesis that the RNA to DNA transition resulted from different viral invasions as proposed by Forterre.
Beyond the controversy opposing "replication first" to metabolism first", the predictive arguments of theories on "catalytic closure" or "compositional heredity" heavily weigh in favour of LUCA's ancestors having emerged as complex, self-replicating entities from which a genetic code arose under natural selection.
Glansdorff, Xu, & Labedan, 2008, Biology Direct

21. Ancestor was hypothesized, based on gene trees and the genetic distance between living cells and fossils to be 3.5 to 3.9 GA
Possible caveats
Some lineages went extinct
genetic heritage of all modern organisms derived through horizontal gene transfer among an ancient community of organisms.
panspermia.

22. Confounding the picture of the three domains of life and the concept of the last common ancestor, is the reality of
Horizontal Gene Transfer

23. Quick facts
When you do phylogenetic reconstruction on rRNA’s, in >15,000 sequences, about 99% of the time, DO NOT appear to horizontally transfer.
Margaret Dayhoff, physical chemist, and the mother of bioinformatics, based all her metrics on the assumption that genes did not move horizontally.

24. How do you find HGT Sequence context (recent events)
G+C content, codon usage
Phylogenetic incongruencies (more ancient events)

25. Doolittle, SciAmer

26. An alternative if to choose metabolic pathways that might have been integral to HGT events and the evolution of life

28. Ability to fix nitrogen found in wide variety of prokaryotes (bacteria and archaea)
Singular origin of nif genes though they show a paraphyletic distribution - horizontal gene transfer (HGT), selective loss?
Nif gene homologs have been recruited from/into many pathways, including bacteriochlorophyll biosynthesis, FeS cluster assembly and insertion, hydrogenase, regulation of heterocyst differentiation
Nif genes sometimes found on plasmids (in rhizobia); facilitation of HGT?

29. Alternative nitrogenases
Nif D, K
NifH
nifH
nifD
niK
nifE
nifN

30. Raymond et al, 2004

32. Interdisciplinary approaches…
To understand the genetic record of earth life and the LCA, we have to understand the ecology in which life evolved… from the individual micro environments that may have been present to the elemental abundances provided by the unique place we occupy in space.

34. Another sample would be nice… really nice.
If we know what to do with it…

35. Janet, did you ever wonder why as we get older we become more careful and less willing to take a chance, when we really have nothing to lose. And young people, they have everything ahead of them, and yet take so many chances… you would have thought evolution would have wired our brains differently than that…
12 January 1927 – 27 October 2007)
Never underestimate the complex, improbable beauty and creative potential of evolution. The conundrums keep us guessing.