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PubMed2003

Locally-adaptive and memetic evolutionary pattern search algorithms.

Recent convergence analyses of evolutionary pattern search algorithms (EPSAs) have shown that these methods have a weak stationary point convergence theory for a broad class of unconstrained and linearly constrained problems. This paper describes how the convergence theory for EPSAs can be adapted to allow each individual in a population to have its own mutation step length (similar to the design of evolutionary programing and evolution strategies algorithms). These are called locally-adaptive EPSAs (LA-EPSAs) since each individual's mutation step length is independently adapted in different local neighborhoods. The paper also describes a variety of standard formulations of evolutionary algorithms that can be used for LA-EPSAs. Further, it is shown how this convergence theory can be applied to memetic EPSAs, which use local search to refine points within each iteration.

Algorithms↗
PubMed2001

A generalized adaptive dynamics framework can describe the evolutionary Ultimatum Game.

Adaptive dynamics describes the evolution of games where the strategies are continuous functions of some parameters. The standard adaptive dynamics framework assumes that the population is homogeneous at any one time. Differential equations point to the direction of the mutant that has maximum payoff against the resident population. The population then moves towards this mutant. The standard adaptive dynamics formulation cannot deal with games in which the payoff is not differentiable. Here we present a generalized framework which can. We assume that the population is not homogeneous but distributed around an average strategy. This approach can describe the long-term dynamics of the Ultimatum Game and also explain the evolution of fairness in a one-parameter Ultimatum Game.

Adaptation, Physiological↗
PubMed1989

Comparative methods for examining adaptation depend on evolutionary models.

Comparisons among taxa provide a powerful means for helping to understand why primate species differ from each other in morphology, behaviour and life history. Comparative tests can also mislead when not applied correctly, and correct application means taking into account the phylogenetic relationships among the species being compared. Adaptation is defined as a comparative concept. The reasons for phenotypic similarity among closely related taxa are summarized. Different models of evolutionary change dictate different methods for reconstructing ancestral character states and for performing comparative analyses on categorical and continuously varying character. All comparative methods rely either implicitly of explicitly on some model of how evolution proceeds. The choice of a particular method of analysis is, therefore, an implicit choice of a model of evolution.

Adaptation, Biological↗
PubMed1990

Haplodiploidy in the Oxyurida: decoupling the evolutionary processes of adaptation and speciation.

Host distribution and life history variation in the Oxyurida are discussed in the context of haplodiploidy. The Oxyurida have the broadest host distribution of any zooparasitic nematode group but have retained a virtually unchanged life cycle. Like other haplodiploids, oxyuridians have life histories that maintain viscous population structures. It is postulated that this has facilitated speciation but may have discouraged major evolutionary innovation in the group.

Adaptation, Physiological↗
PubMed1997

Evolutionary conflicts and adapted psychologies.

Animal information processing and decision making are often considered to be adaptations that allow individuals to behave optimally under particular ecological conditions. Numerous examples demonstrate how cues from the biotic and abiotic environments affect the ways in which animals process information and make decisions. Information gained from interactions with living organisms is the most complex because individuals have to respond to heterospecifics or conspecifics which may decide on what to do depending on the behaviour of a focal individual. Evolutionary conflicts of interest include: (i) interactions between hosts and parasites, predators and prey, and between competitors; (ii) sperm competition interactions between females, male mates and male non-mates, and (iii) interactions between mate-searching females and their potential mates. Brains may evolve particularly rapidly under the influence of evolutionary conflicts and they may enhance the importance of adapted psychologies in these contexts.

Adaptation, Psychological↗
PubMed2026

Complete telomere-to-telomere genome assembly of Guazuma ulmifolia uncovers evolutionary mechanisms, drought adaptation, and flavonoid biosynthesis.

The first T2T reference genome of Guazuma ulmifolia is reported, which serves as a core genomic resource for stress adaptation research and stress-tolerant breeding in cacao wild relatives. Climate change, particularly increased incidence of drought, poses a major threat to food security. Understanding the genomic basis of environmental adaptation in crop wild relatives can provide valuable resources for improving stress resilience. Guazuma ulmifolia, a wild relative of Theobroma cacao with important ecological and medicinal value, lacks high-quality reference genomic resources. Here, we report the first telomere-to-telomere (T2T) chromosome-level genome assembly of G. ulmifolia, with a genome size of 311.31 Mb, contig N50 of 35.19 Mb, and 98.70% BUSCO completeness. Repetitive sequences constitute 27.43% of the G. ulmifolia genome, with LTR retrotransposons as the predominant class. Comparative genomic analyses revealed that genome-size variation among Malvaceae species is associated with differences in polyploidization history and TE dynamics. Ancestral karyotype reconstruction identified five lineage-specific chromosome fusion events distinguishing G. ulmifolia from T. cacao. Comparative analyses further identified tandem duplication-associated expansion of stress-related LEA and GST gene families, suggesting potential genomic features associated with stress responses. Flavonoid biosynthesis genes were largely conserved in copy number but showed tissue-specific expression patterns, providing candidate genes for investigating secondary metabolism. Together, this study establishes a high-quality T2T genome resource for exploring genome evolution, chromosome organization, and stress-related genomic features in Malvaceae.

Genome, Plant↗
PubMed2003

Molecular regulation, evolutionary, and functional adaptations associated with C to U editing of mammalian apolipoproteinB mRNA.

RNA editing encompasses an important class of co- or posttranscriptional nucleic acid modification that has expanded our understanding of the range of mechanisms that facilitate genetic plasticity. Since the initial description of RNA editing in trypanosome mitochondria, a model of gene regulation has emerged that now encompasses a diverse range of biochemical and genetic mechanisms by which nuclear, mitochondrial, and t-RNA sequences are modified from templated versions encoded in the genome. RNA editing is genetically and biochemically distinct from other RNA modifications such as splicing, capping, and polyadenylation although, as discussed in Section I, these modifications may have relevance to the regulation of certain types of mammalian RNA editing. This review will focus on C to U RNA editing, in particular, the biochemical and genetic mechanisms that regulate this process in mammals. These mechanisms will be examined in the context of the prototype model of C to U RNA editing, namely the posttranscriptional cytidine deamination targeting a single nucleotide in mammalian apolipoproteinB (apoB). Other examples of C to U RNA editing will be discussed and the molecular mechanisms--where known--contrasted with those regulating apoB RNA editing.

Animals↗
PubMed1998

Novel evolutionary histories and adaptive features of proteins from hyperthermophiles

The hyperthermophiles include both bacteria and archaea, although the majority of isolates growing above 100 degreesC are archaea. Newly described adaptive features of hyperthermophiles include proteins stable to 200 degreesC, nucleosomes, chaperonins and high-capacity DNA modifying enzymes. The ongoing release of genomic sequence data from hyperthermophiles will continue to accelerate the discovery of novel proteins.

Journal Article↗
PubMed1999

The evolutionary genetics of adaptation: a simulation study.

It is now clear that the genetic basis of adaptation does not resemble that assumed by the infinitesimal model. Instead, adaptation often involves a modest number of factors of large effect and a greater number of factors of smaller effect. After reviewing relevant experimental studies, I consider recent theoretical attempts to predict the genetic architecture of adaptation from first principles. In particular, I review the history of work on Fisher's geometric model of adaptation, including recent studies which suggest that adaptation should be characterized by exponential distributions of gene effects. I also present the results of new simulation studies that test the robustness of this finding. I explore the effects of changes in the distribution of mutational effects (absolute versus relative) as well as in the nature of the character studied (total phenotypic effect versus single characters). The results show that adaptation towards a fixed optimum is generally characterized by an exponential effects trend.

Adaptation, Physiological↗
PubMed2001

Idiopathic osteoporosis: an evolutionary dys-adaptation?

Osteoporosis is characterised by simultaneous net bone growth and net resorption on different surfaces, suggesting that systemic factors are not the sole explanation for the findings. The main clinical consequence is fracturing in the largely trabecular bones of the spine, hip, and radius, and the key problem in these areas is finding an explanation for the preferential loss of transverse trabeculae. In normal bone, local maintenance depends on a negative feedback response to intermittent compression strain, and it is concluded, from biomechanical analysis of the response required to achieve negative feedback, that a preferential loss of transverse trabeculae is indicative of a selective deficiency of radial compression loading. The only significant source of radial compression in humans is the induced strain produced by axial tension. This is a necessary component of the lifestyles of quadrupeds and arboreal primates, but in humans occurs only on the convex side when the bone is offset loaded. The resulting strain is a function of the range of movement. It is suggested that the asymmetrical pattern of bone loss in cortical and trabecular osteoporosis reflects chronic underuse of movement range, resulting from the adoption of a bipedal lifestyle. Exercise regimens based on using the whole of the available movement range should better prepare the skeleton to adjust to other factors hostile to bone maintenance.

Adaptation, Physiological↗
PubMed2005

Evolutionary strategies and adaptations for survival between mosquito-parasitic microsporidia and their intermediate copepod hosts: a comparative examination of Amblyospora connecticus and Hyalinocysta chapmani (Microsporidia: Amblyosporidae).

The epizootiology, transmission dynamics, and survival strategies employed by two mosquito-parasitic microsporidia that utilize copepods as intermediate hosts are examined in relation to the biological attributes of their hosts and the environments in which they inhabit. Amblyospora connecticus Andreadis, 1988, a parasite of Ochlerotatus cantator (Coquillett) and Acanthocyclops vernalis (Fischer) is found in an unstable salt marsh environment that is subject to periodic flooding and drying. Both hosts have distinct non-overlapping generations. A. connecticus exhibits a well-defined seasonal transmission cycle that relies heavily on maternal-mediated transovarial transmission by female O. cantator during the summer, and horizontal transmission via the copepod host during the spring (copepod to mosquito) and fall (mosquito to copepod). Its survival strategies include: delayed virulence, low pathogenicity and high tissue specificity that allow for transstadial transmission of horizontally acquired infections and maximum spore production, reliance on living hosts throughout most of its life cycle with overwintering in the copepod, polymorphic development that is well synchronized with host physiology, and production and dissemination of infectious spores that are coincident with the seasonal occurrence of susceptible stages in each host. Hyalinocysta chapmani Hazard et Oldacre, 1975, a parasite of Culiseta melanura (Coquillett) and Orthocyclops modestus (Herrick) is found in a comparatively stable, subterranean habitat that is inundated with water throughout the year. Copepods are omnipresent and C. melanura has overlapping broods. H. chapmani is maintained in a continuous cycle of horizontal transmission between each host throughout the summer and fall but lacks a developmental sequence leading to transovarial transmission in the mosquito host. It relies on living hosts for most of its life cycle and overwinters in diapausing mosquito larvae. Transstadial transmission does not occur and there is no dimorphic development in the mosquito host. The spatial and temporal overlap of both mosquito and copepod hosts during the summer and fall affords abundant opportunity for continuous horizontal transmission and increases the likelihood that H. chapmani will find a target host, thus negating the need for a transovarial route. It is hypothesized that natural selection has favoured the production of meiospores in larval female mosquitoes rather than congenital transfer of infection to progeny via ovarian infection as a strategy for achieving greater transmission success. Analysis of the molecular phylogeny data suggest that (1) transovarial transmission and the developmental sequence leading to ovarian infection have been secondarily lost in H. chapmani, as they occur in all other closely related genera, (2) the ancestral state included complex life cycles involving transovarial transmission and an intermediate host, and (3) mosquito-parasitic microsporidia are adjusting their life cycles to accommodate host ecological conditions.

Adaptation, Biological↗
PubMed2001

The rhythm of microbial adaptation.

The evolutionary biologist "studies the steps by which the miraculous adaptations so characteristic of every aspect of the organic world have evolved". But the general nature of such adaptive steps is still unclear. Evolution is often thought to be random and dependent on unpredictable events. In this light, one might expect the steps taken by adaptation to be completely random, both biologically and temporally. Here I present a mathematical derivation to show that, on the contrary, adaptive steps can have fairly strong rhythm. I find that the strength of the adaptive rhythm, that is its relative temporal regularity, is equal to a constant that is the same for all microbial populations. As a consequence, numbers of accumulated adaptations are predicted to have a universal variance/mean ratio. The theory derived here is potentially applicable to the study of molecular evolution.

Adaptation, Physiological↗