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Under assumptions on initial wave-packet spreads and particle interactions, different mass particles scattering off one another will have the product sigma(2)(i)m(i) converge to a common value, where sigma(i) is the spread and m(i) is the mass of the ith particle. When this relation is satisfied, kinematic entanglement vanishes.
Given the unique thermal history of the Antarctic continent, fishes of dominant suborder Notothenioidei offer a remarkable opportunity to study the physiological and biochemical characters gained and, conversely, lost during their evolutionary history and to map this information on the species phylogenetic trees. The availability of phylogenetically related notothenioid taxa living in a wide range of latitudes (in the Antarctic, sub-Antarctic and temperate regions) allows to look into the molecular bases of environmentally driven gene birth and death. This evolutionary perspective has also been supported by comparison of some features of the hemoprotein devoted to the oxygen transport in fish species living in the other polar region, the Arctic. The Arctic and Antarctic marine ichthyofaunas differ by age and isolation. Fishes of the two polar regions have undergone different regional histories which have engineered the physiological diversities, so that Antarctic fish are much more stenothermal than Arctic ones. Understanding the mechanisms of phenotypic response to cold exposure in species living at different latitudes in polar habitats offers fundamental insights into environmental adaptations. This review aims at surveying the current knowledge of molecular structure, functional features, phylogeny and adaptations of the hemoglobin of fish thriving in the Antarctic, sub-Antarctic and Arctic regions (with some excursions in the temperate latitudes). Investigating the evolutionary adaptations of hemoglobins to these environments can provide new insights into adaptation currently studied merely in temperate organisms, and can shed light into the convergent processes that evolved in response to thermal adaptations.
Endocannabinoid system evolution was estimated by searching for functional orthologs in the genomes of twelve phylogenetically diverse organisms: Homo sapiens, Mus musculus, Takifugu rubripes, Ciona intestinalis, Caenorhabditis elegans, Drosophila melanogaster, Saccharomyces cerevisiae, Arabidopsis thaliana, Plasmodium falciparum, Tetrahymena thermophila, Archaeoglobus fulgidus, and Mycobacterium tuberculosis. Sequences similar to human endocannabinoid exon sequences were derived from filtered BLAST searches, and subjected to phylogenetic testing with ClustalX and tree building programs. Monophyletic clades that agreed with broader phylogenetic evidence (i.e., gene trees displaying topographical congruence with species trees) were considered orthologs. The capacity of orthologs to function as endocannabinoid proteins was predicted with pattern profilers (Pfam, Prosite, TMHMM, and pSORT), and by examining queried sequences for amino acid motifs known to serve critical roles in endocannabinoid protein function (obtained from a database of site-directed mutagenesis studies). This novel transfer of functional information onto gene trees enabled us to better predict the functional origins of the endocannabinoid system. Within this limited number of twelve organisms, the endocannabinoid genes exhibited heterogeneous evolutionary trajectories, with functional orthologs limited to mammals (TRPV1 and GPR55), or vertebrates (CB2 and DAGLbeta), or chordates (MAGL and COX2), or animals (DAGLalpha and CB1-like receptors), or opisthokonta (animals and fungi, NAPE-PLD), or eukaryotes (FAAH). Our methods identified fewer orthologs than did automated annotation systems, such as HomoloGene. Phylogenetic profiles, nonorthologous gene displacement, functional convergence, and coevolution are discussed.
Ca(2+)-regulated motility is essential to numerous cellular functions, including muscle contraction. Systems with troponin C, myosin light chain, or calmodulin as the Ca(2+) receptor have evolved in striated muscle and other types of cells to transduce the cytoplasm Ca(2+) signals into allosteric conformational changes of contractile proteins. While these Ca(2+) receptors are homologous proteins, their coupling to the responding elements is quite different in various cell types. The Ca(2+) regulatory system in vertebrate striated muscle represents a highly specialized such signal transduction pathway consisting of the troponin complex and tropomyosin associated with the actin filament. To understand the molecular mechanism in the Ca(2+) regulation of muscle contraction and cell motility, we have revealed a preserved ancestral close linkage between the genes encoding two of the troponin subunits, troponin I and troponin T, in the genome of mouse. The data suggest that the troponin I and troponin T genes may have originated from a single locus and evolved in parallel to encode a striated muscle-specific adapter to couple the Ca(2+) receptor, troponin C, to the actin-myosin contractile machinery. This hypothesis views the three troponin subunits as two structure-function domains: the Ca(2+) receptor and the signal transducing adapter. This model may help to further our understanding of the Ca(2+) regulation of muscle contraction and the structure-function relationship of other potential adapter proteins which are converged to constitute the Ca(2+) signal transduction pathways governing nonmuscle cell motility.
Clonal evolution which characterizes malignant tumors is the consequence of two antagonizing forces acting on the tumor cell population, namely, forces of diversion and conversion. The former makes cells to diverge through genetic and epigenetic instabilities which are the built-in characteristics of malignant cells. Possible causes of genetic instability are discussed. These include mistakes in DNA synthesis by an error-prone DNA polymerase, the nucleotide pool distartion and the overreplication of replication origins, abnormal DNA repair, high rate recombination, by expression of fragile sites and possibly by expression of retrotransposons, frequent nondisjunction of chromosomes as a consequence of gene dosage inbalance, and abnormal DNA methylation. The second force makes the resulting tumor cell population with heterogenous phenotypes to converge through selection by host defence mechanisms, competition for nutrients and oxygen among tumor cells, to cell interactions within tumor and between surrounding normal tissues. Genetic tagging of tumor cells with pSV 2neo facilitates the analysis of clonal evolution which results from diversion and conversion of tumor cells. Selective growth and metastasis of a clone in a mouse sarcoma population was demonstrated. Generation of dominant clones as well as drug resistant clones in tumor can be studied with this method.
The brain of the La Plata dolphin, Pontoporia blainvillei, was studied with methods of quantitative morphology. The volumes and the progression indices of the main brain structures were determined and compared with corresponding data of other Cetacea, Insectivora and Primates. In Pontoporia, encephalization and neocorticalization are clearly greater than in primitive ("basal") Insectivora. The indices are in the lower part of the range for simian monkeys. The paleocortex is regressive in accordance with the total reduction of the olfactory bulb and olfactory tract. In contrast to the situation in primates, the septum, schizocortex and archicortex are not progressive in Pontoporia. The striatum and cerebellum are strongly progressive, corresponding to the efficiency and importance of the motor system in the three-dimensional habitat. The diencephalon, mesencephalon and medulla oblongata show considerable progression. Obviously, this is correlated with the extensive development of structures of the acoustic system. The superficial correspondence of the brains of dolphins and primates in relative size and in the degree of gyrencephaly is rather a rough morphological convergence than a sign of functional equivalence. It is coupled to a strongly divergent development of the various functional systems in the two mammalian orders according to their specific evolution.
Although molecular and phenotypic evolution have been studied extensively in Drosophila melanogaster and its close relatives, phylogenetic relationships within the D. melanogaster species subgroup remain unresolved. In particular, recent molecular studies have not converged on the branching orders of the D. yakuba-D. teissieri and D. erecta-D. orena species pairs relative to the D. melanogaster-D. simulans-D. mauritiana-D. sechellia species complex. Here, we reconstruct the phylogeny of the melanogaster species subgroup using DNA sequence data from four nuclear genes. We have employed "vectorette PCR" to obtain sequence data for orthologous regions of the Alcohol dehydrogenase (Adh), Alcohol dehydrogenase related (Adhr), Glucose dehydrogenase (Gld), and rosy (ry) genes (totaling 7164 bp) from six melanogaster subgroup species (D. melanogaster, D. simulans, D. teissieri, D. yakuba, D. erecta, and D. orena) and three species from subgroups outside the melanogaster species subgroup [D. eugracilis (eugracilis subgroup), D. mimetica (suzukii subgroup), and D. lutescens (takahashii subgroup)]. Relationships within the D. simulans complex are not addressed. Phylogenetic analyses employing maximum parsimony, neighbor-joining, and maximum likelihood methods strongly support a D. yakuba-D. teissieri and D. erecta-D. orena clade within the melanogaster species subgroup. D. eugracilis is grouped closer to the melanogaster subgroup than a D. mimetica-D. lutescens clade. This tree topology is supported by reconstructions employing simple (single parameter) and more complex (nonreversible) substitution models.
A model of the P-M system of hybrid dysgenesis is presented which incorporates single-site transposition of P factors in M cytotype, determination of offspring cytotype by both maternal cytotype and maternal or offspring nuclear genotype, and strong fertility selection in dysgenic individuals. The conditions required for the initial invasion of P factors into a pure M population, information concerning stable polymorphisms, and results of numerical iterations depicting the dynamic, nonequilibrium behavior of the system are summarized. While conditions for initial increase are independent of the rate of cytotype switching, the rate of evolution is accelerated by increased production of dysgenic individuals. If the transposition rate is sufficiently high to overcome the fertility barrier opposing P factors introduced into M populations, then convergence to high frequencies of the P factor occurs very rapidly. Under intense fertility depression, the phase of rapid increase may be preceded by an extended period of gradual increase at low frequencies.
A new version of an ant colony optimization (ACO) algorithm has been proposed. A modified ACO algorithm is proposed to select variables in QSAR modeling and to predict inhibiting action of some diarylimidazole derivatives on cyclooxygenase (COX) enzyme. As a comparison to this method, the evolution algorithm (EA) was also tested. Experimental results have demonstrated that the modified ACO is a useful tool for variable selection that needs few parameters to be adjusted and converges quickly toward the optimal position.
The author begins by briefly retracing the causes and the evolution of sinistrosis. He defines the concept and point out its ambiguities. The clinical aspect affect on the north african migrant is then discussed. The body is appeared the converging point for the different psychological social and cultural dimension involved. The conclusion is that the complexity of the transferential and counter transferential phenomena leads to a continue reflexion about the therapeutic models to be used.
M6P/IGF2R imprinting first appeared approximately 150 million years ago following the divergence of prototherian from therian mammals. Although M6P/IGF2R is clearly imprinted in opossums and rodents, its imprint status in humans remains ambiguous. It is also still unknown if M6P/IGF2R imprinting was an ancestral mammalian epigenotype or if it evolved convergently. We report herein that M6P/IGF2R is imprinted in Artiodactyla, as it is in Rodentia and Marsupialia, but that it is not imprinted in Scandentia, Dermoptera and Primates, including ringtail lemurs and humans. These results are most parsimonious with a single ancestral origin of M6P/IGF2R imprinting followed by a lineage-specific disappearance of M6P/IGF2R imprinting in Euarchonta. The absence of M6P/IGF2R imprinting in extant primates, due to its disappearance from the primate lineage over 75 million years ago, demonstrates that imprinting at this locus does not predispose to human disease. Moreover, the divergent evolution of M6P/IGF2R imprinting predicts that the success of in vitro embryo procedures such as cloning may be species dependent.
The time process of transport on randomly evolving trees is investigated. By introducing the notions of living and dead nodes, a model of random tree evolution is constructed which describes the spreading in time of objects corresponding to nodes. It is assumed that at t=0 the tree consists of a single living node (root), from which the evolution may begin. At a certain time instant tau> or =0, the root produces v> or =0 living nodes connected by lines to the root which becomes dead at the moment of the offspring production. In the evolution process each of the new living nodes evolves further like a root independently of the others. By using the methods of the age-dependent branching processes we derive the joint distribution function of the numbers of living and dead nodes, and determine the correlation between these node numbers as a function of time. It is proved that the correlation function converges to square root of 3/2 independently of the distributions of v and tau when q1-->1 and t-->infinity. Also analyzed are the stochastic properties of the end nodes; and the correlation between the numbers of living and dead end nodes is shown to change its character suddenly at the very beginning of the evolution process. The survival probability of random trees is investigated and expressions are derived for this probability.
Inferences of phylogenies and dates of divergence rely on accurate modeling of evolutionary processes; they may be confounded by variation in substitution rates among sites and changes in evolutionary processes over time. In vertebrate mitochondrial genomes, substitution rates are affected by a gradient along the genome of the time spent being single-stranded during replication, and different types of substitutions respond differently to this gradient. The gradient is controlled by biological factors including the rate of replication and functionality of repair mechanisms; little is known, however, about the consistency of the gradient over evolutionary time, or about how evolution of this gradient might affect phylogenetic analysis. Here, we evaluate the evolution of response to this gradient in complete primate mitochondrial genomes, focusing particularly on A-->G substitutions, which increase linearly with the gradient. We developed a methodology to evaluate the posterior probability densities of the response parameter space, and used likelihood ratio tests and mixture models with different numbers of classes to determine whether groups of genomes have evolved in a similar fashion. Substitution gradients usually evolve slowly in primates, but there have been at least two large evolutionary jumps: on the lineage leading to the great apes, and a convergent change on the lineage leading to baboons (Papio). There have also been possible convergences at deeper taxonomic levels, and different types of substitutions appear to evolve independently. The placements of the tarsier and the tree shrew within and in relation to primates may be incorrect because of convergence in these factors.
The restriction endonuclease (R.BsuFI) of Bacillus subtilis recognizes the target DNA sequence 5' CCGG. The R.BsuFI gene was found in close proximity to the cognate M.BsuFI gene, which had previously been characterized (1). Cloning of the R.BsuFI gene in E.coli was only possible with the M.BsuFI Mtase gene present on a compatible plasmid. The cloned R.BsuFI gene was expressed in E. coli and restriction activity was observed in vivo and in vitro. The R.BsuFI gene consists of 1185 bp, coding for a protein of 395 amino acids with a calculated molecular weight of 45.6 kD. The R.BsuFI enzyme was purified to homogeneity following overexpression. It presumably works as a dimer and cleaves the 5' CCGG target sequence between the two cytosines to produce sticky ends with 5' CG overhangs, like the isoschizomers R.MspI and R.HpaII. The relatedness between R.BsuFI and R.MspI is reflected by significant similarities of the amino acid sequences of both enzymes. This is the first case where such similarities have been observed between isoschizomeric restriction endonucleases which belong to 5mC specific R/M systems. This observation suggests that R.BsuFI and R.MspI genes derive from a common ancestor. In spite of such functional and evolutionary relatedness, the R/M systems differ in the arrangement of their R and M genes. In the BsuFI system transcription of the two genes is convergent, whereas divergent transcription occurs in the MspI system.
Clear cell sarcoma of tendons and aponeuroses (CCS) is an uncommon malignancy characterized by a t(12;22)(q13;q12) causing a fusion of the EWS and ATF1 genes. We describe the cytogenetic and molecular genetic analyses of two lung metastases from a CCS patient. Both lesions presented the defining t(12;22) and a type 1 EWS/ATF1 chimeric transcript. The additional cytogenetic changes present in the two lesions allowed us to obtain some insight into the pathogenetic basis of disease progression. Four related clones were identified in the right lung metastasis, permitting a partial reconstitution of the stepwise clonal evolution, whereas the left lung metastasis presented yet another subclone. The comparison of the two karyotypes enabled us to pinpoint which changes occurred in the primary tumor and which emerged independently after the two metastases had been established. We conclude that both clonal divergence and convergence may be operative during tumor progression of CCS.
We formulate two single-locus Mendelian models, one for androdioecy and the other one for gynodioecy, each with 3 parameters: t the male (female) fertility rate of males (females) to hermaphrodites, s the fraction of the progeny derived from selfing; and g the fitness of inbreeders. Each model is expressed as a transformation of a 3 dimensional zygotic algebra, which we interpret as a rational map of the projective plane. We then study the dynamics for the evolution of each reproductive system; and compare our results with similar published models. In this process, we introduce a general concept of fitness and list some of its properties, obtaining a relative measure of population growth, computable as an eigenvalue of a mixed mating transformation for a population in equilibrium. Our results concur with previous models of the evolution of androdioecy and gynodioecy regarding the threshold values above which the sexual polymophism is stable, although the previous models assume constant the fraction of ovules from hermaphrodites that are self pollinated, while we assume constant the fraction of the progeny derived from selfing. A stable androdioecy requires more stringent conditions than a stable gynodioecy if the amount of pollen used for selfing is negligible in comparison with the total amount of pollen produced by hermaphrodites. Otherwise, both models are identical. We show explicitly that the genotype fitnesses depend linearly on their frequencies. Simulations show that any population not at equilibrium always converges to the equilibrium point of higher fitness. However, at intermediate steps, the fitness function occasionally decreases.
Although the mathematical principles underpinning population-level evolution are now well studied, the origin and evolution of morphological novelties has received far less attention. Here, a broad but general theory for how this sort of change takes place is outlined, relying on functional continuity, least-constrained components of morphology, redundancy and preadaptation. At least four distinct sorts of redundancy are identified: (i) redundancy arising through duplication (amplification); (ii) redundancy arising through regionalisation (parcellation); (iii) redundancy arising through functional convergence; and (iv) redundancy arising from shared function (functional degeneracy). Although organisms are here recognised to be functionally constrained ("burdened", in Riedl's terminology), these constraints can be overcome through the combination of the four principles given above. Contrary to its common treatment, functional constraint is neither an ever-increasing restriction on the scope of evolution, nor does it require drastic events to overcome or "break" it. Rather, it is an evolutionary quantity, subject to selection at some level. The rules that govern morphological evolution are the primary controls on what is allowed to happen in the evolution of the overall genotype-phenotype system, suggesting strong controls on the sorts of developmental changes that might be associated with macroevolution. This model, then, sees organism functionality as the primary control on evolvability, with exact genetic make-up being of secondary importance. It should prove possible to recast traditional notions of body-plan evolution into the formulations of complex system analysis, which in the future may prove a unifying discipline for fields as disparate as palaeontology and gene regulatory networks. In particular, understanding how morphology can evolve may provide the critical link between the ecological and morphological networks that are currently the intense focus of evolutionary investigations.
The local density of gene structures and single nucleotide polymorphisms (SNPs) along human chromosomes appears inhomogeneous. In chromosome 1, the density patterns from both these elements are shown here to exhibit similar scale invariant clustering, as well as long-ranged and scale invariant auto- and cross-correlations. The local densities of these elements sites can be accurately represented by the scale invariant exponential dispersion models, a group of stochastic models that act as limiting distributions for a wide range of generalized linear models. The scale invariant Poisson-gamma (PG) distribution is the most applicable of these models, since it describes the above findings and it lends itself to a stochastic mechanism for the accumulation of segmental chromosomal changes. This PG model describes the summation of neutral chromosomal mutations, deletions, rearrangements and recombinations, within chromosomal segments that are distinguished by their evolutionary genealogies. Scale invariance is a necessary property if such a description is to remain valid at different measurement scales. The observed density patterns, and proposed model, presumably represent the convergent summation of multiple stochastic processes within the evolutionary history of the chromosome.