From birth to christening

A brief history of comparative studies of nucleic acids for systematic purposes is given. These studies were initiated by a group of Moscow State University scientists headed by A. N. Belozersky. Based mostly on comparative DNA studies, some main dogmas of a new branch of systematics were gradually developed. In Russia, this new branch of systematics is called "genosystematics". Some of the main results obtained by genosystematics since its birth (1957) and up to its "christening" (1974) are described.     

Genosystematics: From E. Chargaff and A.N. Belozersky To the Present

This review considers the history of genosystematics (macromolecular systematics) from early studies of E. Chargaff and A.N. Belozersky up to the present, with emphasis on the most important discoveries in the field. The potential and limitations of genosystematics and possible ways of further development are analyzed using plants as an example. The future of genosystematics depends to a great extent on adequate employment of its methods in studying the problems of phylogeny and taxonomy. Analysis of recent publications shows that this requirement is not always met. It is no less important to design and improve the methods of genosystematics, especially those for comparing complete genomes.__________Translated from Molekulyarnaya Biologiya, Vol. 39, No. 4, 2005, pp. 581–589.Original Russian Text Copyright © 2005 by Antonov.     

The development of A. N. Belozersky's ideas in polyphosphate biochemistry

This review covers some trends and approaches to the study of inorganic polyphosphates that originated from the fruitful ideas and pioneering works of A. N. Belozersky. This is, first of all, the elucidation of a close relationship between these biopolymers and nucleic acids in organisms at different evolutionary stages; second, the study of "fossil" reactions in polyphosphate metabolism that permit an understanding of their role in the evolution of phosphorus turnover and cell bioenergetics; third, the possible use of the conservative enzymes of polyphosphate metabolism, e.g., exopolyphosphatases, as molecular chronometers for obtaining additional data concerning the theory of the endosymbiotic origin of eukaryotic cells from prokaryotes.     

RNA world and its evolution

The early idea of A. N. Belozersky on the precedence of RNA in the origin of life on Earth is developed. Basing on the present knowledge of functional omnipotence of RNA, the author considers three novel mechanisms that could play a critical role in the origin and evolution of the ancient RNA world: (1) the reaction of spontaneous transesterification of polyribonucleotides in aqueous media, discovered by A.B. Chetverin, which could result in elongation of primary short oligoribonucleotides and generation of sequence variants for subsequent selection; (2) compartmentation of functional RNA ensembles in the form of mixed molecular colonies on moist solid surfaces, in the absence of membranes and any other coats; (3) systematic exponential enrichment of RNA population in functionally "the best" molecules by means of alternately dissolving the colonies upon flooding and forming new ones upon drying a pool ("primordial natural SELEX").     

Naupliar and Metanaupliar Development of Thysanoessa raschii (Malacostraca,Euphausiacea) from Godth?bsfjord,Greenland, with a Reinstatement of the Ancestral Status of the Free-Living Nauplius in Malacostracan Evolution

The presence of a characteristic crustacean larval type, the nauplius, in many crustacean taxa has often been considered one of the few uniting characters of the Crustacea. Within Malacostraca, the largest crustacean group, nauplii are only present in two taxa, Euphauciacea (krill) and Decapoda Dendrobranchiata. The presence of nauplii in these two taxa has traditionally been considered a retained primitive characteristic, but free-living nauplii have also been suggested to have reappeared a couple of times from direct developing ancestors during malacostracan evolution. Based on a re-study of Thysanoessa raschii (Euphausiacea) using preserved material collected in Greenland, we readdress this important controversy in crustacean evolution, and, in the process, redescribe the naupliar and metanaupliar development of T. raschii. In contrast to most previous studies of euphausiid development, we recognize three (not two) naupliar (= ortho-naupliar) stages (N1-N3) followed by a metanauplius (MN). While there are many morphological changes between nauplius 1 and 2 (e.g., appearance of long caudal setae), the changes between nauplius 2 and 3 are few but distinct. They involve the size of some caudal spines (largest in N3) and the setation of the antennal endopod (an extra seta in N3). A wider comparison between free-living nauplii of both Malacostraca and non-Malacostraca revealed similarities between nauplii in many taxa both at the general level (e.g., the gradual development and number of appendages) and at the more detailed level (e.g., unclear segmentation of naupliar appendages, caudal setation, presence of frontal filaments). We recognize these similarities as homologies and therefore suggest that free-living nauplii were part of the ancestral malacostracan type of development. The derived morphology (e.g., lack of feeding structures, no fully formed gut, high content of yolk) of both euphausiid and dendrobranchiate nauplii is evidently related to their non-feeding (lecithotrophic) status.     

Evolutionary advances in the higher fungi

In this report the phrase evolutionary advances; is used in three ways: 1. to describe monophyletic changes perceived within a lineage; 2. to describe evolutionary sequences that appear to have become parallel/convergent; 3. to describe major transitions inferred between primary taxa. In monophyletic evolution the changes occur within a specific lineage that arises from a common ancestor, e.g., modern Man, horses, rusts. In parallel/convergent evolution different lineages respond similarly over time to environmental challenges and opportunities and come to acquire a great deal of comparability (e.g., Webster, 1987). Such lineages may be designated as separate taxa, e.g., similarities in marsupial and placental carnivores, or, if the polyphyleticism is cryptic, as a collective taxon, e.g., Aves, the class of birds, the obsolete Amentiferae for catkin bearing plants, the Gasteromycetes, and lichens. In major transitions there are significant paradigm shifts in which evolutionary changes from one predominant life style pattern to another are accompanied by increases in complexity (see Smith & Szatháry, 1995), e.g., symbiosis, the water to land transition, the changes between the phyla of land fungi. Three particular terms are used in evaluating evolutionary relationships (Moore, 1996a): homology, paramology, and analogy. Homology, from Darwin';s theory of common descent, is the phenomenon of having a common historical origin but not necessarily the same final structure or function (e.g., vertebrate forelimbs). Paramology (Moore, 1971) applies to inferred relationships in evolutionary schemes based on contemporary forms that lack fossil antecedents, e.g., the various phylogenetic interpretations of prokaryotes, algae, and fungi; Boekhout et al. (1993) have evaluated the taxonomic resolution of a variety of morphologic, biochemical, physiological, and molecular characters (Table 1). Analogy is generally applied to similar forms that are unrelated, e.g., insect/vertebrate wings; prokaryote/eukaryote flagella. It should also be borne in mind that, in a given taxon, biotrophism (Coffey, 1975) is an advanced character (Heath, 1987) over, respectively, weaker parasitism, symbiotism, commensalism, and freeliving and that seemingly simple or less differentiated forms can be, and more than likely than not are, reduced, polyphyletic, and specialized rather than ancient and rudimentary, e.g., yeasts (Hoog et al., 1988; Kurtzman & Fell, 1996; Moore, 1988b; 1996a).     

Genomics and genosystematics

A survey of publications dealing with comparative analysis of genomes shows that modern genomics has naturally evolved from gene systematics--an area whose formation and development was greatly influenced by the scientific school of A.N. Belozersky.     

Phylogeography of rusty-necklaced partridge (Alectoris magna) in northwestern China

Rusty-necklaced partridges (Alectoris magna) are found in Qinghai, Ningxia and Gansu provinces of northwestern China, distributed in mountainous areas that were heavily affected by cyclical climate changes throughout the Pleistocene. We investigated the potential impact of Pleistocene range shifts on phylogeographic patterns using 458 nucleotides of mitochondrial control-region from 102 individuals sampled from 10 populations across the current range. We found 31 haplotypes defined by 33 polymorphic positions. Phylogenetic analyses revealed two robustly supported clades, one corresponding to the Chaidamu Basin and the other including all individuals from all other populations. At the population level we also found significant evidence of differentiation. The phylogeographic structure of the rusty-necklaced partridge is consistent with the "phylogenetic discontinuity, spatial separation" pattern outlined by Avise et al. [Avise, J.C., Arnold, J., Ball, R.M., Bermingham, E., Lamb, T., Niegel, J.E., Reeb, C.A., Saunders, N.C., 1987. Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Ann. Rev. Ecol. Syst. 18, 489-522].     

哺乳动物系统发育基因组学研究进展

哺乳动物是一类最进化并在地球上占主导地位的动物类群,重建其系统发育关系一直是分子系统学的研究热点。随着越来越多物种全基因组测序的完成,在基因组水平上探讨该类动物的系统发育关系与进化成为研究的热点。本文从全基因组序列,稀有基因组变异及染色体涂染等几个方面简要介绍了当前系统发育基因组学在现生哺乳动物分子系统学中的应用,综合已有的研究归纳整理了胎盘亚纲的总目及目间的系统发育关系,给出了胎盘动物19 个目的系统发育树。本文还分析了哺乳动物系统发育基因组学目前所面临的主要问题及未来的发展前景。     

The phylogeny,evolutionary developmental biology,and paleobiology of the Deuterostomia: 25 years of new techniques,new discoveries,and new ideas

Over the past 25 years, new techniques, new discoveries, and new ideas have profoundly impacted our understanding of deuterostome interrelationships and, ultimately, deuterostome evolution. During the late 1980s and early 1990s morphological cladistic analyses made predictions about both taxonomic history and homology, predictions that would be tested independent of the morphological characters themselves with the advent of molecular systematics, the rise of evolutionary developmental biology, and continued exploration of the fossil record. Thanks to these three areas of inquiry, we have gone from scenarios where animals like mobile enteropneust hemichordates and chordates were derived from sessile filter-feeding animals like modern lophophorates, echinoderms, and pterobranch hemichordates, to a new perspective where hemichordates are recognized as the nearest living relative of the echinoderms, and that vagile gill-bearing animals like Cambrian vetulicolians are seen—at least by some—as close to the deuterostome last common ancestor, with both sessility and filter-feeding convergent features of deuterostomes (e.g., echinoderm) and non-deuterostomes (e.g., lophophorates) alike. Although much of the backbone of the new deuterostome phylogeny is supported by multiple independent data sets, as are statements of homology of several different morphological characters, in particular the homology of gill slits across Deuterostomia, nonetheless, the next quarter century of study on this remarkable group of animals promises to be as equally illuminating and exciting as the past quarter century.     

The sea-skater Halobates (Heteroptera: Gerridae) – probable cause for extinction in the Mediterranean and potential for re-colonisation following climate change

Sea-skaters in the genus Halobates Eschscholtz 1822 include some of the most specialised water striders and are found in tropical and subtropical seas around the world. Even though species of Halobates occur in both the Atlantic Ocean and the Red Sea, no extant sea-skater has been reported from the Mediterranean Sea. A fossil, Halobates ruffoi Andersen et al., 1994, described from Middle–Upper Eocene (45 Ma) Italy indicates that sea skaters were present in this part of the world in the past. Other geological evidence points to dramatic changes in the Mediterranean Sea during the Tertiary and Quaternary that may have led to their later extinction. In this paper we review briefly the distribution, systematics, evolution and ecology of Halobates, and discuss the potential for the Mediterranean to be recolonised following expected environmental changes due to global warming.     

Avian molecular systematics on the rebound: a fresh look at modern shorebird phylogenetic relationships

The study of avian molecular systematics currently lags behind that of mammals in several ways. Little phylogenetic resolution is observed among orders and phylogenetic studies below the ordinal level largely remain based on fast evolving mitochondrial sequences. New papers by Paton et al., Ericson et al., and Thomas et al. provide avian molecular systematics with a badly needed boost. These studies indicate that sampling more taxa and slower evolving nuclear genes yields strong phylogenetic resolution among the major shorebird (order Charadriiformes) families. The new data show surprising overall consensus and converge on certain novel clades. If correct, this newly obtained phylogenetic framework has tremendous implications for our understanding of the evolution of shorebird morphology, ecology and behaviour.     

Ontogenetic systematics: The synthesis of taxonomy, phylogenetics, and evolutionary developmental biology

The main purpose of the present review is to draw attention to growing problems in the modern systematics and phylogenetics which are presently underestimated by the professional community. The dramatic reduction of the importance of ontogeny and morphology in phylogenetic studies of the second part of the 20th century is considered among the major factors of the modern taxonomic and evolutionary paradigm. The deep contradiction of modern approaches, which either merely consider systematics and phylogeny as genealogy or even in a neotypolgical manner irrespective of the evolutionary idea, is demonstrated. Thus, despite the widespread opinion that the evolutionary theory is the major basis for taxonomy, the processes, which in fact caused the origin and formation of the systematic hierarchy are often considered as redundant for the procedure of classification. In this respect, the classical, but well forgotten statement that evolution is a modification of ontogeny is specially highlighted. Tight relationships between evolution, ontogeny, systematics, and phylogenetics are prima facie obvious, but also presently underestimated, although the field of the evo-devo is continuously growing. Paradoxically, even despite the outburst of various molecular ontogenetic approaches, the commonly accepted evolutionary paradigm still lacks a general theory for changes in the shape of organisms. As a step towards the development of such a theory, a synthesis (or more exactly, resynthesis) of still largely independently developing major biological fields, i.e., ontogenetic and evolutionary studies, on the one hand, and traditional taxonomy, on the other hand, a new concept of ontogenetic systematics is proposed. The new concept is intended for integration of supposedly ??immobile?? traditional taxonomy with the dynamics, but predominantly considered as hypothetical, evolutionary field based on the process of ontogeny, which, in contrast to the evolution itself, can be observed in the real time. Therefore, it is concluded that, for instance, the evolution of the main group of living organisms Metazoa, is primarily the evolution of a very limited number of ontogenetic cycles that were formed as early as the Early Cambrian. A significant underestimation of cyclic properties of ontogeny in the evolution and systematics is shown. Using two model groups, echinoderms of the class Ophiuroidea and dorid nudibranch mollusks (Gastropoda: Doridacea), practical importance of the integrative approach developed here is demonstrated. The ??disruption?? of the ancestral ontogenetic cycle and further formation of a new descendant cycle (which implies some continuity of ancestral and descendant characters) is considered to be a major evolutionary pattern. The model proposed implies either progressive (addition of stages and characters) or regressive (reduction of already existing stages and structures) modification of ancestral taxon, the diagnosis of which corresponds to the model of its ontogenetic cycle. In the extreme cases of disruption of the ancestral ontogenetic cycle, adult characters of descendants are substituted by juvenile ancestral features, demonstrating paedomorphoses in the narrow sense. Within the framework of the approach proposed, the evolutionary and ontogenetic models of ancestral ontogenetic cycles of brittle stars and dorid nudibranchs are developed and discussed. Based on the original material of the extinct Paleozoic ophiuroid group Oegophiurida, the origin of key evolutionary novelties is discussed. A major conclusion of the present review is the high necessity of integration of new molecular data with already well-established taxonomic hierarchy and ontogenetic information as a basis for the development of the general theory of transformations of organisms, i.e., the theory of evolution in its true sense.     

Testing the new animal phylogeny: first use of combined large-subunit and small-subunit rRNA gene sequences to classify the protostomes

Although the small-subunit ribosomal RNA (SSU rRNA) gene is widely used in the molecular systematics, few large-subunit (LSU) rRNA gene sequences are known from protostome animals, and the value of the LSU gene for invertebrate systematics has not been explored. The goal of this study is to test whether combined LSU and SSU rRNA gene sequences support the division of protostomes into Ecdysozoa (molting forms) and Lophotrochozoa, as was proposed by Aguinaldo et al. (1997) (Nature 387:489) based on SSU rRNA sequences alone. Nearly complete LSU gene sequences were obtained, and combined LSU + SSU sequences were assembled, for 15 distantly related protostome taxa plus five deuterostome outgroups. When the aligned LSU + SSU sequences were analyzed by tree-building methods (minimum evolution analysis of LogDet-transformed distances, maximum likelihood, and maximum parsimony) and by spectral analysis of LogDet distances, both Ecdysozoa and Lophotrochozoa were indeed strongly supported (e.g., bootstrap values >90%), with higher support than from the SSU sequences alone. Furthermore, with the LogDet-based methods, the LSU + SSU sequences resolved some accepted subgroups within Ecdysozoa and Lophotrochozoa (e.g., the polychaete sequence grouped with the echiuran, and the annelid sequences grouped with the mollusc and lophophorates)-subgroups that SSU-based studies do not reveal. Also, the mollusc sequence grouped with the sequences from lophophorates (brachiopod and phoronid). Like SSU sequences, our LSU + SSU sequences contradict older hypotheses that grouped annelids with arthropods as Articulata, that said flatworms and nematodes were basal bilateralians, and considered lophophorates, nemerteans, and chaetognaths to be deuterostomes. The position of chaetognaths within protostomes remains uncertain: our chaetognath sequence associated with that of an onychophoran, but this was unstable and probably artifactual. Finally, the benefits of combining LSU with SSU sequences for phylogenetic analyses are discussed: LSU adds signal, it can be used at lower taxonomic levels, and its core region is easy to align across distant taxa-but its base frequencies tend to be nonstationary across such taxa. We conclude that molecular systematists should use combined LSU + SSU rRNA genes rather than SSU alone.     

An integrated approach to taphonomy and faunal change in the Shungura formation (Ethiopia) and its implication for hominid evolution

Environmental and faunal changes through time have been recorded for many African Plio-Pleistocene sites. Fossil evidence suggests that there is a continuous, if not uniform, transformation of the fauna and flora from the Pliocene through the end of Pleistocene. However, discerning major biotic turnovers and linking them to global and regional climatic changes have been complicated by many factors, notably taphonomy and discontinuity of the fossil evidence, notwithstanding the considerable work of some researchers (e.g., Vrba, E.S., 1988. Late Pliocene climatic events and hominid evolution, in: Grine, F. (Ed.), Evolutionary History of the "Robust" Australopithecines. De Gruyter, New York, pp. 405-426, Vrba, E.S., 1995. The fossil record of African (Mammalia, Bovidae) in relation to human evolution and paleoclimate, in: Vrba, E.S., Denton, G.H., Partridge, T.C., Burkle, L.H. (Eds.), Paleoclimate and Evolution, with Emphasis on Human Origins. Yale University Press, New Haven, pp. 385-424). A sample of over 22,000 fossils collected by the French Omo Expedition, from the Shungura Formation of Ethiopia, was analyzed using an integrated approach to investigate taphonomic and faunal change patterns. The following results are obtained: (1) Univariate and multivariate studies support continuous faunal change from Member A through Member G of the Shungura sequence; (2) Correspondence analysis (CA) on extant bovids in African game parks shows that bovid tribes and genera are generally characterized by habitat specificity; (3) Taphonomic studies demonstrate that the relative abundance of different skeletal elements varies according to depositional environment; (4) CA on 73 localities of the Shungura Formation and 19 mammalian taxa points to a major faunal change around the base of Member G dated to ca. 2.3 Ma. This transformation is characterized by a change to open and edaphic grassland as a dominant type of environment; (5) This major faunal change correlates in time with the appearance of A. boisei. It is tentatively suggested that this major biome change is associated with an anagenetic speciation from A. aethiopicus to A. boisei.     

The historical assembly of continental biotas: Late Quaternary range-shifting, areas of endemism, and bio-geographic structure in the North American mammal fauna

A controversial question in biogeography and ecology involves the extent to which vicariance and dispersal interact to determine the structure of continental biotic assemblages, Accumulating evidence of" distributional changes during the past 40 000 yr (Late Quaternary) has suggested to ecologists that changes in geographic ranges during the Pleistocene were of sufficient magnitude to erode prior associations between earth and biotic evolution in continental biotas. This paper first argues that this question can only he addressed by examining the magnitude of Late Quaternary range-shifting at the spatial scale established within the framework of historical historical geography (e.g., areas of endemism) rather than that of ecology (e.g., local community assemblages); and second reassesses patterns of range-shifting in the FAUNMAP data base recording Late Quaternary distributions of North American mammals. At the scale of geo-morphological provinces. North American rodents have exhibited highly stable distributions during this time frame, suggesting that previous inferences drawn from analyses of stability at a local community scale are not relevant to questions of congruence between earth and biotic history at regional or continental scales, A comprehensive understanding of processes underlying the assembly of continental biotas still requires incorporation of biogeographic patterns developed well before episodes of Late Quaternary climatic turbulence.     

Mechanism of flavin mononucleotide cofactor binding to the Desulfovibrio vulgaris flavodoxin. 2. Evidence for cooperative conformational changes involving tryptophan 60 in the interaction between the phosphate- and ring-binding subsites

A mechanism has been proposed for the binding of flavin mononucleotide (FMN) and riboflavin to the apoflavodoxin from Desulfovibrio vulgaris [Murray, T. A., and Swenson, R. P. (2003) Biochemistry 42, 2307-2316]. In this model, the binding of the flavin isoalloxazine ring is dependent on the presence of a phosphate moiety in the phosphate-binding subsite, suggesting a cooperative interaction between that region and the ring-binding subsite. In the absence of inorganic phosphate, FMN can bind through the initial association of its 5'-phosphate group in the phosphate-binding subsite followed by insertion of the flavin ring. Because riboflavin lacks the 5'-phosphate group, it is unable to bind to this apoprotein in the absence of inorganic phosphate in solution. However, inorganic phosphate can enhance the rate of ring binding by occupying the phosphate-binding subsite. In this paper, NMR, near-UV circular dichroism (CD), and fluorescence spectroscopy provide evidence for a phosphate-induced conformational change within the isoalloxazine ring-binding subsite. Phosphate-dependent changes in the chemical shifts of 22 amide groups were observed in (1)H-(15)N HSQC NMR spectra. The majority of these groups are proximal to the phosphate-binding subsite or the loops that constitute the isoalloxazine ring-binding site. Also, a phosphate-dependent change in the environment or position of the Trp60 side chain was apparent in the NMR data and was confirmed by associated changes in the near-UV CD and tryptophan fluorescence spectra when compared to the spectra of the W60A mutant. These data suggest that phosphate, either the 5'-phosphate of the FMN or inorganic phosphate from solution, facilitates the movement of the side chain of Trp60 out of the isoalloxazine ring-binding site and other associated conformational changes, creating a population of apoflavodoxin that is capable of binding the isoalloxazine ring. This conformational switch may explain why some apoflavodoxins cannot bind riboflavin and also supports the "aromatic gate" model proposed from the crystal structure of the Anabaena apoflavodoxin [Genzor, C. G., Perales-Alcon, A., Sancho, J., and Romero, A. (1996) Nat. Struct. Biol. 3, 329-332].     

Genomics and Genosystematics

A survey of publications dealing with comparative analysis of genomes shows that modern genomics has naturally evolved from gene systematics—an area whose formation and development was substantially influenced by the scientific school of A.N. Belozersky.     

Problems in polychaete systematics

Some of the intriguing issues in current polychaete systematics are reviewed. (1) The root of the `polychaete' tree. Currently there are two major hypotheses concerning the root position among polychaetes. One is based on rooting cladograms with outgroups such as Mollusca and result in simple-bodied taxa such as Opheliidae and Questidae forming a basal annelid grade along with Clitellata. Other hypotheses do not use outgroup rooting but involve scenarios on the evolution of the group and would place taxa in Aciculata as basal annelids, thus making Aciculata and Phyllodocida paraphyletic. Molecular sequence data has been of little help in resolving this issue thus far, largely due to limited taxon sampling. (2) Paraphyly. Owing, in part, to a tradition involving the emphasis on differences among taxa, and the application of Linnean ranks (e.g., family), paraphyly is undoubtedly a widespread phenomenon in polychaete systematics. An example of this has been proposed already for Spionidae. If the tree topology and rooting used by Blake & Arnofsky (1999) is correct, Spionidae is made paraphyletic by the recognition of the following four family-ranked taxa; Trochochaetidae, Poecilochaetidae, Longosomatidae and Uncispionidae. Another possible example is seen with Cirratulidae. A preliminary cladistic analysis shows that it is entirely possible that seven other taxa recognised as families may be nested within Cirratulidae. These include Acrocirridae, Ctenodrilidae, Fauveliopsidae, Flabelligeridae, Flotidae, Poeobiidae and Sternaspidae. (3) Problematic taxa. Apart from the problems exposed by the analysis of Cirratuliformia, the position of some of these groups, such as Aberranta, Alciopidae, Hesionides,Lopadorhynchidae, Microphthalmus,Nerillidae, Spinther,Tomopteridae and Sabellariidae, is discussed.