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The molecular basis of the evolution of sex.

Traditionally, sexual reproduction has been explained as an adaptation for producing genetic variation through allelic recombination. Serious difficulties with this explanation have led many workers to conclude that the benefit of sex is a major unsolved problem in evolutionary biology. A recent informational approach to this problem has led to the view that the two fundamental aspects of sex, recombination and outcrossing, are adaptive responses to the two major sources of noise in transmitting genetic information, DNA damage and replication errors. We refer to this view as the repair hypothesis, to distinguish it from the traditional variation hypothesis. On the repair hypothesis, recombination is a process for repairing damaged DNA. In dealing with damage, recombination produces a form of informational noise, allelic recombination, as a by-product. Recombinational repair is the only repair process known which can overcome double-strand damages in DNA, and such damages are common in nature. Recombinational repair is prevalent from the simplest to the most complex organisms. It is effective against many different types of DNA-damaging agents, and, in particular, is highly efficient in overcoming double-strand damages. Current understanding of the mechanisms of recombination during meiosis suggests that meiosis is designed for repairing DNA. These considerations form the basis for the first part of the repair hypothesis, that recombination is an adaptation for dealing with DNA damage. The evolution of sex can be viewed as a continuum on the repair hypothesis. Sex is presumed to have arisen in primitive RNA-containing protocells whose sexual process was similar to that of recombinational repair in extent segmented, single-stranded RNA viruses, which are among the simplest known organisms. Although this early form of repair occurred by nonenzymatic reassortment of replicas of undamaged RNA segments, it evolved into enzyme-mediated breakage and exchange between long DNA molecules. As some lines of descent became more complex, their genome information increased, leading to increased vulnerability to mutation. The diploid stage of the sexual cycle, which was at first transient, became the predominant stage in some lines of descent because it allowed complementation, the masking of deleterious recessive mutations. Out-crossing, the second fundamental aspect of sex, is also maintained by the advantage of masking mutations. However, outcrossing can be abandoned in favor of parthenogenesis or selfing under conditions in which the costs of mating are very high.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

Evo-devo and constraints on selection.

Developmental bias, or genetic channeling, can influence the tempo and direction of evolution and, thus, become reflected in patterns of biodiversity. Twenty years ago, this notion rested on armchair descriptions of potential constraints on evolution. Now, a broad evo-devo approach involving both evolutionary and developmental genetics provides experimental analysis of such bias, revealing how shared genetic or developmental pathways among morphological traits contribute to the evolution of complexity and diversity, and that developmental bias itself evolves, generating variation in evolvability. As I discuss here, it is now possible to determine the relative importance of natural selection and of genetical and developmental architecture as determinants of organic diversity, particularly for examples of adaptive radiations and parallel evolution.

Animals↗

Phylogenetics by likelihood: evolutionary modeling as a tool for understanding the genome.

Molecular evolutionary studies provide a means of investigating how cells function and how organisms adapt to their environment. The products of evolutionary studies provide medically important insights to the source of major diseases, such as HIV, and hold the key to understand the developing immunity of pathogenic bacteria to antibiotics. They have also helped mankind understand its place in nature, casting light on the selective forces and environmental conditions that resulted in modern humans. The use of likelihood as a framework for statistical modeling in phylogenetics has played a fundamental role in studying molecular evolution, enabling rigorous and robust conclusions to be drawn from sequence data. The first half of this article is a general introduction to the likelihood method for inferring phylogenies, the properties of the models used, and how it can be used for statistical testing. The latter half of the article focuses on the emerging new generation of phylogenetic models that describe heterogeneity in the evolutionary process along sequences, including the recoding of protein coding sequence data to amino acids and codons, and various approaches for describing dependencies between sites in a sequence. We conclude with a detailed case study examining how modern modeling approaches have been successfully employed to identify adaptive evolution in proteins.

Animals↗

From genetics to epigenetics.

In the post human-genome area, the challenge is to derive details of heritable variation in relation to how human variation reflects adaptation to the different environments. Heterozygote advantage represents a superior genetic adaptation presumably explaining the presence of the allele at frequencies above those to be expected from a simple replacement of a homozygous lethal allele by mutation alone (Saugstad 1977a, 1975b, 1972). Mean birthweight of unaffected offspring of parents heterozygous for the phenylketonuria (PKU) allele averaged significantly above mean weight of all Norwegian births, rendering unaffected offspring more viable at birth and thus improving the chance for survival of the allele. A successful adaptation requires natural selection acting on that part of the body that makes a difference in survival. Skin colour variation is such a successful adaptation, for the North as opposed to the dark skins of the equator. Human Evolution in Africa and subsequent adaptations have enabled human survival all over the world with highly different light intensity (Jablonski & Chaplin 2000). That continuous variables, height, pubertal age and brain development, are multifactorially inherited and affected by epigenetic factors, was nicely demonstrated in the increase in height in Norway 1860-1960 with at the same time a reduction in pubertal age by 4yrs which may have affected the final stage in brain development. This created an increased need for brain food, N-3, to secure optimal brain function. Body growth is not brain growth. Given that the consumption of brain food (N-3) has declined to 20% only of the level 100yrs ago, what disorders are to be expected with an N-3 dietary deficit: in pregnancy, infancy and later in life? In this paper I discuss the significance of prepubertal selective pruning of excitatory synapses compared to delayed pruning and suggest relationships with brain disorders.

Adaptation, Physiological↗

Initial characteristics of psychological development and evolution of the young autistic child.

This longitudinal study assessed multidisciplinary data on 219 children with autistic spectrum disorders from the median age of 5 (Time 1) to 8 years old (Time 2). The evolution of psychological and adaptive data was subjected to cluster analysis. Four clinically meaningful clusters emerged. The first group (21%) demonstrated the most important psychological transformations between the two times of the research. The second group (24%) made progress but less than group 1. The third and biggest group (30%) kept the same developmental slope. The fourth group (25%) showed no significant evolution between the two times of the research. This study highlights important differences among children with autism and the necessity of using a developmental view when considering the autistic syndrome.

Adaptation, Psychological↗

Human semilunar cardiac valve remodeling by activated cells from fetus to adult: implications for postnatal adaptation, pathology, and tissue engineering.

BACKGROUND: The evolution of cell phenotypes and matrix architecture in cardiac valves during fetal maturation and postnatal adaptation through senescence remains unexplored. METHODS AND RESULTS: We hypothesized that valvular interstitial (VIC) and endothelial cell (VEC) phenotypes, critical for maintaining valve function, change throughout life in response to environmental stimuli. We performed quantitative histological assessment of 91 human semilunar valves obtained from fetuses at 14 to 19 and 20 to 39 weeks' gestation; neonates minutes to 30 days old; children aged 2 to 16 years; and adults. A trilaminar architecture appeared by 36 weeks of gestation but remained rudimentary compared with that of adult valves. VECs expressed an activated phenotype throughout fetal development. VIC density, proliferation, and apoptosis were significantly higher in fetal than adult valves. Pulmonary and aortic fetal VICs showed an activated myofibroblast-like phenotype (alpha-actin expression), abundant embryonic myosin, and matrix metalloproteinase-collagenases, which indicates an immature/activated phenotype engaged in matrix remodeling versus a quiescent fibroblast-like phenotype in adults. At birth, the abrupt change from fetal to neonatal circulation was associated with a greater number of alpha-actin-positive VICs in neonatal aortic versus pulmonary valves. Collagen content increased from early to late fetal stages but was subsequently unchanged, whereas elastin significantly increased postnatally. Collagen fiber color analysis revealed a progressive temporal decrease in thin fibers and a corresponding increase in thick fibers. Additionally, collagen fibers were more aligned in adult than fetal valves. CONCLUSIONS: Fetal valves possess a dynamic/adaptive structure and contain cells with an activated/immature phenotype. During postnatal life, activated cells gradually become quiescent, whereas collagen matures, which suggests a progressive, environmentally mediated adaptation.

Adaptation, Physiological↗

Evolution and revolution in child psychiatry: ADHD as a disorder of adaptation.

Current knowledge about early plasticity and children's responsiveness to environmental modifications as well as the atheoretical nature of current nosological systems necessitate alternative models to explain the phenomena of childhood behavioral and emotional disturbances. Evolutionary biology provides one such framework. It organizes data from the behavioral and cognitive sciences and parallels similar efforts in other areas of medicine and biology. Through an evolutionary biological lens, some mental disorders are better viewed as an adaptive response to early pathogenic environments and/or reflect the optimization of brain function to some environments at the cost of poorer response to the demands of other environments. As an example, the authors examine attention-deficit/hyperactivity disorder (ADHD) in relation to evolutionary theories of psychology and biology and clarify the potentially adaptive nature of characteristics of inattention, impulsivity, and motoric hyperactivity, depending on the nature of child's environments. Reframing ADHD characteristics according to evolutionary theory has important treatment implications for clinicians and offers researchers opportunities for novel scientific discoveries.

Adaptation, Psychological↗

Theoretical analysis of mutation-adaptive evolutionary algorithms.

Adaptive evolutionary algorithms require a more sophisticated modeling than their static-parameter counterparts. Taking into account the current population is not enough when implementing parameter-adaptation rules based on success rates (evolution strategies) or on premature convergence (genetic algorithms). Instead of Markov chains, we use random systems with complete connections - accounting for a complete, rather than recent, history of the algorithm's evolution. Under the new paradigm, we analyze the convergence of several mutation-adaptive algorithms: a binary genetic algorithm, the 1/5 success rule evolution strategy, a continuous, respectively a dynamic (1+1) evolutionary algorithm.

Algorithms↗

Cooperation and conflict in the evolution of multicellularity.

Multicellular organisms probably originated as groups of cells formed in several ways, including cell proliferation from a group of founder cells and aggregation. Cooperation among cells benefits the group, but may be costly (altruistic) or beneficial (synergistic) to individual cooperating cells. In this paper, we study conflict mediation, the process by which genetic modifiers evolve that enhance cooperation by altering the parameters of development or rules of formation of cell groups. We are particularly interested in the conditions under which these modifiers lead to a new higher-level unit of selection with increased cooperation among group members and heritable variation in fitness at the group level. By sculpting the fitness variation and opportunity for selection at the two levels, conflict modifiers create new functions at the organism level. An organism is more than a group of cooperating cells related by common descent; organisms require adaptations that regulate conflict within. Otherwise their continued evolution is frustrated by the creation of within-organism variation and conflict between levels of selection. The evolution of conflict modifiers is a necessary prerequisite to the emergence of individuality and the continued well being of the organism. Conflict leads--through the evolution of adaptations that reduce i--to greater individuality and harmony for the organism.

Animals↗

Elucidating sequence codes: three codes for evolution.

The sequences are related to evolution in several ways. First, they carry traces of a distant past. Two sequence features point to the earliest sequence organization. The universal hidden GCU-periodical pattern in mRNA suggests the earliest codons: GCU and its nine-point-change derivatives. They code for seven amino acids that by several criteria are also the oldest. Together it makes the earliest form of the triplet code, still recognizable in the extant sequences. Another feature present in the sequences, apparently, since separation of prokaryotes and eukaryotes, is hidden genome segmentation. Both protein-coding and noncoding sequences appear to have been formed by fusion of standard size units, about 360 bp (120 aa) in eukaryotes and 450 bp (150 aa) in prokaryotes. Presumably, the units have been functioning at some stage of evolution as autonomous single-gene size elements. There are sequence designs that promote evolution. One such design suitable for fast adaptation is the tandem repetition of identical sequences, so that their copy numbers in the repeat arrays would modulate (tune) the expression of nearby genes. The tandem repeat expansion diseases illustrate this mechanism in a dramatic way: overtuning of the respective gene expression leads to the disease.

Adaptation, Biological↗

Optimum tracking with evolution strategies.

Evolutionary algorithms are frequently applied to dynamic optimization problems in which the objective varies with time. It is desirable to gain an improved understanding of the influence of different genetic operators and of the parameters of a strategy on its tracking performance. An approach that has proven useful in the past is to mathematically analyze the strategy's behavior in simple, idealized environments. The present paper investigates the performance of a multiparent evolution strategy that employs cumulative step length adaptation for an optimization task in which the target moves linearly with uniform speed. Scaling laws that quite accurately describe the behavior of the strategy and that greatly contribute to its understanding are derived. It is shown that in contrast to previously obtained results for a randomly moving target, cumulative step length adaptation fails to achieve optimal step lengths if the target moves in a linear fashion. Implications for the choice of population size parameters are discussed.

Adaptation, Biological↗

The process of coping following child sexual abuse:a qualitative study.

This research employed both quantitative and qualitative approaches to studying the immediate and long-term coping strategies adopted by survivors of child sexual abuse, focusing on how strategies evolve over time. Qualitative findings showed that coping with child sexual abuse is not static, but changes over time. The narratives of these nonclinical survivors suggest that an adaptive outcome may be associated with a particular evolution of strategies across time, i.e., survivors reported coping predominantly by engaging in psychological escape methods initially, and then adopting cognitive appraisal and positive reframing strategies in the longer term. It appears that coping processes can affect psychological outcome following child sexual abuse. This study offers insight into the evolution of coping methods associated with an adaptive outcome.

Adaptation, Psychological↗