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Convergence time for the linkage learning genetic algorithm.

This paper identifies the sequential behavior of the linkage learning genetic algorithm, introduces the tightness time model for a single building block, and develops the connection between the sequential behavior and the tightness time model. By integrating the first-building-block model based on the sequential behavior, the tightness time model, and the connection between these two models, a convergence time model is constructed and empirically verified. The proposed convergence time model explains the exponentially growing time required by the linkage learning genetic algorithm when solving uniformly scaled problems.

Algorithms↗

[Time from the viewpoint of Cantor's and post-Cantorian set theory--a contribution to the founding of chronobiology].

There is given a survey of the evolution of the idea of time in the mankind's thinking from the beginning down to the term's application in sciences and in the philosophy. As one can point out from some languages, living as well as extincted ones, the words for time are derived etymologically from several roots or stems, respectively, which mostly represent different meanings. But by increasing abstraction in all civilized languages, the process of stripping the different words of their concrete accompaniments led up to a narrow of the diverse meanings which converged towards the common understanding of time in modern sciences. Nevertheless time is no unequivocal term as one can show by linguistic and mathematical analysis. Especially by means of the theory of differential equations and the set theory, the chimerical nature of time is demonstrable, so that time is only an abstraction of abstractions.

Biological Evolution↗

Parallel evolution of larval morphology and habitat in the snail-killing fly genus Tetanocera.

In this study, we sequenced one nuclear and three mitochondrial DNA loci to construct a robust estimate of phylogeny for all available species of Tetanocera. Character optimizations suggested that aquatic habitat was the ancestral condition for Tetanocera larvae, and that there were at least three parallel transitions to terrestrial habitat, with one reversal. Maximum likelihood analyses of character state transformations showed significant correlations between habitat transitions and changes in four larval morphological characteristics (cuticular pigmentation and three characters associated with the posterior spiracular disc). We provide evidence that phylogenetic niche conservatism has been responsible for the maintenance of aquatic-associated larval morphological character states, and that concerted convergence and/or gene linkage was responsible for parallel morphological changes that were derived in conjunction with habitat transitions. These habitat-morphology associations were consistent with the action of natural selection in facilitating the morphological changes that occurred during parallel aquatic to terrestrial habitat transitions in Tetanocera.

Animals↗

Geographical variation in a quantitative character.

A model for the evolution of the local averages of a quantitative character under migration, selection, and random genetic drift in a subdivided population is formulated and investigated. Generations are discrete and nonoverlapping; the monoecious, diploid population mates at random in each deme. All three evolutionary forces are weak, but the migration pattern and the local population numbers are otherwise arbitrary. The character is determined by purely additive gene action and a stochastically independent environment; its distribution is Gaussian with a constant variance; and it is under Gaussian stabilizing selection with the same parameters in every deme. Linkage disequilibrium is neglected. Most of the results concern the covariances of the local averages. For a finite number of demes, explicit formulas are derived for (i) the asymptotic rate and pattern of convergence to equilibrium, (ii) the variance of a suitably weighted average of the local averages, and (iii) the equilibrium covariances when selection and random drift are much weaker than migration. Essentially complete analyses of equilibrium and convergence are presented for random outbreeding and site homing, the Levene and island models, the circular habitat and the unbounded linear stepping-stone model in the diffusion approximation, and the exact unbounded stepping-stone model in one and two dimensions.

Biological Evolution↗

Critically attained threshold of cerebral hypoperfusion: the CATCH hypothesis of Alzheimer's pathogenesis.

This review discusses the experimental and clinical data which indicate that chronic cerebral hypoperfusion can affect metabolic, anatomic, and cognitive function adversely. In aged but not young animals, chronic brain hypoperfusion results in regional pre- and post-synaptic changes, protein synthesis abnormalities, energy metabolic dysregulation, reduced glucose utilization, cholinergic receptor loss, and visuo-spatial memory deficits. Additionally, aging animals that are kept for prolonged periods of time after chronic brain hypoperfusion, also develop brain capillary degeneration in CA1 hippocampus and neuronal damage extending from the hippocampal region to the temporo-parietal cortex where neurodegenerative tissue atrophy eventually forms. All these pathologic events occur in rodents in the absence of senile plaques and neurofibrillary tangles. Alzheimer brains reveal similar biochemical and structural changes as those experimentally induced in aging animals. Moreover, regional cerebral hypoperfusion is one of the earlier (if not the earliest) clinical manifestations in both the sporadic and familial forms of Alzheimer's disease. In addition, therapy that improves or increases cerebral perfusion is generally of some benefit to Alzheimer patients. Conversely, a variety of disorders with different etiologies that impair or diminish cerebral perfusion are reported to be risk factors for this dementia. These findings have prompted us to propose the concept that advanced aging in the presence of a vascular risk factor can converge to create a critically attained threshold of cerebral hypoperfusion (CATCH) that triggers regional brain microcirculatory disturbances and impairs optimal delivery of energy substrates needed for normal brain cell function. The outcome of this defect generates a chain of events leading to the progressive evolution of brain metabolic, cognitive and tissue pathology that characterize Alzheimer's disease. The possible role of CATCH in familial and early onset Alzheimer's disease is briefly discussed from a theoretical vantagepoint. The growing and most recent evidence in support of the CATCH concept is the focus of this review.

Alzheimer Disease↗

Developmental phenotypic plasticity: where ecology and evolution meet molecular biology.

The plastic response of phenotypic traits to environmental change is a common research focus in several disciplines-from ecology and evolutionary biology to physiology and molecular genetics. The use of model systems such as the flowering plant Arabidopsis thaliana has facilitated a dialogue between developmental biologists asking how plasticity is controlled (proximate causes) and organismal biologists asking why plasticity exists (ultimate causes). Researchers studying ultimate causes and consequences are increasingly compelled to reject simplistic, 'black box' models, while those studying proximate causes and mechanisms are increasingly obliged to subject their interpretations to ecological 'reality checks.' We review the successful multidisciplinary efforts to understand the phytochrome-mediated shade-avoidance and light-seeking responses of flowering plants as a pertinent example of convergence between evolutionary and molecular biology. In this example, the two-way exchange between reductionist and holist camps has been essential to rapid and sustained progress. This should serve as a model for future collaborative efforts towards understanding the responses of organisms to their constantly changing environments.

Arabidopsis↗

Different strategies to recover the activity of monomeric triosephosphate isomerase by directed evolution.

A monomeric version of triosephosphate isomerase from Trypanosoma brucei, MonoTIM, has very low activity, and the same is true for all of the additional monomeric variants so far constructed. Here, we subjected MonoTIM to directed evolution schemes to achieve an activity improvement. The construction of a suitable strain for genetic selection provided an effective way to obtain active catalysts from a diverse population of protein variants. We used this tool to identify active mutants from two different strategies of mutagenesis: random mutagenesis of the whole gene and randomization of loop 2. Both strategies converged in the isolation of mutations Ala43 to Pro and Thr44 to either Ala or Ser, when randomizing the entire gene or to Arg in the case of randomization of loop 2. The kinetic characterization of the two more active mutants showed an increase of 11-fold in k(cat) and a reduction of 4-fold in K(m) for both of them, demonstrating the sensitivity of the selection method. A small difference in growth rate is observed when both mutant genes are compared, which seems to be attributable to a difference in solubility of the expressed proteins.

Amino Acid Sequence↗

The phylogeny of the cercomeria (Platyhelminthes: Rhabdocoela) and general evolutionary principles.

The unified theory of evolution is an expansion of Darwinian theory that asserts that evolution is driven by entropic accumulation of genetic information that is constrained and organized primarily by the genealogical effects of phylogenetic history and developmental integration, and secondarily by ecological effects, or natural selection in its classical mode. Phylogenetic systematic analysis of the 8 major groups of parasitic rhabdocoelous platyhelminths permits empirical macroevolutionary evaluation of these postulates. Of the 131 characters considered, 127 are phylogenetically constrained, and 4 show evidence of 1 case of convergence each. Data from different developmental stages are phylogenetically congruent, despite differences in ecology among those stages. Ecological diversification, indicated by phylogenetic association of definitive hosts and parasites, and by changes in ecological components of life cycle patterns, is more conservative evolutionarily than diversification in developmental patterns, indicated by the appearance of unique larval stages, asexual proliferation of larvae, polyembryony, and heterochronic changes. These observations support the macroevolutionary postulates of the unified theory.

Animals↗

Reconstruction of ancestral protosplice sites.

Most of the eukaryotic protein-coding genes are interrupted by multiple introns. A substantial fraction of introns occupy the same position in orthologous genes from distant eukaryotes, such as plants and animals, and consequently are inferred to have been inherited from the common ancestor of these organisms. In contrast to these conserved introns, many other introns appear to have been gained during evolution of each major eukaryotic lineage. The mechanism(s) of insertion of new introns into genes remains unknown. Because the nucleotides that flank splice junctions are nonrandom, it has been proposed that introns are preferentially inserted into specific target sequences termed protosplice sites. However, it remains unclear whether the consensus nucleotides flanking the splice junctions are remnants of the original protosplice sites or if they evolved convergently after intron insertion. Here, we directly address the existence of protosplice sites by examining the context of introns inserted within codons that encode amino acids conserved in all eukaryotes and accordingly are not subject to selection for splicing efficiency. We show that introns are either predominantly inserted into specific protosplice sites, which have the consensus sequence (A/C)AG/Gt, or that they are inserted randomly but are preferentially fixed at such sites.

Amino Acid Sequence↗

The narrow-leaf syndrome: a functional and evolutionary approach to the form of fog-harvesting rosette plants.

Plants that use fog as an important water-source frequently have a rosette growth habit. The performance of this morphology in relation to fog interception has not been studied. Some first-principles from physics predict that narrow leaves, together with other ancillary traits (large number and high flexibility of leaves, caudices, and/or epiphytism) which constitute the "narrow-leaf syndrome" should increase fog-interception efficiency. This was tested using aluminum models of rosettes that differed in leaf length, width and number and were exposed to artificial fog. The results were validated using seven species of Tillandsia and four species of xerophytic rosettes. The total amount of fog intercepted in rosette plants increased with total leaf area, while narrow leaves maximized interception efficiency (measured as interception per unit area). The number of leaves in the rosettes is physically constrained because wide-leafed plants can only have a few blades. At the limits of this constraint, net fog interception was independent of leaf form, but interception efficiency was maximized by large numbers of narrow leaves. Atmospheric Tillandsia species show the narrow-leaf syndrome. Their fog interception efficiencies were correlated to the ones predicted from aluminum-model data. In the larger xerophytic rosette species, the interception efficiency was greatest in plants showing the narrow-leaf syndrome. The adaptation to fog-harvesting in several narrow-leaved rosettes was tested for evolutionary convergence in 30 xerophytic rosette species using a comparative method. There was a significant evolutionary tendency towards the development of the narrow-leaf syndrome the closer the species grew to areas where fog is frequently available. This study establishes convergence in a very wide group of plants encompassing genera as contrasting as Tillandsia and Agave as a result of their dependence on fog.

Aluminum↗

Aquatic ape theory and fossil hominids.

While most older palaeo-anthropological studies emphasise the similarities of the fossil hominids with modern man, recent studies often stress the unique and the apelike features of the australopithecine dentitions, skulls and postcranial bones. It is worth reconsidering the features of Australopithecus, Homo erectus and Homo neanderthalensis in the light of the so-called Aquatic Ape Theory (AAT) of Hardy and Morgan, and to compare the skeletal parts of our fossil relatives with those of (semi)aquatic animals. Possible convergences are observed with proboscis monkeys, beavers, sea-otters, hippopotamuses, seals, sea-lions, walruses, sea-cows, whales, dolphins, porpoises, penguins and crocodiles.

Animals↗

Exhaustive sample set among Viverridae reveals the sister-group of felids: the linsangs as a case of extreme morphological convergence within Feliformia.

Although molecular studies have helped to clarify the phylogeny of the problematic family Viverridae, a recent phylogenetic investigation based on cytochrome b (cyt b) has excluded the Asiatic linsangs (genus Prionodon) from the family. To assess the phylogenetic position of the Asiatic linsangs within the Feliformia, we analysed an exhaustive taxonomic sample set with cyt b and newly produced transthyretin intron I sequences (TR-I-I). TR-I-I alone and cyt b +TR-I-I combined (maximum-likelihood analysis) highly support the position of Asiatic linsangs as sister-group of the Felidae. The estimation of minimum divergence dates from molecular data suggests a splitting event ca. 33.3 million years (Myr) ago, which lends support to historical assertions that the Asiatic linsangs are "living fossils" that share a plesiomorphic morphotype with the Oligocene feliform Paleoprionodon. The African linsang is estimated to appear more than 20 Myr later and represents the sister-group of the genus Genetta. Our phylogenetic results illustrate numerous morphological convergences of "diagnostic" characters among Feliformia that might be problematic for the identification of fossil taxa. The morphotype reappearance from the Asiatic to the African linsangs suggests that the genome of the Feliformia conserved its potential ability of expression for a peculiar adaptive phenotype throughout evolution, in this case arboreality and hypercarnivory in tropical forest.

Animals↗

Accurate evolutions of orbiting black-hole binaries without excision.

We present a new algorithm for evolving orbiting black-hole binaries that does not require excision or a corotating shift. Our algorithm is based on a novel technique to handle the singular puncture conformal factor. This system, based on the Baumgarte-Shapiro-Shibata-Nakamura formulation of Einstein's equations, when used with a "precollapsed" initial lapse, is nonsingular at the start of the evolution and remains nonsingular and stable provided that a good choice is made for the gauge. As a test case, we use this technique to fully evolve orbiting black-hole binaries from near the innermost stable circular orbit regime. We show fourth-order convergence of waveforms and compute the radiated gravitational energy and angular momentum from the plunge. These results are in good agreement with those predicted by the Lazarus approach.

Journal Article↗

Neural mechanisms for synthesizing sensory information and producing adaptive behaviors.

The ability to integrate information from different sensory systems is a fundamental characteristic of the brain. Because different bits of information are derived from different sensory channels, their synthesis markedly enhances the detection and identification of external stimuli. The neural substrate for such "multisensory" integration is provided by neurons that receive convergent input from two or more sensory modalities. Many such multisensory neurons are found in the superior colliculus (SC), a midbrain structure that plays a significant role in overt attentive and orientation behaviors. The various principles governing the integration of visual, auditory, and somatosensory inputs in SC neurons have been explored in several species. Thus far, the evidence suggests a remarkable conservation of integrative features during vertebrate evolution. One of the most robust of these principles is based on spatial relationships: a striking enhancement in activity is induced in a multisensory neuron when two different sensory stimuli (e.g., visual and auditory) are in spatial concordance, whereas a profound response depression can be induced when these cues are spatially discordant. The most extensive physiological observations have been made in cat, and in this species the same principles that have been shown to govern multisensory integration at the level of the individual SC neuron have also been shown to govern overt attentive and orientation responses to multisensory stimuli. Most surprising, however, is the critical role played by association (i.e. anterior ectosylvian) cortex in facilitating these midbrain processes. In the absence of the modulating corticotectal influences, multisensory SC neurons in cat are unable to integrate the different sensory cues converging upon them in an adult-like fashion, and are unable to mediate overt multisensory behaviors. This situation appears quite similar to that observed during early postnatal life. When multisensory SC neurons first appear, they are able to respond to multiple sensory inputs but are unable to synthesize these inputs to significantly enhance or degrade their responses. During ontogeny, individual multisensory neurons develop this capacity abruptly, but at very different ages, until the mature population condition is reached after several postnatal months. It appears likely that the abrupt onset of this capacity in any individual SC neuron reflects the maturation of inputs from anterior ectosylvian cortex. Presumably, the functional coupling of cortex with an individual SC neuron is essential to initiate and maintain that neuron's capability for multisensory integration throughout its life.

Adaptation, Physiological↗

Genomic Footprints of Historical Introgression Between Ancient Lineages of Wild Oryza AA-Genome Species With Widely Separated Contemporary Distributions.

Phylogenetic incongruence is increasingly recognized as pervasive, yet the extent to which reticulate evolution occurs between groups separated by substantial geographical distances and deep phylogenetic divergence remains poorly characterized. In the Oryza AA-genome group-a model for plant speciation and domestication-the traditional bifurcation model posits that Australian Oryza meridionalis and African Oryza longistaminata occupy basal branches, distinct from the more recently diversified monophyletic clade comprising Asian and other African lineages, including major cultivars. However, recent evidence from endogenous viral sequences has hinted at unexpected genetic relatedness between African O. longistaminata and Asian Oryza sativa, which are geographically and phylogenetically distant. Here, we conducted a genome-wide survey across 11 Oryza species to systematically identify genomic regions exhibiting phylogenetic incongruence. Widespread phylogenetic discordance was observed, notably involving genomic segments in which O. longistaminata showed phylogenetic proximity to Asian species, contradicting their established deep divergence. To distinguish between introgression and incomplete lineage sorting, we performed four-taxon ABBA-BABA tests, which provided statistical support for introgression. Furthermore, divergence time estimates for these incongruent regions were younger than the species divergence times, suggesting historical introgression between the ancestors of lineages that are currently separated by vast geographical distances. Systematic assessments indicated that potential analytical artifacts, such as compositional bias and substitution saturation, were unlikely to explain the observations. These convergent lines of evidence suggest that ancient introgression had occurred between currently geographically separated and evolutionarily divergent Oryza lineages, leaving detectable footprints across their modern genomes.

Oryza↗

Human genetic variation associates with infection by derived Ugandan M. tuberculosis lineage.

BACKGROUND: Several studies have examined host and pathogen genetic influences on tuberculosis (TB) susceptibility separately, but relatively few studied their combined effects. However, host-pathogen interactions or co-evolution may explain the inability to replicate many reported human genetic effects across global populations and provide additional insight into TB risk. In this study, we address such possible interactions by focusing on the outcome of infection with the L4-Uganda M. tuberculosis sub-lineage and human genetic variants as independent variables. This is possible because the L4-Uganda sub-lineage is both restricted to Uganda and nearby locations and is recent there, compared to other more ancestral L4 lineages. METHODS: Our study consisted of 276 culture-confirmed adult TB cases from a long-standing household contact study. We conducted a genome-wide association study, with infection with L4-Uganda versus L4-NonUganda as the outcome. RESULTS: Multiple loci with results suggestive of association (p<10-5) also demonstrated convergent relevant evidence for strain specific infection via: evidence of gene expression in relevant cells and lung tissue, signatures of natural selection, eQTL expression, and CRISPR screens for immunity-related genes. We also replicated previously published host-pathogen interaction effects, demonstrating that effects seen for other sub-lineages were also present for L4-Uganda. CONCLUSIONS: These results provide evidence for host-pathogen co-evolution in TB, consistent with our previous work, and indicate these interactions involve genes highly relevant to the host immune response to Mycobacterium infection.

GWAS↗

Formation, stability, and breakup of nanojets

Atomistic molecular dynamics simulations reveal the formation of nanojets with velocities up to 400 meters per second, created by pressurized injection of fluid propane through nanoscale convergent gold nozzles with heating or coating of the nozzle exterior surface to prevent formation of thick blocking films. The atomistic description is related to continuum hydrodynamic modeling through the derivation of a stochastic lubrication equation that includes thermally triggered fluctuations whose influence on the dynamical evolution increases as the jet dimensions become smaller. Emergence of double-cone neck shapes is predicted when the jet approaches nanoscale molecular dimensions, deviating from the long-thread universal similarity solution obtained in the absence of such fluctuations.

Journal Article↗

A physico-chemical survey of inland lakes and saline ponds: Christmas Island (Kiritimati) and Washington (Teraina) Islands, Republic of Kiribati.

The equatorial Pacific Ocean atoll islands of Kiritimati and Teraina encompass great physical, chemical and biological variability within extreme lacustrine environments. Surveys of lake chemistry and sediments revealed both intra- and inter-island variability. A survey of more than 100 lakes on Kiritimati found salinities from nearly fresh to 150 ppt with the highest values occurring within the isolated, inland portions of the island away from the influence of groundwater or extreme tides. Dissolved oxygen (DO) and pH values also showed considerable variability with a less regular spatial pattern, but were both generally inversely related to salinity. Series of lakes, progressively more isolated from marine communication, present a modern analog to the chemical and morphologic evolution of presently isolated basins. Sediments on both islands consist of interbedded red and green silt, possibly degraded bacterial mat, overlying white, mineralogenic silt precipitate. Variability may be indicative of shifts in climatological parameters such as the El Niño Southern Oscillation (ENSO) or the Pacific Intertropical Convergence Zone (ITCZ).

Journal Article↗