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PubMed2005

An evolutionary scenario for the origin of pentaradial echinoderms-implications from the hydraulic principles of form determination.

The early evolutionary history of echinoderms was reconstructed on the basis of structural-functional considerations and application of the quasi-engineering approach of 'Konstruktions-Morphologie'. According to the presented evolutionary scenario, a bilaterally symmetrical ancestor, such as an enteropneust-like organism, became gradually modified into a pentaradial echinoderm by passing through an intermediate pterobranch-like stage. The arms of a pentaradial echinoderm are identified as hydraulic outgrowths from the central coelomic cavity of the bilateral ancestor which developed due to a shortening of the body in length but widening in the diameter. The resulting pentaradial symmetry is a consequence of mechanical laws that dictate minimal contact surface areas among hydraulic pneumatic entities. These developed in the coelomic cavity (metacoel) in the bilaterally symmetrical ancestor, when from the already U-shaped mesentery with the intestinal tract two additional U-shaped bows developed directly or subsequently. During the subsequent development tensile chords of the mesentery 'sewed' the gut with the body wall first in three and secondly in five 'seams'. During the direct development five 'seams' between tensile chords and body wall developed straightly. These internal tensile chords subdivide the body coelom into five hydraulic subsystems ('pneus'), which eventually arrange in a pentaradial pattern. The body could then enlarge only between the tensile chords, which means that five hydraulic bulges developed. These bulges initially supported the tentacles and finally each of them enclosed the tentacle until only the feather-like appendages of the tentacles projected over the surface. The tentacles with their feathers were transformed into the ambulacral system, and the bulges become the arms. These morphological transformations were accompanied and partly determined by specific histological modifications, such as the development of mutable connective tissues and skeletal elements that fused to ossicles and provided shape stabilization in form of a calcareous skeleton in the body wall. The organism resulted was an ancestral echinoderm ('Ur-Echinoderm') with an enlarged metacoel, stabilized by hydraulic pressure working against a capsule of mutable connective tissue, skeletal elements and longitudinal muscles. In regard to these reconstructions, the body structure of echinoderms can be understood as a hydraulic skeletal capsule.

Animals↗
PubMed2005

Multi-alignment of orthologous genome regions in five species provides new insights into the evolutionary make-up of mammalian genomes.

Evidence has shown that bacterial genomes have undergone random shuffling of genomic elements consisting of one to two genes. In order to delineate such genome-shuffling events in mammals, we constructed a high-resolution map of Sus scrofa chromosome 3 (SSC3) with a total of 116 genes/markers. Alignment of this pig map to orthologous regions in human, dog, mouse and rat led to the identification of 31 provisional conserved ancestral blocks (CABs) in these five species. Among them, only 3 CABs (<10%) had one gene, indicating that one-gene shuffling is not frequent in mammals. The sizes of CABs vary significantly within a species, but each may be relatively consistent in different species with a scale to species-genome evolution. The type and frequency of rearrangement events that takes place, either intra- or interchromosomal, depends on the evolutionary regions and species under comparison. Characterization of 36 tentative breakpoint regions flanking these 31 CABs indicated that they occupied approximately 43 Mb in length and featured genome deserts, gene duplications, and birth/death of species-specific genes in humans. Identification of CABs provides an alternative for further determination of the evolutionary make-up of mammalian genomes.

Animals↗
PubMed2006

Evolutionary studies on an alpha-amylase gene segment in bats and other mammals.

Comparative studies of salivary glands showed that they maybe related to the adaptive radiation of bats, especially in the family Phylostomidae. In this study we have been searching for a likely relationship between different feeding habits found in bats and possible adaptive changes in a coding segment of the alpha-amylase enzyme. We have also tested some hypothesis about the phylogenetic relationship of bats and other mammals. A 663 bp segment of the alpha-amylase gene, corresponding to the exon 4 and part of the intron c, was sequenced in nine bat species. The exon 4 was also sequenced in further ten mammalian species. The phylogenetic trees generated with different methods produced the same results. When the intron c and the exon 4 were independently analyzed, they showed distinct topologies involving the bat species Sturnira lilium, different from the traditional bat phylogeny. Phylogenetic analysis of bats, primates and rodents supports the Euarchontoglires-Laurasiatheria hypothesis about the relationship among these groups. Selection tests showed that the alpha-amylase exon 4 is under strong purifying selection, probably caused by functional constraints. The conflicting bat phylogenies could not be explained by evolutionary convergence due to adaptive forces, and the different topologies may be likely due to the retention of plesiomorphic characters or the independent acquisition by evolutionary parallelism.

Amino Acid Sequence↗
PubMed2005

ENPDA: an evolutionary structure-based de novo peptide design algorithm.

One of the goals of computational chemists is to automate the de novo design of bioactive molecules. Despite significant advances in computational approaches to ligand design and binding energy evaluation, novel procedures for ligand design are required. Evolutionary computation provides a new approach to this design endeavor. We propose an evolutionary tool for de novo peptide design, based on the evaluation of energies for peptide binding to a user-defined protein surface patch. Special emphasis has been placed on the evaluation of the proposed peptides, leading to two different evaluation heuristics. The software developed was successfully tested on the design of ligands for the proteins prolyl oligopeptidase, p53, and DNA gyrase.

Algorithms↗
PubMed2005

Reverse-engineering gene-regulatory networks using evolutionary algorithms and grid computing.

OBJECTIVE: Living organisms regulate the expression of genes using complex interactions of transcription factors, messenger RNA and active protein products. Due to their complexity, gene-regulatory networks are not fully understood.However, by building computational models it is possible to gain insight into their function and operation. METHODS: Evolutionary algorithms are used to create computational models of gene-regulatory networks based on observed microarray data. These algorithms can be computationally intensive. They will be implemented within an existing grid computing infrastructure, that has been developed for data mining purposes, and which is able to deliver the required compute power. RESULTS: We discuss how models can built achieved using distributed and grid computing technology. In particular we investigate how Condor and JavaSpaces technology is suited to the requirements of our modeling approach. CONCLUSIONS: Determining network models of gene-regulatory networks using evolutionary algorithms not only requires considerable computational power, but also a modeling formalism that can explain the underlying dynamics.

Algorithms↗
PubMed2004

Evolutionary and cross-cultural perspectives on gambling.

Few attempts have been made to incorporate evolutionary and cross-cultural perspectives on gambling. This paper begins with the assumption that gambling represents a risky endeavor undertaken for the purpose of winning stakes. This assumption leads to the derivation from evolutionary theory of two hypotheses concerning the socio-demographic characteristics of gamblers: (1) gambling should be over-represented among males, and (2) among young adults. To test these hypotheses, data are drawn from three sources. A cross-cultural sample of 60 societies reveals that males are more often identified as gamblers than females, and these results do not appear to reflect reporting biases. The data are insufficient to enable conclusions about age patterns associated with gambling within this cross-cultural sample. Nationally representative studies of problem and pathological gamblers drawn from seven nation states show that such gamblers tend to be over-represented by young males, as predicted. Lastly, available demographic data on casino gambling hint at sex differences in the games played and the stakes wagered, but require further research for robust conclusions to be drawn.

Age Factors↗
PubMed2005

Why disease persists: an evolutionary nosology.

Although natural selection might be expected to reduce the incidence and severity of disease, disease persists. Natural selection leads to increases in the mean fitness of populations and so will reduce the frequency of disease-associated alleles, but other evolutionary processes, such as mutation and gene flow, may introduce or increase the frequency of these deleterious alleles. The pleiotropic actions of genes and the epistatic interactions between them complicate the relationship between genotype and phenotype, and may result in the preservation of disease-associated alleles. Deleterious alleles may also be maintained because of linkage to beneficial alleles. The inability of natural selection to eliminate diseases of aging is a reminder that fitness -- success in producing progeny, or in contributing genes to the population gene pool -- is not equivalent to the absence of disease. Nutritional or psychosocial cues may lead to life history strategies that maximize survival to reproductive maturity at the expense of disease later in life. Natural selection acts on genes, cells, and groups, as well as on organisms; the outcome of evolution reflects selection at different levels of biological organization. Finally, the human environment is constantly changing, largely because of the evolution of our parasites and because of changes in cultural beliefs and practices; genetic evolution is comparatively slow and lags behind environmental change. An evolutionary nosology complements traditional medical nosologies and enhances our understanding of the persistence of disease and the meaning of human variation.

Environment↗
PubMed2006

Evolutionary computation and multimodal search: a good combination to tackle molecular diversity in the field of peptide design.

The awesome degree of structural diversity accessible in peptide design has created a demand for computational resources that can evaluate a multitude of candidate structures. In our specific case, we translate the peptide design problem to an optimization problem, and use evolutionary computation (EC) in tandem with docking to carry out a combinatorial search. However, the use of EC in huge search spaces with different optima may pose certain drawbacks. For example, EC is prone to focus a search in the first good region found. This is a problem not only because of the undesirable and automatic rejection of potentially good search space regions, but also because the found solution may be extremely difficult to synthesize chemically or may even be a false docking positive. In order to avoid rejecting potentially good solutions and to maximize the molecular diversity of the search, we have implemented evolutionary multimodal search techniques, as well as the molecular diversity metric needed by the multimodal algorithms to measure differences between various regions of the search space.

Algorithms↗
PubMed2006

Fixation of strategies for an evolutionary game in finite populations.

A stochastic evolutionary dynamics of two strategies given by 2x 2 matrix games is studied in finite populations. We focus on stochastic properties of fixation: how a strategy represented by a single individual wins over the entire population. The process is discussed in the framework of a random walk with site dependent hopping rates. The time of fixation is found to be identical for both strategies in any particular game. The asymptotic behavior of the fixation time and fixation probabilities in the large population size limit is also discussed. We show that fixation is fast when there is at least one pure evolutionary stable strategy (ESS) in the infinite population size limit, while fixation is slow when the ESS is the coexistence of the two strategies.

Biological Evolution↗
PubMed1990

On the evolutionary history of the circumsporozoite protein in plasmodia.

We report the complete nucleotide sequence of the circumsporozoite (CS) gene of Plasmodium brasilianum and present an analysis of its evolutionary profile. Despite the lack of a reliable time scale, the analysis of the number and distribution of fixations among seven taxa provides a first glimpse of the evolutionary history of the CS gene, and suggests that the branching events of this gene are completely unconnected with--and far precede in time--the speciation event of the parasite's vertebrate hosts.

Amino Acid Sequence↗
PubMed1990

Is the pseudo-dyad in retroviral proteinase monomers structural or evolutionary?

A pseudo-dyad was found to exist in the monomers of the crystal structures of the proteinases from Rous sarcoma virus and the human immunodeficiency virus. This dyad, also discovered earlier in pepsin-like aspartic proteinases and considered to be of probable evolutionary origin, has been shown to arise as a result of the topology and the folding of the proteinase monomers and may not therefore have much evolutionary significance.

Avian Sarcoma Viruses↗
PubMed1986

Sex steroid hormones in natural populations of a sexual whiptail lizard Cnemidophorus inornatus, a direct evolutionary ancestor of a unisexual parthenogen.

The lizard genus Cnemidophorus consists of both sexual species and unisexual, all-female species. We characterized changes in circulating levels of gonadal sex steroid hormones in males and females in one of the sexual species, C. inornatus, to compare them to previously measured levels in a unisexual, parthenogenetic species, C. uniparens. Reproductively active male C. inornatus have high levels of dihydrotestosterone and somewhat lower levels of testosterone. These levels are highest immediately after females become sexually receptive and decrease later at the onset of testicular regression. Female C. inornatus have high levels of estradiol and low levels of progesterone during the previtellogenic and vitellogenic phases of the ovarian cycle. During the postovulatory phase, they have low levels of estradiol and high levels of progesterone. We could not detect circulating levels of androgen at any phase of the ovarian cycle. The patterns of hormone secretion in the female C. inornatus are virtually identical to those of its direct evolutionary descendant, C. uniparens. This confirms our previous conclusion that the evolution of the parthenogenetic mode of reproduction and expression of male-like pseudosexual behavior that are characteristic of the unisexual C. uniparens has not been accomplished by evolutionary modifications in the pattern of sex steroid hormone secretion. Rather it is the response to this pattern of secretion that has been modified.

Animals↗
PubMed1993

Cosmogenic and nucleogenic isotopic changes in Mars: their rates and implications to the evolutionary history of Martian surface.

We present calculations of rates of production of several nuclides in the Martian atmosphere and in the regolith due to nuclear interactions of cosmic ray and radiogenic particles and consider their implications to the evolutionary history of Mars. Nuclides selected are those which, considering their chemical properties, may be useful as tracers for delineating the past histories of the Martian atmosphere and regolith. Calculations are presented for different assumed atmospheric pressures. The regolith production rates for the present thin Martian atmosphere (approximately 20 g cm-2) are expected to be fairly robust because they are based primarily on observed cosmogenic effects in the Moon, for which semiempirical estimates of nuclide production rates have been provided earlier by Reedy (1981). Uncertainties which arise in the calculations of nuclide production rates for an earlier hypothetical Martian atmosphere of approximately 300-500 g cm-2 thickness are discussed. Compared to cosmic ray production rates, the nucleogenic production rates are smaller by several orders of magnitude. However, the nucleogenic production extends to much deeper levels, whereas the cosmogenic production is essentially confined to the top 750-1000 g cm-2 depth. Important examples of nucleogenic production are discussed. Isotopes of neon and argon appear to be very promising for delineating relative magnitudes of a number of planetary processes related to the temporal changes in the thickness of the atmosphere, as well as their release from the regolith. However, quantification of the processes would require higher-precision isotopic data for the atmosphere and also direct measurements of isotopic ratios in the Martian regolith, along with supplementary information on changes in the isotopic compositions of hydrogen, carbon, and nitrogen, which are affected by a variety of mechanisms of escape of gases from the atmosphere. Cosmogenic effects are minimal in these cases. We show that although we can at present draw but limited inferences, the planet Mars presents a unique opportunity to use cosmogenic nuclides as tools to delineate the evolutionary history of the planet as a whole, as well as its regolith and the atmosphere. This arises because of two factors: minimal degassing of the planet, and a fairly intense chemical weathering history of the upper surface. Consequently, an appreciable fraction of some of the isotopes of volatile elements is contributed by nuclear reactions.

Argon↗
PubMed1994

Evolutionary expansion of the Monogenea.

The evolutionary expansion of the monogeneans has taken place in parallel with the diversification of the fish-like vertebrates. In this article the main trends in monogenean evolution are traced from a hypothetical skin-parasitic ancestor on early vertebrates. Special consideration is given to the following topics: early divergence between skin feeders and blood feeders; diversification and specialization of the haptor for attachment to skin; transfer from host to host, viviparity and the success of the gyrodactylids; predation on skin parasites and camouflage; colonization of the buccal and branchial cavities; diversification and specialization of the haptor for attachment to the gills; phoresy in gill parasites; the development of endoparasitism and the origin of the cestodes; the success of dactylogyroidean gill parasites; the uniqueness of the polyopisthocotyleans; ovoviviparity and the colonization of the tetrapods. Host specificity has been the guiding force of coevolution between monogeneans and their vertebrate hosts, but the establishment of monogeneans on unrelated hosts sharing the same environment (host-switching) may have been underestimated. Host-switching has provided significant opportunities for evolutionary change of direction and is probably responsible for the establishment of monogeneans on cephalopod molluscs, on the hippopotamus and possibly on chelonians. There are indications that host-switching may be more common in monogeneans that spread by direct transfer of adults/juveniles from host to host. A limitation on the further expansion of monogeneans is the need for water for the dispersal of the infective larva (oncomiracidium).

Animals↗
PubMed1994

The evolutionary expansion of the Sporozoa.

The sporozoans comprise a coherent group of protozoans, with characteristic and complex life cycles, containing 4-5000 species parasitic in invertebrates, particularly annelids and arthropods, and vertebrates. The group is a very successful one but neither its origins nor evolution are well understood. Considerations of traditional life cycles combined with newer methodologies have thrown some light on the evolutionary expansions of the main groups of sporozoans, the gregarines, coccidia, haemosporidians and piroplasms. The sporozoans of economic importance such as the coccidia, malaria parasites and piroplasms have received most attention but the data obtained have also thrown new light on the possible evolution of less well studied groups and it is concluded that conclusions based on simple comparisons of life cycles will have to be modified. It is also clear that humans have played a major part in affecting the distribution and present abundance of many sporozoans of economic significance and probably also those of less importance, and that the rates of evolutionary expansion are much more rapid than previously thought.

Animal Population Groups↗
PubMed1996

Parasites as host [corrected] evolutionary prints: insights into host evolution from parasitological data.

The close relationships which link parasitic organisms to their hosts have led to the use of parasites as biological tags. Most studies on this topic refer to parasites as host ecological tags. Recent development of molecular methods which give access to the genomic structures of populations have provided new information on the evolutionary biology of parasites. In this paper, we have attempted to review whether parasites can be considered as "host evolutionary prints", and focus our discussion on host biodiversity and biogeography.

Animals↗
PubMed1988

Influenza B virus evolution: co-circulating lineages and comparison of evolutionary pattern with those of influenza A and C viruses.

Sequence analyses and comparison of the genes coding for the nonstructural (NS) and hemagglutinin (HA) proteins of different influenza B viruses isolated between 1940 and 1987 reveal that the number of substitutions is not always proportional to the time between isolates. Examination of 14 influenza B virus NS gene and 10 HA gene sequences by the maximum parsimony method suggested that--as with influenza C viruses--there are multiple evolutionary lineages which can coexist for considerable periods of time. Comparison of the sequence divergence among genes of viruses belonging to type A, B, and C virus suggests that, in man, influenza B viruses evolve slower than A viruses and faster than C viruses. We propose an evolutionary model for influenza B viruses that is intermediate between the pattern for human influenza A viruses and that for influenza C viruses.

Amino Acid Sequence↗
PubMed1990

Cocirculation of two distinct evolutionary lineages of influenza type B virus since 1983.

During 1988-1989 two highly distinct antigenic variants of influenza type B were recognized in hemagglutination-inhibition tests with postinfection ferret serum. These viruses were antigenically related to either B/Victoria/2/87, the most recent reference strain, or B/Yamagata/16/88, a variant that was isolated in Japan in May 1988. All influenza B viruses isolated in the United States during an epidemic in the winter of 1988-1989 were antigenically related to B/Victoria/2/87. However, in several countries in Asia, both B/Victoria/2/87-like viruses and B/Yamagata/16/88-like viruses were isolated. Sequence analysis of the hemagglutinin (HA) genes of several influenza B isolates from 1987 to 1988 indicated that the HA1 domains of the B/Yamagata/16/88-like viruses and B/VI/87-like viruses isolated in 1988 differed by 27 amino acids. Evolutionary relationships based on this sequence data indicated that the B/Yamagata/16/88-like viruses were more closely related to epidemic viruses from 1983 (B/USSR/100/83-like viruses) than to more recent reference strains such as B/Victoria/2/87. All other Asian strains, as well as selected isolates from the United States in 1988, were confirmed by sequence analysis as being genetically related to B/Victoria/2/87. These data provide clear evidence that two parallel evolutionary pathways of influenza type B have existed since at least 1983 and that viruses from each of the separate lineages were isolated from cases of influenza B in 1988. This finding is similar to earlier observations for type A H1N1 and H3N2 influenza viruses.

Amino Acid Sequence↗