Origin and Evolution of Early Eukaryotes
National University of Ireland Maynooth,
August 25th, 2009,
And the LORD God made all kinds of
trees grow out of the ground--trees
that were pleasing to the eye and
good for food. In the middle of the
garden were the tree of life and the
tree of the knowledge of good and
Hypothesis Implied Relationship s Phylogenetic signals expected in genomic
analys e s
Tree of lifea Archaea and Eukaryota Eukaryotic genes should show 3
are sister groups. monophyletic domains or Eukaryota
Eukaryota- Eukaryota is the first Most eukaryotic genes should not have a
firstb diverging domain, while prokaryotic homologue. Others should
Eubacteria and Archaea show 3 monophyletic domains or
are sister groups. Eukaryota with Archaebacteria .
Eocytec Eukaryota is the sister Eukaryotic genes with Crenarchaeota .
group of Crenarchaeota .
Phagotrophyd Eukaryota and Archaea Eukaryotic genes with Archaebacteria,
are sister groups. This and these two with Actinobacteria.
group stemmed from
Serial Symbiosis of a Eukaryotic genes with Thermoplasma,
endosymbiosise Thermoplasma-like spirochetes or -Proteobacteria .
archaeon and a spirochete
Mitochondria probably via
symbiosis with an -
Syntrophy-1f Eukaryota originated Eukaryotic genes with methanogenic
through the symbiosis of a Archaea (or within Euryarchaeota), - or
methanogen and a - -Proteobacteria.
Hydrogen Eukaryota originated Eukaryotic genes with methanogenic
Hypothesisg through the symbiosis of a Archaea (or within Euryarchaeota) or -
methanogen and an - Proteobacteria .
Syntrophy-2h Eukaryota originated Eukaryotic genes with Thermoplasmatales
through the symbiosis of a (or within Euryarchaeota) or -
sulfur-methabolising Proteobacteria .
euryarchaeote and an -
Ring of lifei Eukaryota originated Eukaryotic genes with Crenarchaeota or
through the symbiosis of a -Proteobacteria.
Crenarchaeota and an -
Comparisons of the same bacterial
E. coli K12 E. Coli 0157:H7
Horizontal gene transfer
does occur between species
McInerney, J.O., Cotton, J.A. and Pisani, D. (2008) The Prokaryotic Tree of Life:
Past, Present...and Future? Trends in Ecology and Evolution 23 (5) 276-281
Doubts concerning a universal tree
…most archaeal and bacterial genomes (and
the inferred ancestral eukaryotic nuclear
genome) contain genes from multiple
…If "chimerism" or "lateral gene transfer"
cannot be dismissed as trivial in extent or
limited to special categories of genes, then
no hierarchical universal classiﬁcation can
be taken as natural. Ford Doolittle
Phylogenetic classification and the universal tree.
Doolittle WF. Science. 1999 Nov 19;286(5444):1443
The importance of congruence
• “The importance, for
classification, of trifling
characters, mainly depends on
their being correlated with
several other characters of more
or less importance. The value
indeed of an aggregate of
characters is very evident ...a
classification founded on any
single character, however
important that may be, has
• Charles Darwin
• Origin of Species, Ch. 13
Fitzpatrick, D.A., Creevey, C.J. and McInerney, J.O. (2006). Genome Phylogenies Indicate a Meaningful α-Proteobacterial Phylogeny and
Support A Grouping of the Mitochondria With the Rickettsiales. Molecular Biology and Evolution 23: 74-85.
The mitochondrion is
descended from a common
ancestor with the
Pisani, D., Cotton, J.A. and McInerney, J.O. (2007). Supertrees Disentangle the Chimerical
Origin of Eukaryote Genomes. Molecular Biology and Evolution. 24(8):1752–1760.
• All Saccharomyces cerevisiae proteins
subjected to homology search against
Caenorhabditis elegans, Arabidopsis thaliana,
Schizosaccharomyces pombe, Neurospora
crassa, Ashbya gossypii, Trypanosoma cruzi.
• Multiple alignment of resulting significant hits and
profile search against prokaryotic genomes (197
bacterial, 22 archaebacterial).
• Two datasets used:
– Phylogeny independent
• 2,460 out of 6,704 genes have prokaryotic
• 1,980 genes have a eubacterial best hit,
• 952 genes have only eubacterial
homologs, 216 only archaebacterial.
So there is a larger role for
• Which is more important….
– An informational or an operational gene?
– A highly-expressed gene or a lowly-
– A gene that is central to metabolism or
one that is peripheral?
– A gene that is lethal upon knockout or one
that is not?
• We describe associations between factors using
the odds ratio.
• e.g., the odds of being archaebacterial for
informational genes is calculated as the
probability of an informational gene having an
archaebacterial homolog, divided by the
probability of the gene having a eubacterial
• We can similarly calculate the odds of being
archaebacterial for operational genes, and the
odds ratio is the ratio of these two odds.
Confirmation of informational
• We confirm a significant bias towards
archaebacterial homology for genes with
informational functions (odds ratio
(or)=2.37; 95% confidence interval
(ci)=1.59-3.52), although genes with
archaebacterial homologs are found across
most gene ontology biological processes.
Link between lethality and
• Lethal genes are almost three times as
likely to have archaebacterial homologs
than bacterial ones (or=2.96; 2.32-3.77).
• Informational genes are significantly more
likely to be lethal than operational genes
Link between lethality and
• Lethality of archaebacterial genes is almost
identical across the two categories (for
informational genes, or=2.01; 0.92-4.41; for
operational genes, or=1.89; 1.43-2.47)
DATATYPE Bact Arch All p-value
L phase, number of SAGE tags sequenced 1.76 (1.43,2.17) 3.42 (2.15,5.16) 1.96 (1.74,2.21) 0.0034
S phase, number of SAGE tags sequenced 1.93 (1.59,2.33) 2.97 (1.94,4.35) 2.05 (1.82,2.30) 0.0395
G2/M phase boundary, number of SAGE tags 1.55 (1.27,1.88) 2.99 (1.97,4.39) 2.04 (1.81,2.28) 0.0028
Closeness Centrality in interaction network 0.314 0.324 0.316 < 0.0001
(0.312,0.316) (0.321,0.327) (0.315,0.317)
Degree in interaction network 15.91 20.90 18.02 < 0.0001
(15.20,16.62) (19.33,22.48) (17.60,18.48)
Number of homologs in yeast genome 13.13 8.02 (6.89,9.22) 7.58 (7.14,8.04) 1
P-values are bootstrap probabilities for the mean of the statistic in archaebacteria
being less than or equal to the mean in eubacteria, based on 10,000 replicates.
• Eukaryote “Tree”
– Davide Pisani
– James Cotton
– Angela McCann
• Prokaryotic “Tree”
– Chris Creevey
– David Fitzpatrick
– Mary O’Connell
– Melissa Pentony
– Simon Travers
– Rhoda Kinsella
– Gayle Philip
– Jennifer Commins
– Thomas Keane
• Supertree Theory
– Dr. Mark Wilkinson,
Natural History Museum.
• Irish Centre for High End Computing
• NUIM HPC
– Marie Curie