148
4 Molecular Evolution
3. "Evolutionary systematics" is also based on
phylogenetic relationships but takes into
account phenetic similarity. The important
proponents of this system are Simpson and
Mayr [198].
A large problem in the analysis of phylogenetic
relationships is the fact that similarities in a particular character may not simply be due to a common origin (homology), but rather to the development of similar characters in two independent
evolutionary lines (paraUel evolution) or to the
adaptation of characters to similar functional
requirements (convergence). In the face of these
difficulties, the phenetic school makes the
assumption that the analysis of a large enough
number of characters reduces the influence of
parallel evolution or convergence on the results.
The other two schools attempt to recognize the
existence of parallel evolution and convergence,
in particular by examining the agreement
between cladograms constructed using different
characters (congruence criteria) [198, 385].
The basic unit of biological systematics is the
species. The definition of this term already presents large problems. Comprehensible in real
terms for bisexual organisms is the population,
whose members form a reproductive community
and can freely exchange genes. In this connection,
a species may be defined biologically as a group of
individuals that actually or potentially forms a
reproductive community and which is reproductively isolated from other such groups. As this
definition applies only to organisms with bisexual
reproduction, and as, furthermore, a "potential"
reproductive community cannot be determined, a
phenetic species concept is normally applied in
practice, according to which the members of one
species are distinguished from another species by
particular (diagnostic) characters. Groups of species are brought together in higher taxa as genera,
families, orders, classes, phyla and kingdoms; further classification may be into sub-orders or superfamilies. The assignment of a taxon to one of these
categories is based on different rules in the different schools of systematics: according to the estimated degree of similarity in the phenetic school;
based on the phylogenetic age in the phylogenetic
school; and taking into account the number of
species and the heterogeneity in the evolutionary
school. Whatever the case, taxa of the same rank
in different parts of the system are not directly
comparable [198, 385].
In accordance with the international rules of
nomenclature, each organism is known by a Latin
name consisting of at least two parts, the genus
and the species; where necessary, the name of the
subspecies is also added. The genus name is
always written with an initial capital letter,
whereas the species or subspecies name starts
with a lower-case letter. In order to refer completely and unambiguously to a species, the name of
the first describer should be given. Unfortunately,
biochemical texts frequently break the rules of
biological nomenclature and the organisms in
question are often very carelessly named. Trivial
names, such as "frog", "toadfish" or "locust", are
often applied to very different species and in no
way clearly define the species actually under examination. Because considerable biochemical differences can exist between various species, biochemical results lacking exact reference to the
organisms involved are quite worthless.
4.5.1 The Evolutionary Distance Between
Amino Acid or Nucleotide Sequences
The simplest measurement of the difference
between two amino acid sequences is the number
of varying amino acids. If, however, by evolutionary distance is meant the number of nucleotide
substitutions that have become fixed during the
diversifying evolution of two structural genes,
then it must be taken into account that one, two
or three substitutions may be required for one
amino acid exchange, depending on the degree of
difference in the codons. The minimum sum of
substitutions, calculated from the genetic code, to
explain the transformation of one amino acid
sequence into another was described by Fitch in
1967 as the "minimum mutation distance"
(MMD) [120]. The MMD, however, gives only an
incomplete estimate of the genetic distance
between the structural genes. It takes no account
of synonymous substitutions that do not lead to
amino acid exchange, and cannot deal with multiple, parallel and back mutations (Fig. 4.9).
In the last two decades numerous methods
have been developed for the determination of
evolutionary distances between proteins, and the
relative suitability of these has been the subject of
vigorous debate. Conclusions drawn from differences in two amino acid sequences about the corresponding structural genes are questionable,
because information is clearly lost during translation; the information content decreases from
3 . log24 = 6 bits for a triplet to log220 = 4.32 bits
for one amino acid. On the other hand, it is not
only the selection pressure on the protein that is
4 Molecular Evolution
3. "Evolutionary systematics" is also based on
phylogenetic relationships but takes into
account phenetic similarity. The important
proponents of this system are Simpson and
Mayr [198].
A large problem in the analysis of phylogenetic
relationships is the fact that similarities in a particular character may not simply be due to a common origin (homology), but rather to the development of similar characters in two independent
evolutionary lines (paraUel evolution) or to the
adaptation of characters to similar functional
requirements (convergence). In the face of these
difficulties, the phenetic school makes the
assumption that the analysis of a large enough
number of characters reduces the influence of
parallel evolution or convergence on the results.
The other two schools attempt to recognize the
existence of parallel evolution and convergence,
in particular by examining the agreement
between cladograms constructed using different
characters (congruence criteria) [198, 385].
The basic unit of biological systematics is the
species. The definition of this term already presents large problems. Comprehensible in real
terms for bisexual organisms is the population,
whose members form a reproductive community
and can freely exchange genes. In this connection,
a species may be defined biologically as a group of
individuals that actually or potentially forms a
reproductive community and which is reproductively isolated from other such groups. As this
definition applies only to organisms with bisexual
reproduction, and as, furthermore, a "potential"
reproductive community cannot be determined, a
phenetic species concept is normally applied in
practice, according to which the members of one
species are distinguished from another species by
particular (diagnostic) characters. Groups of species are brought together in higher taxa as genera,
families, orders, classes, phyla and kingdoms; further classification may be into sub-orders or superfamilies. The assignment of a taxon to one of these
categories is based on different rules in the different schools of systematics: according to the estimated degree of similarity in the phenetic school;
based on the phylogenetic age in the phylogenetic
school; and taking into account the number of
species and the heterogeneity in the evolutionary
school. Whatever the case, taxa of the same rank
in different parts of the system are not directly
comparable [198, 385].
In accordance with the international rules of
nomenclature, each organism is known by a Latin
name consisting of at least two parts, the genus
and the species; where necessary, the name of the
subspecies is also added. The genus name is
always written with an initial capital letter,
whereas the species or subspecies name starts
with a lower-case letter. In order to refer completely and unambiguously to a species, the name of
the first describer should be given. Unfortunately,
biochemical texts frequently break the rules of
biological nomenclature and the organisms in
question are often very carelessly named. Trivial
names, such as "frog", "toadfish" or "locust", are
often applied to very different species and in no
way clearly define the species actually under examination. Because considerable biochemical differences can exist between various species, biochemical results lacking exact reference to the
organisms involved are quite worthless.
4.5.1 The Evolutionary Distance Between
Amino Acid or Nucleotide Sequences
The simplest measurement of the difference
between two amino acid sequences is the number
of varying amino acids. If, however, by evolutionary distance is meant the number of nucleotide
substitutions that have become fixed during the
diversifying evolution of two structural genes,
then it must be taken into account that one, two
or three substitutions may be required for one
amino acid exchange, depending on the degree of
difference in the codons. The minimum sum of
substitutions, calculated from the genetic code, to
explain the transformation of one amino acid
sequence into another was described by Fitch in
1967 as the "minimum mutation distance"
(MMD) [120]. The MMD, however, gives only an
incomplete estimate of the genetic distance
between the structural genes. It takes no account
of synonymous substitutions that do not lead to
amino acid exchange, and cannot deal with multiple, parallel and back mutations (Fig. 4.9).
In the last two decades numerous methods
have been developed for the determination of
evolutionary distances between proteins, and the
relative suitability of these has been the subject of
vigorous debate. Conclusions drawn from differences in two amino acid sequences about the corresponding structural genes are questionable,
because information is clearly lost during translation; the information content decreases from
3 . log24 = 6 bits for a triplet to log220 = 4.32 bits
for one amino acid. On the other hand, it is not
only the selection pressure on the protein that is