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PubMed1999

Explaining the universe: Herbert Spencer's attempt to synthesize political and evolutionary ideas.

Herbert Spencer's evolutionary ideas related not just to the biological world but to the universe and everything in it. Human societies were also viewed through his evolutionary lens so that Spencer's evolutionary and political ideas are inextricably entwined. This essay looks at some of Spencer's ideas and attempts to locate them in the social and intellectual context of his youth. It also speculates on the rise and fall of Spencer's reputation.

Biological Evolution↗
PubMed1998

Typing of European strains of parvovirus B19 by restriction endonuclease analyses and sequencing: identification of evolutionary lineages and evidence of recombination of markers from different lineages.

European isolates of parvovirus B19 were analyzed by restriction enzyme analysis of PCR products of the VP1/2 coding region and sequencing of the same amplified region, five cloned fragments from each PCR product. Two main groupings were found based on three perfectly linked point deviations. On the assumption that identical point deviations causing the various restriction patterns regardless of time and origin of virus isolation were unlikely to emerge independently in different evolutionary lineages, traits of evolutionary lineages were identified, suggesting a clonal population structure of global circulating B19 strains. However, combinations of markers from different evolutionary lineages were also found, particularly in a strain derived from an individual chronically infected with B19 for more than 7 years. As chronically infected individuals might be subject to superinfections due to contacts or possibly due to blood transfusions or the administration of gamma-globulin, it is suggested that coexistence of, and recombination between variants of B19 of different phylogenetic origin incidentally occur in such individuals.

Capsid↗
PubMed2000

Towards a new evolutionary synthesis.

New concepts and information from molecular developmental biology, systematics, geology and the fossil record of all groups of organisms, need to be integrated into an expanded evolutionary synthesis. These fields of study show that large-scale evolutionary phenomena cannot be understood solely on the basis of extrapolation from processes observed at the level of modern populations and species. Patterns and rates of evolution are much more varied than had been conceived by Darwin or the evolutionary synthesis, and physical factors of the earth's history have had a significant, but extremely varied, impact on the evolution of life.

Journal Article↗
PubMed1997

Human aggression in evolutionary psychological perspective.

This article proposes an evolutionary psychological account of human aggression. The psychological mechanisms underlying aggression are hypothesized to be context-sensitive solutions to particular adaptive problems of social living. Seven adaptive problems are proposed for which aggression might have evolved as a solution--co-opting the resources of others, defending against attack, inflicting costs on same-sex rivals, negotiating status and power hierarchies, deterring rivals from future aggression, deterring mates from sexual infidelity, and reducing resources expended on genetically unrelated children. We outline several of the contexts in which humans confront these adaptive problems and the evolutionary logic of why men are cross-culturally more violently aggressive than women in particular contexts. The article concludes with a limited review of the empirical evidence surrounding each of the seven hypothesized functions of aggression and discusses the status and limitations of the current evolutionary psychological account.

Aggression↗
PubMed1997

Evolutionary physiology: history, principles.

1) The history of comparative and evolutionary physiology since the early XIX century is given; 2) The methods of evolutionary physiology are described; 3) Principles of the evolution of function are discussed at every level of physiological organization (cellular, functional units of the organ, the organ itself, functional systems) as they apply to the kidney and to the regulation of salt and water balance; and 4) General questions of evolutionary physiology covering physico-chemical factors in evolution of functions, the development of the integrity of an organism, the origin of physiological adaptation, the development of interconnection of physiological systems are discussed.

Animals↗
PubMed2003

Evolutionary optimization, backpropagation, and data preparation issues in QSAR modeling of HIV inhibition by HEPT derivatives.

Artificial neural networks (ANNs) can be utilized to generate predictive models of quantitative structure-activity relationships between a set of molecular descriptors and activity. Evolutionary computation provides a means to appropriately search for the set of weights and bias terms associated with artificial neural networks that minimize selected functions of the error between the actual and desired outputs. This method is demonstrated by evolutionary training of artificial neural networks capable of predicting anti-HIV activity for a set of 1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymine (HEPT) derivatives. The results of this work further confirm the growing indication that evolutionary computation can outperform backpropagation as a method of artificial neural network training. The results also indicate the degree to which bias in the initial training and testing data can affect performance and the importance of bootstrapping.

Algorithms↗
PubMed1997

Interplay of causation between suppliers and consumers in evolutionary trophic dynamics.

Natural selection, conceived as the process of small causes making small effects on the level of molecular evolutionary dynamics of a population, can yield global effects on the level of evolutionary trophic dynamics of populations, including those of mass extinctions. Occurrence of mass extinctions is due to the interplay of causation between suppliers and consumers in trophic dynamics. If the case of supplier causation is available such that resource exploitation by consumers on the upper trophic level follows in time resource presentation by suppliers on the lower, instead of resource exploitation followed by resource presentation, mass extinctions could be a norm of the evolutionary trophic dynamics.

Biological Evolution↗
PubMed2000

Evolutionary strategies of human T-cell lymphotropic virus type II.

Human T-cell lymphotropic virus type II (HTLV-II) primarily infects two different populations in which the virus is transmitted in very diverse ways. In endemically infected populations, the virus is propagated through sexual contact, and by mother to child transmission via breast-feeding, among intravenous drug users (IDUs), spread is mainly due to blood-borne transmission via needle sharing. The phylogeny of HTLV-II strains isolated from American Indian and Pygmy tribes and strains from IDUs, reveal that the virus originated on the African continent as a result of a simian to human transmission at least 400,000 years ago. HTLV-II was very likely introduced into the American continent during one or more migrations of HTLV-II infected Asian populations over the Bering land bridge, some 15,000-35,000 years ago. During the last few decades, HTLV-II has been transmitted from native American Indians to IDUs at least twice, followed by a rapid spread of the virus in the drug users population world-wide due to the practice of needle sharing. Molecular clock analysis showed that HTLV-II has two different evolutionary rates, with the molecular clock for the virus in IDUs ticking 150-350 times faster than the one in endemically infected tribes: 2.7x10(-4) compared to 1.7/7.3x10(-7) nucleotide substitutions per site per year in the LTR region. Although many of the HTLV-II infected drug users are co-infected with HIV, the dramatic acceleration of the evolutionary rate seems to be mainly related to the different modes of transmission in the two populations. These contrasting evolutionary rates correlate with an endemic spread of HTLV-II in infected tribes compared to an epidemic spread in IDUs.

Animals↗
PubMed2002

Amino acid composition of genomes, lifestyles of organisms, and evolutionary trends: a global picture with correspondence analysis.

Can we infer the lifestyle of an organism from the characteristic properties of its genome? More precisely, what are the relations between easily quantifiable properties from genomic sequences, such as amino-acid compositions, and more subtle characteristics concerning for example lifestyles or evolutionary trends? Here, we seek a global picture for such properties, based on a large number (56) of complete genomes, including significant numbers of representatives from the three domains of life. We consider the amino acid compositions of the predicted proteomes, and we use correspondence analysis, as a multivariate method to extract the relevant information from the large-scale data. From these analyses we derive a series of conclusions, concerning lifestyles, as well as physico-chemical and evolutionary trends: (1) correspondence analysis of the amino acid compositions permits discrimination between the three known lifestyles (mesophily/thermophily/hyperthermophily). (2) For various organisms, amino-acid composition properties are essentially driven by GC content, and to a significantly lesser extent by growth temperatures associated with lifestyles. Roughly speaking, the respective contributions of these two components are 57 and 20%. It is notable that these proportions are essentially unchanged with respect to a previous analysis (Nature 393 (1998) 537), which involved only 15 genomes, available at the time. (3) In terms of amino acid compositional biases, two specific 'signatures' for thermophily (in a broad sense, including hyperthermophily) can be detected. First, thermophilic species display a relative abundance in glutamic acid (Glu), concomitantly with the depletion in glutamine. Second, in thermophilic species, the relative abundance in Glu (negative charge) is significantly correlated (Pearson correlation coefficient r=0.83 with P<0.0001), with the increase in the lumped 'pool' lysine+arginine (positive charges). This correlation (absent in mesophiles) could be interpreted on a physico-chemical basis, relevant to the thermostability of proteins. (4) Statistically significant differences are observed between the average lengths of the genes in the surveyed species, which follow their distribution between the three domains of life. Also a significant difference is observed between the average lengths of thermophilic (283.0+/-5.8) versus mesophilic (340+/-9.4) genes. It is thus possible that the 'general' shortening of the primary sequences in thermophilic proteins plays a role in thermostability. (5) Considering various combinations of conservation properties (genes conserved exclusively in eukaryotes, in archaea, in bacteria, in combinations of two domains, etc.) correspondence analysis reveals a trend towards thermophilic-hyperthermophilic profiles for the most conserved subset of genes (ancient genes). (6) When limited to the subset of species-specific genes, correspondence analysis leads to a different picture for the clustering of genomes following amino-acid compositions: for example, the 'core' specific part of a genome can bear lifestyle signatures different from those of the complete genome.Various results are discussed both on methodological and biological grounds. The evolutionary perspectives opened by our analyses are noted.

Amino Acids↗
PubMed1997

Mammalian mitochondrial D-loop region structural analysis: identification of new conserved sequences and their functional and evolutionary implications.

This paper reports the first comprehensive analysis of Displacement loop (D-loop) region sequences from ten different mammalian orders. It represents a systematic evolutionary study at the molecular level on regulatory homologous regions in organisms belonging to a well defined class, mammalia, which radiated about 150 million years ago (Mya). We have aligned and analyzed 26 complete D-loop region sequences available in the literature and the fat dormouse sequence, recently determined in our laboratory. The novelty of our alignment consists of the extensive manual revision of the preliminary output obtained by computer program to optimize sequence similarity, particularly for the two peripheral domains displaying heterogeneity in length and the presence of repeated sequences. The multialignment is available at the WWW site: http://www.ba.cnr.it/dloop.html. Our comparative study has allowed us to identify new conserved sequence blocks present in all the species under consideration and events of insertion/deletion which have important implications in both functional and evolutionary aspects. In particular we have detected two blocks, about 60 bp long, extended termination associated sequences (ETAS1 and ETAS2) conserved in all the organisms considered. Evaluation against experimental work suggests a possible functional role of ETAS1 and ETAS2 in the regulation of replication and transcription and targeted experimental approaches. The analyses on conserved sequence blocks (CSBs) clearly indicate that CSB1 is the only very essential element, common to all mammalian mt genomes, while CSB2 and CSB3 could be involved in different though related functions, probably species specific, and thus more linked to nuclear mitochondrial coevolutionary processes. Our hypothesis on the different functional implications of the conserved elements, CSBs and TASs, reported so far as main regulatory signals, would explain the different conservation of these elements in evolution. Moreover the intra-order comparison of the D-loop regions highlights peculiar features useful to define the evolutionary dynamics of this region in closely related species.

Animals↗
PubMed1999

The differential pattern of tissue-specific expression of ruminant pancreatic type ribonucleases may help to understand the evolutionary history of their genes.

Molecular evolutionary analyses of mammalian ribonucleases have shown that gene duplication events giving three paralogous genes occurred in ruminant ancestors. The enzymes of the bovine species encoded by these genes, isolated from pancreas, brain and seminal vesicles, present similar enzymological properties but distinct structural features. In other ruminant species, genomic sequences orthologous to the bovine genes of pancreas and brain ribonucleases encode active enzymes. In mammalian species other than ruminant artiodactyls, only one gene encoding ribonuclease of the pancreatic type is generally present. In this work, we describe a differential pattern of transcriptional expression of the pancreas and brain ribonuclease genes in the ox species and report transcription of the human ribonuclease gene in brain as well as in pancreas and in mammary gland. We also report the molecular cloning of the gene encoding the bovine seminal ribonuclease in which the structural organization already described for the two paralogous genes is conserved. The seminal RNAase is exclusively expressed in seminal vesicles of Bos taurus, whereas in other ruminant species, the orthologous sequence is a pseudogene. Previous studies from a number of research groups demonstrated that, unlike other mammalian ribonucleases, the seminal enzyme is a covalent dimer, and its unique quaternary structure correlates with special biological activities. The major determinant of dimer formation, i.e. the presence of two adjacent cysteine residues, is absent in the pseudogenes. We advance the hypothesis that the differentiation of distinct expression patterns could represent an important evolutionary determinant for the genes encoding pancreas and brain ribonucleases in ruminants, whereas the differentiation of a quaternary structure endowed with new biological functions could be the main determinant for the evolutionary success of the seminal gene in the bovine species.

Amino Acid Sequence↗
PubMed2001

Developmental and evolutionary hypotheses for the origin of double fertilization and endosperm.

The discovery of a second fertilization event that initiates endosperm in flowering plants, just over a century ago, stimulated intense interest in the evolutionary history and homology of endosperm, the genetically biparental embryo-nourishing tissue that is found only in angiosperms. Two alternative hypotheses for the origin of double fertilization and endosperm have been invoked to explain the origin of the angiosperm reproductive syndrome from a typical non-flowering seed plant reproductive syndrome. Endosperm may have arisen from a developmental transformation of a supernumerary embryo derived from a rudimentary second fertilization event that first evolved in the ancestors of angiosperms (endosperm homologous with an embryo). Conversely, endosperm may represent the developmental transformation of the cellular phase of non-flowering seed plant female gametophyte ontogeny that was later sexualized by the addition of a second fertilization event in a strongly progenetic female gametophyte (endosperm homologous with a female gametophyte). For the first time, explicit developmental and evolutionary transitions for both of these hypotheses are examined and compared. In addition, current data that may be congruent with either of these hypotheses are discussed. It is clear that much remains to be accomplished if the evolutionary significance of the process of double fertilization and the formation of endosperm is to be fully understood.

Biological Evolution↗
PubMed2000

Evolutionary weighting of image features for diagnosing of CNS tumors.

This paper concerns an application of evolutionary feature weighting for diagnosis support in neuropathology. The original data in the classification task are the microscopic images of ten classes of central nervous system (CNS) neuroepithelial tumors. These images are segmented and described by the features characterizing regions resulting from the segmentation process. The final features are in part irrelevant. Thus, we employ an evolutionary algorithm to reduce the number of irrelevant attributes, using the predictive accuracy of a classifier ('wrapper' approach) as an individual's fitness measure. The novelty of our approach consists in the application of evolutionary algorithm for feature weighting, not only for feature selection. The weights obtained give quantitative information about the relative importance of the features. The results of computational experiments show a significant improvement of predictive accuracy of the evolutionarily found feature sets with respect to the original feature set.

Algorithms↗
PubMed2003

Nuclear medical PET-study in the causal relationship between mastication and brain function in human evolutionary and developmental processes.

The principal author (Kubote 1995, 1997, 1998, 1999, 2000 a, b) has proposed that chewing food well from infancy will lead to a clear-headed and robust person, following which the same concept has been presented to the general public by the mass media. Unfortunately, however, there does not yet seem to be any direct evidence to support this claim. It is thus necessary to review mastication from the standpoint of the new concept of evidence-based medicine (EBM) and to create a new direction in medicodental research and treatment from the viewpoint of human evolution, because the causal relationship between mastication and brain function has never been clarified either in fossil science research or in the modem scientific bibliography. To confirm the human historical fossil record in regard to the causal relationship between the development of mastication and brain function in human evolutionary processes, the effect of gum chewing on brain reaction was examined in humans by means of a positron-emission tomography (PET) camera (Momose et al. 1997) after an antecubital intravenous injection of H215O. Powerful activation of the cortical cells was demonstrated in multiple cortical areas involving the marginal areas of the bilateral central sulci of the cerebral cortex (Fig. 1), and the activated areas coincided with our previous results in region of interest (ROI) analysis (Momose et al. 1887). Three-dimensionally, numerous cortical cells were shown to form nuclei on relief maps (Fig. 2). As diets and feeding habits changed in a stepwise manner from frugivorous to omnivorous via herbivorous and carnivorous over the lengthy progress of evolution, the brain concomitantly grew and the cranial capacity gradually increased in volume from 500 cm3, food from plant sources to animal sources (700 cm3), and then to both (1500 cm3), during the human evolutionary and developmental processes. Gradual increases in the cranial capacity of human fossils during the developmental stage have been demonstrated also by PET images of the human brain acquired by means of a PET camera and an antecubital intravenous injection of H215O during mastication that showed powerful activation of cortical cells in multiple areas. It could be concluded that human fossils give us concrete information on how to feed our children in the modern human life style from infancy to adulthood, so that we should bring children up by adhering to images of the principal feeding habits discovered during this research on human evolutionary and developmental processes.

Brain↗
PubMed1999

Comparative genomics and evolutionary biology.

Data of large-scale DNA sequencing are relevant to some of the most fundamental issues in evolutionary biology: suboptimality, homology, hierarchy, ancestry, novelties, the role of natural selection, and the relative importance of directional versus stabilizing selection. Already, these data provided the best available evidence for some evolutionary phenomena, and in several cases led to refinement of old concepts. Still, the Darwinian evolutionary paradigm will successfully accommodate comparative genomics.

Animals↗
PubMed1994

A molecular evolutionary framework for eukaryotic model organisms.

BACKGROUND: Implicit in the characterization of a model organism is the hope that insights into its biology can be extended to other species. For this hope to be fulfilled, the phylogenetic position of the model organism within a larger evolutionary framework must be known. We focus here on major model organisms of developmental genetics and cell biology. We first consider the positions of the nematode Caenorhabditis elegans and the arthropod Drosophila melanogaster within a phylogeny of the major advanced metazoan groups. Then we consider the evolutionary relationships between fungi (represented by Saccharomyces cerevisiae and Schizosaccharomyces pombe), plants, and animals. RESULTS: We show, by a direct comparison with small subunit ribosomal RNA (18 S rRNA), that RNA polymerase II is an appropriate molecule for addressing the phylogenetic branchings in the early evolution of eukaryotes. The results from the analyses of newly determined and previously published sequences of the two largest subunits of RNA polymerase II suggest the following. Firstly, that plants and animals share a last common ancestor that excludes fungi, the lineage of which originated earlier. Secondly, that the lineage leading to the nematode Caenorhabditis elegans diverged earlier from the Metazoa than the lineages of arthropods, deuterostomes, annelids and molluscs. Finally, that deuterostomes arose from within protostomes. CONCLUSIONS: RNA polymerase II is well-suited for the elucidation of the evolutionary relationships among eukaryotes. We emphasize the implications of our results for other biological disciplines in addition to molecular evolution, as a phylogenetic framework allows predictions and inferences to be made about the existence of fundamental biological mechanisms elucidated in model organisms.

Amino Acid Sequence↗
PubMed2002

Evolutionary patterns of the gypsy and bilbo retrotransposon families in the Drosophila species of the obscura group.

We analyse in this paper the evolutionary patterns of two types of Drosophila retrotransposons, gypsy (a virus-like element), and bilbo (a LINE-like element), in host species from the Drosophila and Scaptomyza genus. Phylogenetic analysis of the retrotransposon sequences amplified by PCR, revealed concordance with the phylogeny of the Drosophila host species from the obscura group, which is consistent with vertical transmission during differentiation of the species. However, in the species outside of the obscura group, horizontal transmission can be considered. The amplified sequences that presented intact open reading frames were used in an analysis of the evolutionary constraints on the amino acid sequences. The analysed sequences seem to be functional, and the selective constraints are evidenced, especially when sequences from distant species are compared. Comparison of the evolutionary rates of both retrotransposons in the same species, suggests that bilbo seems to evolve more rapidly than gypsy.

Animals↗
PubMed2002

An evolutionary treatment of the morphology and physiology of circulatory organs in insects.

An overview from an evolutionary perspective is presented on the research of the past 2 decades on insect circulatory organs. Based on various functional morphology it is clear that the flow mode of the dorsal vessel ('heart') has changed during the evolution of hexapods. In all apterygotes and mayflies the flow is bidirectional. In most pterygote insects, however, it is unidirectional. In some endopterygote insects, the direction of the flow alternates. This is achieved by heartbeat reversal, which may have various physiological functions and is a derived condition that probably occurred several times during the course of insect evolution. Special attention is given to the hemolymph flow in body appendages. In ancestral hexapods, they are supplied by arteries, whereas circulation in appendages of higher insects is accomplished by accessory pulsatile organs. These auxiliary hearts are autonomous pumps and exhibit a great diversity in their functional morphology. They represent evolutionary innovations which evolved by recruitment of building blocks from various organ systems and were assembled into new functional units. Almost all pulsatile circulatory organs in insects investigated exhibit a myogenic automatism with a superimposed neuronal control. The neuroanatomy of insect circulatory organs has been investigated only in a small number of species but in considerable detail. Numerous potential peptidergic and a few aminergic mediators could be demonstrated by immunocytochemical and biochemical methods. The cardiotropic effectiveness of these mediators may vary among species and it can be stated that there is no uniform picture of the control of the various circulatory organs in insects. A possible explanation for the differences may lie in the different evolutionary origins of the muscular components. Furthermore, insect circulatory organs may represent important neurohemal releasing sites.

Animal Structures↗