This proposal by Woese has profoundly changed the way
we consider the evolution of prokaryotes. His choice of a
conserved, universal, marker that nevertheless contained
variations helped reshape the phylogeny and taxonomy
of prokaryotes, characterize microbial habitats, identify
non-culturable pathogens, and propose evolutionary
scenarios that are regularly revisited in the light of
developments in molecular biology. However, a weakness
of this proposal is that it is based on one marker, the 16S
ribosomal RNA, and a too limited number of phenotypic
markers. It should also be noted that the term chosen for one
of the two prokaryotic domains (Archaea) suggests a greater
antiquity of these microorganisms. However, the current
data cannot in any case be used to infer that the Archaea
are the ancestral forms of life nor of course that would have
had a hyperthermophilic archaeal origin from which the
other prokaryotes would have derived. The characteristics
of the last common ancestor (“last universal common
CAMBRIAN
ORDOVICIAN
SILURIAN
DEVONIAN
CARBONIFEROUS
PERMIAN
TRIASSIC
PALEOZOIC
JURASSIC
CRETACEOUS
MESOZOIC
CENOZOIC
600 million years
500
440
400
350
270
225
135
180
70
00
Shark
Carp
Newt
Chicken Echidna Kangaroo
Dog
Man
Shark
Carp
Newt
Chicken
Echidna
Kangaroo
Dog
% difference between amino
acid sequences
46,1
44,0
59,4
61,4
59,7
60,4
55,4
56,8
53,2
51,4
53,6
50,7
47,9
48,6
53,2
44,7
50,4
47,5
34,0
29,1
31,2
24,8
34,8
29,8
26,2
23,4
19,1
16,3
Fig. 5.3 Protein sequence alignment (partial) of the alpha hemoglobin
of man, dog, kangaroo, echidna, chicken, newt, carp, and shark. The
sequences of morphologically similar organisms are closer. From the
calculation of genetic distances (% difference between the amino acid
sequences in the protein), a distance matrix was generated and a
phylogenetic tree was created, wherein the length of the branches
corresponds to the number of differences. On the left side of the figure,
a geological scale shows the probable age of the common ancestor of
the different taxa (neighbor joining, distances according to Kimura
1968)
Box 5.3: Molecular Clock
Celine Brochier-Armanet
This well-known hypothesis relies on the assumption
that molecular sequences (DNA and proteins) evolve
at a constant rate, meaning that their evolutionary rate
(r) is constant over time. The molecular clock hypothesis was postulated in the early 1960s based on the
first analyses of protein sequences (hemoglobin,
cytochrome C, fibrinopeptides, etc.) which showed
that the divergence observed between two sequences
is proportional to the divergence time between the
corresponding species. This is due to the fact that
C. Brochier-Armanet (*)
Laboratoire de Biome ´trie et Biologie E ´ volutive,
UMR CNRS 5558, Universite ´ Claude Bernard Lyon 1,
69622 Villeurbanne Cedex, France
(continued)
5 Systematic and Evolution of Microorganisms: General Concepts
117
we consider the evolution of prokaryotes. His choice of a
conserved, universal, marker that nevertheless contained
variations helped reshape the phylogeny and taxonomy
of prokaryotes, characterize microbial habitats, identify
non-culturable pathogens, and propose evolutionary
scenarios that are regularly revisited in the light of
developments in molecular biology. However, a weakness
of this proposal is that it is based on one marker, the 16S
ribosomal RNA, and a too limited number of phenotypic
markers. It should also be noted that the term chosen for one
of the two prokaryotic domains (Archaea) suggests a greater
antiquity of these microorganisms. However, the current
data cannot in any case be used to infer that the Archaea
are the ancestral forms of life nor of course that would have
had a hyperthermophilic archaeal origin from which the
other prokaryotes would have derived. The characteristics
of the last common ancestor (“last universal common
CAMBRIAN
ORDOVICIAN
SILURIAN
DEVONIAN
CARBONIFEROUS
PERMIAN
TRIASSIC
PALEOZOIC
JURASSIC
CRETACEOUS
MESOZOIC
CENOZOIC
600 million years
500
440
400
350
270
225
135
180
70
00
Shark
Carp
Newt
Chicken Echidna Kangaroo
Dog
Man
Shark
Carp
Newt
Chicken
Echidna
Kangaroo
Dog
% difference between amino
acid sequences
46,1
44,0
59,4
61,4
59,7
60,4
55,4
56,8
53,2
51,4
53,6
50,7
47,9
48,6
53,2
44,7
50,4
47,5
34,0
29,1
31,2
24,8
34,8
29,8
26,2
23,4
19,1
16,3
Fig. 5.3 Protein sequence alignment (partial) of the alpha hemoglobin
of man, dog, kangaroo, echidna, chicken, newt, carp, and shark. The
sequences of morphologically similar organisms are closer. From the
calculation of genetic distances (% difference between the amino acid
sequences in the protein), a distance matrix was generated and a
phylogenetic tree was created, wherein the length of the branches
corresponds to the number of differences. On the left side of the figure,
a geological scale shows the probable age of the common ancestor of
the different taxa (neighbor joining, distances according to Kimura
1968)
Box 5.3: Molecular Clock
Celine Brochier-Armanet
This well-known hypothesis relies on the assumption
that molecular sequences (DNA and proteins) evolve
at a constant rate, meaning that their evolutionary rate
(r) is constant over time. The molecular clock hypothesis was postulated in the early 1960s based on the
first analyses of protein sequences (hemoglobin,
cytochrome C, fibrinopeptides, etc.) which showed
that the divergence observed between two sequences
is proportional to the divergence time between the
corresponding species. This is due to the fact that
C. Brochier-Armanet (*)
Laboratoire de Biome ´trie et Biologie E ´ volutive,
UMR CNRS 5558, Universite ´ Claude Bernard Lyon 1,
69622 Villeurbanne Cedex, France
(continued)
5 Systematic and Evolution of Microorganisms: General Concepts
117