RECONSTRUCTING A “UNIVERSAL TREE”
All living things share same common ancestor
Classical view
Prokaryotes
Eukaryotes
1977: C. Woese
3 “primordial kingdoms” (or domains)
Archaea
Bacteria
Eucarya
- based on ribosomal RNA
sequence comparisons
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
1989: Iwabe - rooting the universal tree
- if set of duplicated genes is present in all 3 lineages,
then duplication must have occurred in their common ancestor
Fig. 5.40
- can use one gene (eg. Gene A2) as an outgroup when comparing
the other one (Gene A1) in all 3 lineages
- 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
Fig. 5.41
Bacterial lineage diverged prior to archaeal & eukaryotic ones
Plant-animal-fungal trichotomy
Eucarya
Bacteria
Archaea
Fig. 5.39
Where would you place the root on this tree?
Maximum parsimony analysis of a – 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
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….
Fig. 5.45
Dot = divergence point of
a-proteobacterial and mitochondrial
lineages
chloroplast
How do you interpret the
data in this figure?
Phylogenetic tree based on
SSU ribosomal RNA data
mitochondrial
Gray PNAS 86: 2267, 1989
Protists are very diverse grouping
Tree based on
ribosomal RNA data
Certain protists (a few? lineages) lack mitochondria
Fig. 5.39
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
Brown Nat Rev Genet 4:121, 2003
Evolutionary pathway for
origin of eukaryotic cell
Many genes transferred
to nucleus
… a few retained in
organelle
& others lost
Alberts Fig. 14-56
Chimeric nature of eukaryotic nuclear genomes
Eukaryotic genomes have bacterial-type
and archaeal-type genes
Fig. 5.43
Certain genes for DNA replication/repair, transcription/translation…
shared by archaea & eukaryotes (but absent in bacteria)
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
Model for origin of nucleus-cytosol compartmentalization “in the wake
of mitochondrial origin”
Martin & Koonin Nature 44:41, 2006
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)
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
True tree
C
A
B
Inferred tree
C
Fig. 7.22
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
“Web-of-life”
Doolittle “Uprooting the tree
of life” Sci.Amer. 282:90, 2000
www.whoi.edu/cms/images/oceanus/2005/4/v43n
2-teske_edwards1en_8591.gif
Was early cellular life communal?
How rampant was (is) lateral gene transfer - especially among microbes?
“Highways of gene sharing” among prokaryotes?
Transposable elements carry along “foreign genes?”
and Doolittle Science 284: 2124, 1999
Informational genes: machinery for transcription, translation, DNA replication...
Operational genes: “housekeeping genes” for cellular processes (biosynthesis
of amino acids, fatty acids, nucleotides, cell envelope proteins...)
Doolittle Cold Spring Harbor Symp. 2009
“Prokaryotic evolution and the tree of life are two different things”
Bapteste et al. Biol. Direct 4:34, 2009
“A molecular tree-of-life based on
ribosomal RNA sequence comparisons”
Pace “Mapping the Tree of Life: Progress
and Prospects” Microbiol.Mol. Biol. Rev.
73:565, 2009