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At least 757 records · Page 42Linked to original sources
PubMed2006

Symbiotic adaptive neuro-evolution applied to rainfall-runoff modelling in northern England.

This paper uses a symbiotic adaptive neuro-evolutionary algorithm to breed neural network models for the River Ouse catchment. It advances on traditional evolutionary approaches by evolving and optimising individual neurons. Furthermore, it is ideal for experimentation with alternative objective functions. Recent research suggests that sum squared error may not result in the most appropriate models from a hydrological perspective. Models are bred for lead times of 6 and 24 hours and compared with conventional neural network models trained using backpropagation. The algorithm is also modified to use different objective functions in the optimisation process: mean squared error, relative error and the Nash-Sutcliffe coefficient of efficiency. The results show that at longer lead times the evolved neural networks outperform the conventional ones in terms of overall performance. It is also shown that the sum squared error objective function does not result in the best performing model from a hydrological perspective.

Algorithms↗
PubMed1982

H(2) and CO(2) Evolution by Anaerobically Adapted Chlamydomonas reinhardtii F-60.

Using manometric and enzymic techniques, H(2) and CO(2) evolution in darkness and light has been studied in the green alga Chlamydomonas reinhardtii F-60. F-60 is a mutant strain characterized by an incomplete photosynthetic carbon reduction cycle but an intact electron transport chain.In the dark, starch was broken down, and H(2) and CO(2) was released. The uncoupler, carbonyl cyanide m-fluorophenylhydrazone with an optimum concentration of 5 to 10 micromolar, increased the rate of CO(2) release and starch breakdown but depressed H(2) formation. It was suggested that carbonyl cyanide m-fluorophenylhydrazone increased the rate of starch breakdown by making the chloroplast membrane permeable to H(+), removing a rate-limiting step, and leading to an altered fermentative pattern.Photoevolution of H(2) and CO(2), but not starch breakdown, was stimulated by acetate. Maximum stimulation occurred at concentrations from 1 to 10 millimolar. Carbonyl cyanide m-fluorophenylhydrazone stimulated starch breakdown and CO(2) and H(2) release in the light, but not to the extent of acetate. Inasmuch as the uptake and subsequent metabolism of acetate required ATP, it was suggested that acetate, like carbonyl cyanide m-fluorophenylhydrazone, stimulated H(2) photoproduction by removing ATP which limited the sequence of reactions. The contribution of photosystem II to the photoproduction of H(2), as judged from the effect of 10 micromolar 3-(3,4-dichlorophenyl)-1, 1-dimethylurea, was at least 80%.CO(2) photoevolution increased linearly with time, but H(2) photoevolution occurred in two phases: a rapid initial phase followed by a second slower phase. The rate of H(2) release increased hyperbolically with light intensity, but the rate of CO(2) production tended to level off and decrease with increasing light intensity, up to 145 watts per square meter. It was proposed that a changing CO(2) and H(2) ratio is the result of interaction between the carbon and hydrogen metabolism and the photosynthetic electron transport chain.

Journal Article↗
PubMed1995

Experimental tests of the roles of adaptation, chance, and history in evolution.

The contributions of adaptation, chance, and history to the evolution of fitness and cell size were measured in two separate experiments using bacteria. In both experiments, populations propagated in identical environments achieved similar fitnesses, regardless of prior history or subsequent chance events. In contrast, the evolution of cell size, a trait weakly correlated with fitness, was more strongly influenced by history and chance.

Adaptation, Physiological↗
PubMed2024

The genome of Lespedeza potaninii reveals biased subgenome evolution and drought adaptation.

Lespedeza potaninii, a xerophytic subshrub belonging to the legume family, is native to the Tengger Desert and is highly adapted to drought. It has important ecological value due to its drought adaptability, but the underlying molecular mechanisms remain largely unknown. Here, we report a 1.24 Gb chromosome-scale assembly of the L. potaninii genome (contig N50 = 15.75 Mb). Our results indicate that L. potaninii underwent an allopolyploid event with 2 subgenomes, A and B, presenting asymmetric evolution and B subgenome dominance. We estimate that the 2 diploid progenitors of L. potaninii diverged around 3.6 million years ago (MYA) and merged around 1.0 MYA. We revealed that the expansion of hub genes associated with drought responses, such as the binding partner 1 of accelerated cell death 11 (ACD11) (BPA1), facilitated environmental adaptations of L. potaninii to desert habitats. We found a novel function of the BPA1 family in abiotic stress tolerance in addition to the known role in regulating the plant immune response, which could improve drought tolerance by positively regulating reactive oxygen species homeostasis in plants. We revealed that bZIP transcription factors could bind to the BPA1 promoter and activate its transcription. Our work fills the genomic data gap in the Lespedeza genus and the tribe Desmodieae, which should provide theoretical support both in the study of drought tolerance and in the molecular breeding of legume crops.

Genome, Plant↗
PubMed2001

The evolution of intelligence: adaptive specializations versus general process.

Darwin argued that between-species differences in intelligence were differences of degree, not of kind. The contemporary ecological approach to animal cognition argues that animals have evolved species-specific and problem-specific processes to solve problems associated with their particular ecological niches: thus different species use different processes, and within a species, different processes are used to tackle problems involving different inputs. This approach contrasts both with Darwin's view and with the general process view, according to which the same central processes of learning and memory are used across an extensive range of problems involving very different inputs. We review evidence relevant to the claim that the learning and memory performance of non-human animals varies according to the nature of the stimuli involved. We first discuss the resource distribution hypothesis, olfactory learning-set formation, and the 'biological constraints' literature, but find no convincing support from these topics for the ecological account of cognition. We then discuss the claim that the performance of birds in spatial tasks of learning and memory is superior in species that depend heavily upon stored food compared to species that either show less dependence upon stored food or do not store food. If it could be shown that storing species enjoy a superiority specifically in spatial (and not non-spatial) tasks, this would argue that spatial tasks are indeed solved using different processes from those used in non-spatial tasks. Our review of this literature does not find a consistent superiority of storing over non-storing birds in spatial tasks, and, in particular, no evidence of enhanced superiority of storing species when the task demands are increased, by, for example, increasing the number of items to be recalled or the duration of the retention period. We discuss also the observation that the hippocampus of storing birds is larger than that of non-storing birds, and find evidence contrary to the view that hippocampal enlargement is associated with enhanced spatial memory; we are, however, unable to suggest a convincing alternative explanation for hippocampal enlargement. The failure to find solid support for the ecological view supports the view that there are no qualitative differences in cognition between animal species in the processes of learning and memory. We also argue that our review supports our contention that speculation about the phylogenetic development and function of behavioural processes does not provide a solid basis for gaining insight into the nature of those processes. We end by confessing to a belief in one major qualitative difference in cognition in animals: we believe that humans alone are capable of acquiring language, and that it is this capacity that divides our intelligence so sharply from non-human intelligence.

Adaptation, Physiological↗
PubMed2004

Adaptation, co-evolution, and human susceptibility to HIV-1 infection.

Infection with HIV-1, a retrovirus of animal origin, has reached pandemic proportions. For this the virus, characterized by rapid mutation rate, has adapted to the host immunity and to the human cellular environment. Humans are also exerting considerable pressure on HIV-1 through the use of antiretroviral agents. On the other hand, long term exposure of humans to other retroviruses and retroelements may have already shaped the human genome. Thus, despite a recent entry of HIV-1 in humans, this pathogen might be already exerting evolutionary pressure on humans, by selecting a repertoire of restriction genes and susceptibility loci.

Adaptation, Physiological↗
PubMed1999

The effects of density dependence and immigration on local adaptation and niche evolution in a black-hole sink environment.

We examine the effects of density dependence and immigration on local adaptation in a "black-hole sink" habitat, i.e., a habitat in which isolated populations of a species would tend to extinction but where a population is demographically maintained by recurrent one-way migration from a separate source habitat in which the species persists. Using a diploid, one-locus model of a discrete-generation sink population maintained by immigration from a fixed source population, we show that a locally favored allele will spread when rare in the sink if the absolute fitness (or, in some cases, the geometric-mean absolute fitness) of heterozygotes with the favored allele is above one in the sink habitat. With density dependence, the criterion for spread can depend on the rate of immigration, because immigration affects local densities and, hence, absolute fitness. Given the successful establishment of a locally favored allele, it will be maintained by a migration-selection balance and the resulting polymorphic population will be sustained deterministically with either stable or unstable dynamics. The densities of stable polymorphic populations tend to exceed densities that would be maintained in the absence of the favored allele. With strong density regulation, spread of the favored allele may destabilize population dynamics. Our analyses show that polymorphic populations which form subsequent to the establishment of favorable alleles have the capacity to persist deterministically without immigration. Finally, we examined the probabilistic rate at which new favored alleles arise and become established in a sink population. Our results suggest that favored alleles are established most readily at intermediate levels of immigration.

Animals↗
PubMed2004

Physicochemical evolution and molecular adaptation of the cetacean and artiodactyl cytochrome b proteins.

Cetaceans have most likely experienced metabolic shifts since evolutionarily diverging from their terrestrial ancestors, shifts that may be reflected in the proteins such as cytochrome b that are responsible for metabolic efficiency. However, accepted statistical methods for detecting molecular adaptation are largely biased against even moderately conservative proteins because the primary criterion involves a comparison of nonsynonymous and synonymous substitution rates (dN/dS); they do not allow for the possibility that adaptation may come in the form of very few amino acid changes. We apply the MM01 model to the possible molecular adaptation of cytochrome b among cetaceans because it does not rely on a dN/dS ratio, instead evaluating positive selection in terms of the amino acid properties that comprise protein phenotypes that selection at the molecular level may act upon. We also apply the codon-degeneracy model (CDM), which focuses on evaluating overall patterns of nucleotide substitution in terms of base exchange, codon position, and synonymy to estimate the overall effect of selection. Using these relatively new models, we characterize the molecular adaptation that has occurred in the cetacean cytochrome b protein by comparing revealed amino acid replacement patterns to those found among artiodactyls, the modern terrestrial mammals found to be most closely related to cetaceans. Our findings suggest that several regions of the cetacean cytochrome b protein have experienced molecular adaptation. Also, these adaptations are spatially associated with domain structure, protein function, and the structure and function of the cytochrome bc(1) complex and its constituents. We also have found a general correlation between the results of the analytical software programs TreeSAAP (which implements the MM01 model) and CDM (which implements the codon-degeneracy model).

Adaptation, Physiological↗
PubMed2004

Major histocompatibility complex controls the trajectory but not host-specific adaptation during virulence evolution of the pathogenic fungus Cryptococcus neoformans.

Genes of the major histocompatibility complex (MHC) play a critical role in immune recognition and are the most genetically diverse loci known. One hypothesis to explain this diversity postulates that pathogens adapt to common MHC haplotypes and thus favour selection of new or rare alleles. To determine whether the pathogenic yeast Cryptococcus neoformans adapts to MHC-dependent immune responses, it was serially passaged in two independent replicate lines of five B10 MHC-congenic strains and Balb/c mice. All passaged lines increased in virulence as measured by reduced host survival. MHC influenced the rate (trajectory) of virulence increase during passages as measured by significant differences in mortality rate (p < 0.001). However, when the post-passage strains were tested, no MHC differences in mortality rate remained and only minor differences in titres were observed. Also contrary to expectations, increased virulence in three lines passaged in B10 mice had a larger effect in Balb/c mice, and the evolution of virulence in lines passaged in alternating hosts was not retarded. To our knowledge, these data represent the first experimental test of MHC-specific adaptation in a non-viral pathogen. The failure to observe MHC effects despite dramatically increased virulence and host-genotype-specific adaptation to non-MHC genes suggests that escape of MHC-dependent immune recognition may be difficult for pathogens with unlimited epitopes or that other virulence factors can swamp MHC effects.

Adaptation, Biological↗
PubMed2004

Pseudomonas aeruginosa and Burkholderia cepacia in cystic fibrosis: genome evolution, interactions and adaptation.

The Gram-negative bacteria Pseudomonas aeruginosa and Burkholderia cepacia are opportunistic human pathogens that are responsible for severe nosocomial infections in immunocompromised patients and are the major pathogens in cystic fibrosis (CF). The two bacteria not only inhabit the same environmental niches but can also form mixed biofilms in the lungs of CF patients. Hence, it appears very likely that the two organisms are capable of interacting with each other. Work of the past few years has shown that both bacteria utilize quorum-sensing systems, which rely on N-acyl-homoserine lactone signal molecules, to control the expression of virulence factors and biofilm development. Most importantly, evidence has been presented that these signal molecules also serve as a universal language for communication between the two organisms. Moreover, analyses of the diversity in P. aeruginosa revealed the presence of genome islands that contain genes that are highly homologous to genes identified in strains of Burkholderia sp. This finding suggests that there is a frequent exchange of genetic material between the two organisms.

4-Butyrolactone↗
PubMed2002

Evolution of cannibalistic traits: scenarios derived from adaptive dynamics.

The evolution of cannibalistic traits in consumer populations is studied in this paper with the approach of adaptive dynamics theory. The model is kept at its minimum complexity by eliminating some environmental characteristics, like heterogeneity and seasonalities, and by hiding the size-structure of the population. Evolutionary dynamics are identified through numerical bifurcation analysis, applied both to the ecological (resident-mutant) model and to the canonical equation of adaptive dynamics. The result is a rich catalog of evolutionary scenarios involving evolutionary stable strategies and branching points both in the monomorphic and dimorphic dynamics. The possibility of evolutionary extinction of highly cannibalistic populations is also ascertained. This allows one to explain why cannibalism can be a transient stage of evolution.

Adaptation, Physiological↗
PubMed2005

Evolutionary traction: the cost of adaptation and the evolution of sex.

The advantage of sexual reproduction remains a puzzle for evolutionary biologists. Everything else being equal, asexual populations are expected to have twice the number of offspring produced by similar sexual populations. Yet, asexual species are uncommon among higher eukaryotes. In models assuming small populations, high mutation rates, or frequent environmental changes, sexual reproduction seems to have at least a two-fold advantage over asexuality. But the advantage of sex for large populations, low mutation rates, and rare or mild environmental changes remains a conundrum. Here we show that without recombination, rare advantageous mutations can result in increased accumulation of deleterious mutations ('evolutionary traction'), which explains the long-term advantage of sex under a wide parameter range.

Adaptation, Biological↗
PubMed1999

Transposition mediated by RAG1 and RAG2 and the evolution of the adaptive immune system.

The RAG1 and RAG2 proteins together initiate V(D)J recombination by performing cleavage of chromosomal DNA adjacent to antigen receptor gene segments. Like the adaptive immune system itself, RAG1 and RAG2 are found only in jawed vertebrates. The hypothesis that RAG1 and RAG2 arose in evolution as components of a transposable element has received dramatic support from our recent finding that the RAG proteins are a fully functional transposase in vitro. This result strongly suggests that antigen receptor genes acquired their unusual structure as a consequence of the insertion of a transposable element into an ancestral receptor gene by RAG1 and RAG2 approx 450 million years ago.

Animals↗
PubMed2003

Genes that determine flower color: the role of regulatory changes in the evolution of phenotypic adaptations.

A central goal of evolutionary genetics is to trace the causal pathway between mutations at particular genes and adaptation at the phenotypic level. The proximate objective is to identify adaptations through the analysis of molecular sequence data from specific candidate genes or their regulatory elements. In this paper, we consider the molecular evolution of floral color in the morning glory genus (Ipomoea) as a model for relating molecular and phenotypic evolution. To begin, flower color variation usually conforms to simple Mendelian transmission, thus facilitating genetic and molecular analyses. Population genetic studies of flower color polymorphisms in the common morning glory (Ipomoea purpurea) have shown that some morphs are subject to complex patterns of selection. Striking differences in floral color and morphology are also associated with speciation in the genus Ipomoea. The molecular bases for these adaptive shifts can be dissected because the biosynthetic pathways that determine floral pigmentation are well understood and many of the genes of flavonoid biosynthesis have been isolated and extensively studied. We present a comparative analysis of the level of gene expression in Ipomoea for several key genes in flavonoid biosynthesis. Specifically we ask: how frequently are adaptive shifts in flower color phenotypes associated with changes in regulation of gene expression versus mutations in structural genes? The results of this study show that most species differences in this crucial phenotype are associated with changes in the regulation of gene expression.

Adaptation, Physiological↗
PubMed2005

Meeting the demand for innate and adaptive immunities during evolution.

An ideal immune system should provide each individual with rapid and efficient responses, a diverse repertoire of recognition and effector molecules and a certain flexibility to match the changing internal and external environment. It should be economic in cells and genes. Specific memory would be useful. It should not be autoreactive. These requirements, a mixture of innate and adaptive immunity features, are modulated in function of the dominant mode of selection for each species of metazoa during evolution (K or r). From sponges to man, a great diversity of receptors and effector mechanisms, some of them shared with plants, are articulated around conserved signalling cascades. Multiple attempts at combining innate and adaptive immunity somatic features can be observed as new somatic mechanisms provide individualized repertoires of receptors throughout metazoa, in agnathans, prochordates, echinoderms and mollusks. The adaptive immunity of vertebrates with lymphocytes and their specific receptors of the immunoglobulin superfamily, the major histocompatibility complex, developed from innate immunity evolutionary lines that can be traced back in earlier deuterostomes.

Animals↗
PubMed2006

The evolution of thermal adaptation in polar fish.

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.

Acclimatization↗