Rooting a phylogenetic tree requires inclusion in the analysis of what is called an outgroup*, a set of genes that are
homologous to the selected molecular marker, but branching
outside the study group. For the universal tree of life, a major
difficulty arises because all organisms are inside the tree. In
1978, Schwartz and Dayhoff proposed an elegant theoretical
solution to this problem using the protein sequences of
paralogous genes* that have undergone a duplication event
prior to LUCA (Schwartz and Dayhoff 1978). If no gene loss
subsequently occurred during the course of evolution, these
genes should be present in two copies in LUCA and also in the
members of the three domains of life. Inferring the phylogeny
of these paralogues provides a symmetrical phylogenetic tree
in which the phylogeny of one set of paralogues is rooted by
the other paralogous sequences and vice versa (Fig. 4.6b).
This approach was tested independently by two research
groups (Gogarten et al. 1989; Iwabe et al. 1989) who used
the sequences of elongation factors EF-1α and EF-2 and the
sequences of the F and vacuolar H
+
-ATPases, respectively.
Both studies resulted in placing the root in the bacterial
branch (Fig. 4.6a, tree 1).
The position of the root of the universal tree of life in the
bacterial branch was quickly adopted by a majority of the
scientific community because it is consistent with the
hypothesis that LUCA was a prokaryotic organism and that
bacteria form the most ancient evolutionary lineage. However, this result was also very controversial. Some believe
that the amount of phylogenetic information contained in
these markers is not sufficient to infer events as ancient as
these. Indeed, the same markers used with different methods
of analysis can place the universal root in the eukaryotic
branch (Fig. 4.6a, tree 2).
O
O
C
O
O
P
O
O
X
O
C
a
b
c
LIPIDS OF NON HYPERTHERMOPHILIC PROKARYOTES
LIPIDS OF HYPERTHERMOPHILIC ARCHAEA
O
Fatty acids
Hydrophilic group
-
Glycerol
Phytanyl chain
HC
H 2 C
H 2 C
H 2 C
O
HC
CH 2
R
O
O
Biphytanyl chain
O
HC
CH 2
R 1
R 1
O
O
O
O
CH
O
H 2 C
CH 2
CH 2
Fig. 4.5 Sketch showing the
organisation of polar membrane
lipids in Bacteria and Archaea.
(a) In Bacteria, the most
abundant polar lipids are
glycerophospholipids in which
two molecules of fatty acids are
linked by an ester linkage to
glycerol at positions C-1 and C-2.
Phospholipids form a bilayer. (b)
Among non-hyperthermophilic
Archaea, the basic unit of polar
lipids is of the isoprenic glycerol
ether type: two phytanyl
molecules are linked by ether
bonds to a glycerol molecule. In
the cytoplasmic membrane,
diethers are organised in a double
layer (R ¼ phosphate or
aminophosphate with polar head).
Diethers have also been identified
in some thermophilic Bacteria
(Thermodesulfobacterium
commune, Ammonifex degensii,
Aquifex pyrophilus). (c) In
hyperthermophilic Archaea, the
basic structure is glycerol
tetraether: two identical,
saturated, biphytanyl chains in
nC 40 H 82 are linked by an ether
bond to two opposite glycerol
molecules forming a monolayer
(R1 ¼ sugar residue). This type
of molecular organisation
withstands temperatures above
80
C
84
J.-C. Bertrand et al.
homologous to the selected molecular marker, but branching
outside the study group. For the universal tree of life, a major
difficulty arises because all organisms are inside the tree. In
1978, Schwartz and Dayhoff proposed an elegant theoretical
solution to this problem using the protein sequences of
paralogous genes* that have undergone a duplication event
prior to LUCA (Schwartz and Dayhoff 1978). If no gene loss
subsequently occurred during the course of evolution, these
genes should be present in two copies in LUCA and also in the
members of the three domains of life. Inferring the phylogeny
of these paralogues provides a symmetrical phylogenetic tree
in which the phylogeny of one set of paralogues is rooted by
the other paralogous sequences and vice versa (Fig. 4.6b).
This approach was tested independently by two research
groups (Gogarten et al. 1989; Iwabe et al. 1989) who used
the sequences of elongation factors EF-1α and EF-2 and the
sequences of the F and vacuolar H
+
-ATPases, respectively.
Both studies resulted in placing the root in the bacterial
branch (Fig. 4.6a, tree 1).
The position of the root of the universal tree of life in the
bacterial branch was quickly adopted by a majority of the
scientific community because it is consistent with the
hypothesis that LUCA was a prokaryotic organism and that
bacteria form the most ancient evolutionary lineage. However, this result was also very controversial. Some believe
that the amount of phylogenetic information contained in
these markers is not sufficient to infer events as ancient as
these. Indeed, the same markers used with different methods
of analysis can place the universal root in the eukaryotic
branch (Fig. 4.6a, tree 2).
O
O
C
O
O
P
O
O
X
O
C
a
b
c
LIPIDS OF NON HYPERTHERMOPHILIC PROKARYOTES
LIPIDS OF HYPERTHERMOPHILIC ARCHAEA
O
Fatty acids
Hydrophilic group
-
Glycerol
Phytanyl chain
HC
H 2 C
H 2 C
H 2 C
O
HC
CH 2
R
O
O
Biphytanyl chain
O
HC
CH 2
R 1
R 1
O
O
O
O
CH
O
H 2 C
CH 2
CH 2
Fig. 4.5 Sketch showing the
organisation of polar membrane
lipids in Bacteria and Archaea.
(a) In Bacteria, the most
abundant polar lipids are
glycerophospholipids in which
two molecules of fatty acids are
linked by an ester linkage to
glycerol at positions C-1 and C-2.
Phospholipids form a bilayer. (b)
Among non-hyperthermophilic
Archaea, the basic unit of polar
lipids is of the isoprenic glycerol
ether type: two phytanyl
molecules are linked by ether
bonds to a glycerol molecule. In
the cytoplasmic membrane,
diethers are organised in a double
layer (R ¼ phosphate or
aminophosphate with polar head).
Diethers have also been identified
in some thermophilic Bacteria
(Thermodesulfobacterium
commune, Ammonifex degensii,
Aquifex pyrophilus). (c) In
hyperthermophilic Archaea, the
basic structure is glycerol
tetraether: two identical,
saturated, biphytanyl chains in
nC 40 H 82 are linked by an ether
bond to two opposite glycerol
molecules forming a monolayer
(R1 ¼ sugar residue). This type
of molecular organisation
withstands temperatures above
80
C
84
J.-C. Bertrand et al.