1022-7954/02/3808- $27.00 © 2002
Russian Journal of Genetics, Vol. 38, No. 8, 2002, pp. 877–894. Translated from Genetika, Vol. 38, No. 8, 2002, pp. 1043–1062.
Original Russian Text Copyright © 2002 by Petrov, Aleshin.
OF MOLECULAR PHYLOGENETICS
Molecular phylogenetics was born in the early 20th
century, when immunological experiments showed a
very close relationship between humans and apes .
Then, the history of molecular phylogenetics was dis-
continued until the emergence of methods for the deter-
mination of amino-acid sequences of proteins in the
mid-1950s [2, 3], improved immunological methods
, and methods for comparing DNA sequences based
on DNA–DNA hybridization [5–7]. The accumulation
of data that were obtained by these methods have stim-
ulated the development of techniques for sequence
alignment [8–10] and phylogenetic reconstruction
[11–14], as well as extensive phylogenetic studies of
different groups of organisms [15–18].
The development of both methods for the determi-
nation of nucleotide sequences and the cloning tech-
niques for individual genes (especially using poly-
merase chain reaction) have initiated rapid accumula-
tion of data on nucleotide sequences of various genes.
Molecular phylogenetics entered the phase that can be
named the era of 18S rRNA genes, because, by virtue
of a number of reasons , exactly these genes prom-
ised to help in solving many phylogenetic problems.
Certainly, other genes have been also actively used for
this purpose [20, 21] but the scope of phylogenetic
studies using the 5S [22, 23] and 18S rRNA genes is
considerably larger than the scale of similar studies
based on other genes. The available sample of 18S
rRNA gene sequences currently covers all phyla of
metazoans except Loricifera and Lobatocerebrida. The
European Small Subunit Ribosomal RNA database
(http://rrna.uia.ac.be) contains 6000 complete aligned
sequences of the 18S rRNA genes of eukaryotes, of which
more than 1500 organisms belong to metazoans .
The phase of phylogenetic studies using ribosomal
RNA genes seems to approach its end. At present, we
are on the verge of a new era, that of comparison of a
multitude of various genes, and then complete
genomes. In view of this, there is a need to review the
past phase, estimate its advances, detect its weak
points, outline the ways for overcoming these weak
points, and determine the prospects of phylogenetic
studies in the new, genomic era.
Even now, comparative studies of rRNA genes have
signiﬁcantly changed the views on the evolution of
eukaryotes, permitted to resolve some old disputes, and
introduced many new phylogenetic ideas [25–30].
Since the main advances of phylogenetic studies using
rRNA genes of protists  and plants  have
recently been reviewed, our review is devoted to analy-
sis of similar data obtained mostly for metazoans.
ADVANCES OF THE PHASE
OF TRADITIONAL PHYLOGENETICS
The metazoan phylogeny is characterized by a para-
doxical situation: while all main animal phyla have
been described as early as in the 19th century, the rela-
tionships between them are still debated. This situation
can largely be explained by the fact that the famous
Conditionally Neutral Phylogenetic Markers of Major Taxa:
A New Aspect of the Evolution of Macromolecules
N. B. Petrov and V. V. Aleshin
Belozersky Institute of Physicochemical Biology, Moscow State University, Moscow, 119899 Russia;
fax: (095) 939-31-81; e-mail: Petr@belozersky.msu.ru
Received December 4, 2001
—The current phase of molecular phylogenetics can be named the 18S rRNA gene era, which is now
approaching the end. To date, almost all phyla of metazoans and many taxa of protists are represented in data-
bases of 18S rRNA gene sequences. The elements of the phylogenetic tree of Metazoa inferred from 18S rRNA
genes are characterized by unequal validity: some of them seem to be well grounded; others are not adequately
supported, and probably will be revised later. The validity of phylogenetic reconstruction is inﬂuenced by two
main factors: (1) erroneous grouping of long branches that occur because of abnormally high evolution rate;
(2) deﬁcit of phylogenetically informative characters. A method for overcoming these difﬁculties is suggested
in addition to known tools: using phylogenetic markers that are stable within individual taxa and evolve by
punctuated equilibrium. These markers are least inﬂuenced by the convergence caused by a high evolution rate
of the entire gene. The nature of these markers of ancient taxa, paradoxical from the perspective of neutral evo-
lution, is discussed, as well as their importance for establishing monophyly of both new large-scale taxonomic
groups of invertebrates (Bilateria + Rhombozoa + Orthonectida + Myxozoa + Cnidaria + Placozoa and Echin-
odermata + Hemichordata) and some major taxa of Nematoda.