ancestor” LUCA) are difficult to determine, and there is no
consensus on its hyperthermophilic character (Galtier et al.
1999; Di Giulio 2003) or on its belonging to the bacterial or
archaeal phyla, as proposed by Cavalier-Smith (2002a, b)
(cf. Sect. 4.3.3).
Cavalier-Smith (2002a, b), who used different criteria to
expand his vision of the phylogeny and taxonomy of
prokaryotes, proposed taxa and a topology that are far from
unanimously accepted in ICSP (Fig. 5.5). Despite the fact
that they were validly published in the reference journal for
bacterial taxonomy, many of these taxa are therefore not
adopted in this book. The tree of life based on concepts and
latest molecular tools will be presented later (cf. Sect. 5.5).
5.2
Microorganisms: Unicellular
or Multicellular?
Microorganisms as a whole, including eukaryotes, do not
constitute a monophyletic group of organisms (cf. Chap. 7).
However, they can be considered as a well-defined set of
organisms according to their morphology, particularly by
their uni- or almost unicellularity. The notion of
unicellularity (or almost unicellularity), as opposed to multicellularity, is actually much less clear as one may think at
first. Between unicellularity and multicellularity, the boundary is in fact blurred, rather corresponding to a continuum.
In a unicellular organism, the cells are physically isolated
and (at least theoretically) independent. A typical multicellular organism is (1) made by numerous cells; (2) its cells
contain a single nucleus (in the case of a eukaryote); (3) its
cells communicate, in one of several way (pores, synapses,
etc.), allowing them to exchange morphogenetic
informations and chemicals (products of metabolism)
(Fig. 5.6f); and (4) a specialization appears between cells.
A multicellular organism is therefore not an association of
identical and totipotent cells but a set of specialized cells that
can eventually organize themselves into tissues and organs.
As noted above, there are many intermediate cases
between strict unicellularity and strict multicellularity: the
main ones are those of colonial and filamentous organisms
without cell specialization.
The closest organisms to unicellularity are colonial
organisms which are single-celled organisms whose cells
remain associated during their division by extracellular
mucus; hydrodynamism can eventually dissociate them.
Although there may be chemical interactions between
cells, there is no physical communication between them.
The colonial organisms are not multicellular. However, the
question may arise for Labyrinthulobionta (Stramenopiles,
eukaryotes) in which cells move in a common envelope
(labyrinth) that they contribute to secrete (Fig. 5.6c). The
Box 5.3 (continued)
mutations occur randomly and mainly at neutral sites.
Accordingly, mutations will be fixed (leading to
substitutions) at a constant rate (Kumar 2005).
A constant rate r implies a linear relation between
the divergence time (t) and the evolutionary distance
(D) between two homologous sequences. More precisely, under a molecular clock assumption, D ¼ 2 * r
* t. Based on this relation, it is possible to perform
molecular dating, meaning that knowing D, the
evolutionary distance between two homologous
sequences from A to B species, and r, their evolutionary rate r, it is possible to estimate t, the divergence
time between A and B.
In the past few years, the molecular clock hypothesis has been called into question. Indeed, the analysis
of numerous DNA and protein sequences revealed that
there is no universal molecular clock, that is to say that
there is no universal and constant evolutionary rate r.
On the contrary, it was showed that:
1. Each molecular marker evolves at its own rate.
2. The evolutionary rate r of a given sequence can
vary over time, and among lineages, due to selection pressure changes or functional shifts, for
instance, following gene duplication events.
3. r may vary among sites within a given sequence
because selective pressures are not uniform along a
sequence.
For instance, the evolutionary rate of 18S rRNA
sequences from Dasycladales (Chlorobionta) and
Angiosperms (Viridiplantae) is about 0.01
substitutions per 25 million years, whereas it is much
slower in Cyanobacteria. Similarly, the evolutionary
rate of the superoxide dismutase is four time faster in
mammals than in fungi. Finally, the four regions (A,
B, C, and the signal peptide) of the proinsulin, the
protein precursor of insulin, evolve at different rate,
reflecting different selective pressures acting on these
regions.
The concept of molecular clock must be used
wisely and cautiously because recent advances in
molecular evolution demonstrated that there is no
universal molecular clock but a multitude of local
molecular clocks, each having its own features. Far
from being a problem, this offers the possibility to
select accurate chronometers (i.e., genes, proteins,
noncoding DNA, etc.) suitable for each question (e.
g., fast evolving genes to study recent evolutionary
events, slowly evolving genes to study ancient
events, etc.).
118
C.-F. Boudouresque et al.
consensus on its hyperthermophilic character (Galtier et al.
1999; Di Giulio 2003) or on its belonging to the bacterial or
archaeal phyla, as proposed by Cavalier-Smith (2002a, b)
(cf. Sect. 4.3.3).
Cavalier-Smith (2002a, b), who used different criteria to
expand his vision of the phylogeny and taxonomy of
prokaryotes, proposed taxa and a topology that are far from
unanimously accepted in ICSP (Fig. 5.5). Despite the fact
that they were validly published in the reference journal for
bacterial taxonomy, many of these taxa are therefore not
adopted in this book. The tree of life based on concepts and
latest molecular tools will be presented later (cf. Sect. 5.5).
5.2
Microorganisms: Unicellular
or Multicellular?
Microorganisms as a whole, including eukaryotes, do not
constitute a monophyletic group of organisms (cf. Chap. 7).
However, they can be considered as a well-defined set of
organisms according to their morphology, particularly by
their uni- or almost unicellularity. The notion of
unicellularity (or almost unicellularity), as opposed to multicellularity, is actually much less clear as one may think at
first. Between unicellularity and multicellularity, the boundary is in fact blurred, rather corresponding to a continuum.
In a unicellular organism, the cells are physically isolated
and (at least theoretically) independent. A typical multicellular organism is (1) made by numerous cells; (2) its cells
contain a single nucleus (in the case of a eukaryote); (3) its
cells communicate, in one of several way (pores, synapses,
etc.), allowing them to exchange morphogenetic
informations and chemicals (products of metabolism)
(Fig. 5.6f); and (4) a specialization appears between cells.
A multicellular organism is therefore not an association of
identical and totipotent cells but a set of specialized cells that
can eventually organize themselves into tissues and organs.
As noted above, there are many intermediate cases
between strict unicellularity and strict multicellularity: the
main ones are those of colonial and filamentous organisms
without cell specialization.
The closest organisms to unicellularity are colonial
organisms which are single-celled organisms whose cells
remain associated during their division by extracellular
mucus; hydrodynamism can eventually dissociate them.
Although there may be chemical interactions between
cells, there is no physical communication between them.
The colonial organisms are not multicellular. However, the
question may arise for Labyrinthulobionta (Stramenopiles,
eukaryotes) in which cells move in a common envelope
(labyrinth) that they contribute to secrete (Fig. 5.6c). The
Box 5.3 (continued)
mutations occur randomly and mainly at neutral sites.
Accordingly, mutations will be fixed (leading to
substitutions) at a constant rate (Kumar 2005).
A constant rate r implies a linear relation between
the divergence time (t) and the evolutionary distance
(D) between two homologous sequences. More precisely, under a molecular clock assumption, D ¼ 2 * r
* t. Based on this relation, it is possible to perform
molecular dating, meaning that knowing D, the
evolutionary distance between two homologous
sequences from A to B species, and r, their evolutionary rate r, it is possible to estimate t, the divergence
time between A and B.
In the past few years, the molecular clock hypothesis has been called into question. Indeed, the analysis
of numerous DNA and protein sequences revealed that
there is no universal molecular clock, that is to say that
there is no universal and constant evolutionary rate r.
On the contrary, it was showed that:
1. Each molecular marker evolves at its own rate.
2. The evolutionary rate r of a given sequence can
vary over time, and among lineages, due to selection pressure changes or functional shifts, for
instance, following gene duplication events.
3. r may vary among sites within a given sequence
because selective pressures are not uniform along a
sequence.
For instance, the evolutionary rate of 18S rRNA
sequences from Dasycladales (Chlorobionta) and
Angiosperms (Viridiplantae) is about 0.01
substitutions per 25 million years, whereas it is much
slower in Cyanobacteria. Similarly, the evolutionary
rate of the superoxide dismutase is four time faster in
mammals than in fungi. Finally, the four regions (A,
B, C, and the signal peptide) of the proinsulin, the
protein precursor of insulin, evolve at different rate,
reflecting different selective pressures acting on these
regions.
The concept of molecular clock must be used
wisely and cautiously because recent advances in
molecular evolution demonstrated that there is no
universal molecular clock but a multitude of local
molecular clocks, each having its own features. Far
from being a problem, this offers the possibility to
select accurate chronometers (i.e., genes, proteins,
noncoding DNA, etc.) suitable for each question (e.
g., fast evolving genes to study recent evolutionary
events, slowly evolving genes to study ancient
events, etc.).
118
C.-F. Boudouresque et al.