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At least 631 records · Page 35Linked to original sources
PubMed1988

Stone agers in the fast lane: chronic degenerative diseases in evolutionary perspective.

From a genetic standpoint, humans living today are Stone Age hunter-gatherers displaced through time to a world that differs from that for which our genetic constitution was selected. Unlike evolutionary maladaptation, our current discordance has little effect on reproductive success; rather it acts as a potent promoter of chronic illnesses: atherosclerosis, essential hypertension, many cancers, diabetes mellitus, and obesity among others. These diseases are the results of interaction between genetically controlled biochemical processes and a myriad of biocultural influences--lifestyle factors--that include nutrition, exercise, and exposure to noxious substances. Although our genes have hardly changed, our culture has been transformed almost beyond recognition during the past 10,000 years, especially since the Industrial Revolution. There is increasing evidence that the resulting mismatch fosters "diseases of civilization" that together cause 75 percent of all deaths in Western nations, but that are rare among persons whose lifeways reflect those of our preagricultural ancestors.

Alcohol Drinking↗
PubMed2006

Evolutionary model selection with a genetic algorithm: a case study using stem RNA.

The choice of a probabilistic model to describe sequence evolution can and should be justified. Underfitting the data through the use of overly simplistic models may miss out on interesting phenomena and lead to incorrect inferences. Overfitting the data with models that are too complex may ascribe biological meaning to statistical artifacts and result in falsely significant findings. We describe a likelihood-based approach for evolutionary model selection. The procedure employs a genetic algorithm (GA) to quickly explore a combinatorially large set of all possible time-reversible Markov models with a fixed number of substitution rates. When applied to stem RNA data subject to well-understood evolutionary forces, the models found by the GA 1) capture the expected overall rate patterns a priori; 2) fit the data better than the best available models based on a priori assumptions, suggesting subtle substitution patterns not previously recognized; 3) cannot be rejected in favor of the general reversible model, implying that the evolution of stem RNA sequences can be explained well with only a few substitution rate parameters; and 4) perform well on simulated data, both in terms of goodness of fit and the ability to estimate evolutionary rates. We also investigate the utility of several distance measures for comparing and contrasting inferred evolutionary models. Using widely available small computer clusters, our approach allows, for the first time, to evaluate the performance of existing RNA evolutionary models by comparing them with a large pool of candidate models and to validate common modeling assumptions. In addition, the new method provides the foundation for rigorous selection and comparison of substitution models for other types of sequence data.

Algorithms↗
PubMed2005

Evolutionary consequences of gender plasticity in genetically dimorphic breeding systems.

A functional view of gender helps evolutionary biologists evaluate the mechanisms underlying breeding-system evolution. Evolutionary pathways from hermaphroditism to dioecy include the intermediate breeding systems of gynodioecy and androdioecy. These pathways start with the invasion of unisexual mutants, females or males, respectively, followed by alteration of the hermaphrodites to allocate more to the sexual function that the unisexuals lack. Eventually, hermaphrodites become unisexual and dioecy has evolved. Some species evolving along these pathways stop short of completing this second step, or even revert back from dioecy. We evaluate the hypothesis that gender plasticity is involved in these transitions to and from dioecy. Evidence from studies of subdioecious species that have evolved along the gynodioecy pathway suggests that gender plasticity occurs and stabilizes subdioecy by lowering the cost of producing seed. Factors influencing species evolving toward androdioecy, or reverting to androdioecy from dioecy, appear to be more varied and include reproductive assurance, herbivory and gender plasticity. In general, gender specialization appears to be favored in resource-poor environments regardless of which pathway is taken to dioecy.

Biological Evolution↗
PubMed2006

Evolutionary toxicology: population-level effects of chronic contaminant exposure on the marsh frogs (Rana ridibunda) of Azerbaijan.

We used molecular methods and population genetic analyses to study the effects of chronic contaminant exposure in marsh frogs from Sumgayit, Azerbaijan. Marsh frogs inhabiting wetlands in Sumgayit are exposed to complex mixtures of chemical contaminants, including petroleum products, pesticides, heavy metals, and many other industrial chemicals. Previous results documented elevated estimates of genetic damage in marsh frogs from the two most heavily contaminated sites. Based on mitochondrial DNA (mtDNA) control region sequence data, the Sumgayit region has reduced levels of genetic diversity, likely due to environmental degradation. The Sumgayit region also acts as an ecological sink, with levels of gene flow into the region exceeding gene flow out of the region. Additionally, localized mtDNA heteroplasmy and diversity patterns suggest that one of the most severely contaminated sites in Sumgayit is acting as a source of new mutations resulting from an increased mutation rate. This study provides an integrated method for assessing the cumulative population impacts of chronic contaminant exposure by studying both population genetic and evolutionary effects.

Animals↗
PubMed2004

Can fat explain the human brain's big bang evolution?-Horrobin's leads for comparative and functional genomics.

When David Horrobin suggested that phospholipid and fatty acid metabolism played a major role in human evolution, his 'fat utilization hypothesis' unified intriguing work from paleoanthropology, evolutionary biology, genetic and nervous system research in a novel and coherent lipid-related context. Interestingly, unlike most other evolutionary concepts, the hypothesis allows specific predictions which can be empirically tested in the near future. This paper summarizes some of Horrobin's intriguing propositions and suggests as to how approaches of comparative genomics published in Cell, Nature, Science and elsewhere since 1997 may be used to examine his evolutionary hypothesis. Indeed, systematic investigations of the genomic clock in the species' mitochondrial DNA, the Y and autosomal chromosomes as evidence of evolutionary relationships and distinctions can help to scrutinize associated predictions for their validity, namely that key mutations which differentiate us from Neanderthals and from great apes are in the genes coding for proteins which regulate fat metabolism, and particularly the phospholipid metabolism of the synapses of the brain. It is concluded that beyond clues to humans' relationships with living primates and to the Neanderthals' cognitive performance and their disappearance, the suggested molecular clock analyses may provide crucial insights into the biochemical evolution-and means of possible manipulation-of our brain.

Animals↗
PubMed2005

Simple evolutionary pathways to complex proteins.

A recent paper in this journal has challenged the idea that complex adaptive features of proteins can be explained by known molecular, genetic, and evolutionary mechanisms. It is shown here that the conclusions of this prior work are an artifact of unwarranted biological assumptions, inappropriate mathematical modeling, and faulty logic. Numerous simple pathways exist by which adaptive multi-residue functions can evolve on time scales of a million years (or much less) in populations of only moderate size. Thus, the classical evolutionary trajectory of descent with modification is adequate to explain the diversification of protein functions.

Evolution, Molecular↗
PubMed2003

[Extreme divergence of a homeotic gene: the bicoid case].

Evolutionary developmental genetics (evo-devo) reveals that the plasticity of development is so important that every developmental biology project should carefully take this point into consideration. The example of bicoid, the first discovered morphogen, illustrates how an essential gene can change its function during evolution. The search for bicoid homologues showed that this gene is surprisingly specific to flies (cyclorraphan diptera) and absent in other insects. In fact, recent studies demonstrate that bicoid is a very derived Hox3 homeotic gene. During insect evolution, the ancestral Hox3 gene lost its homeotic function and acquired new roles in oocytes and embryonic annexes. Then, in the lineage leading to modern flies, a duplication of this new gene, followed by functional divergence, led to the formation of bicoid and zerknüllt. Both genes are located within the Drosophila Hox complex; however, they have no homeotic function. Thanks to the power of Drosophila genetics, it is possible to suggest that torso and hunchback may constitute the insect primitive anterior organizer. The bicoid evolutionary history reveals several fundamental mechanisms of the evolution of developmental genes, such as changes of gene regulation, modifications of protein sequences and gene duplication. It also shows the need for studying a wider range of model organisms before generalisations can be made from data obtained with one particular species.

Animals↗
PubMed1997

Temporal pattern formation by heterochronic genes.

Heterochrony describes the phylogenetic variation in the relative timing of major developmental events. Such heterochronic variation has been noted across phylogeny, including closely related species, suggesting that particular genetic loci control global aspects of developmental timing, and that variation at those loci may play important roles in evolutionary change. Genetic analyses of heterochronic mutations in the nematode Caenorhabditis elegans reveal that control of temporal patterning is analogous to the dedicated genetic pathways that control the patterning of the spatial axes in Drosophila and other metazoans. These pathways generate graded or binary levels of regulatory factors that pattern particular axes of the developing animal. C. elegans heterochronic genes constitute a regulatory cascade that both generates a temporal decrease in the level of the LIN-14 and LIN-28 proteins and responds to the changes in these gene activities to coordinate the temporal sequence of many cell fates as the animal develops. The temporal regulation of lin-14 and lin-28 gene activities is posttranscriptional and mediated by the antisense RNA product of the lin-4 gene. Hormonal control of developmental timing is a common theme throughout phylogeny. Heterochronic genes that involve hormonal signaling have been identified in vertebrates as well as C. elegans.

Animals↗
PubMed1983

Isozyme assessment of plant genetic resources.

The genetic resources of cultivated plants consist of the genetic diversity present among developed cultivars, in the land races or primitive stocks, and in wild populations of their evolutionary relatives. Genetic evaluation of these resources through isozyme studies provides an important aid in efficient collection, storage, and use. Recent isozyme studies with barley exemplify these points. The allelic isozyme diversity present in 12 land race samples from Iran has been compared with that found in cultivars on the one hand, and natural populations of wild barley (H spontaneum) on the other. The primitive materials were on average more variable than the cultivars but less variable than the wild populations, supporting the view that the land races are or crucial importance in genetic conservation. Some roles for isozyme data in the manipulation of genetic resources have been outlined.

Agriculture↗
PubMed1975

Structure and regulation of immunoglobulins: kappa allotypes in the rat have multiple amino-acid differences in the constant region.

Immunoglobulin kappa chains from various inbred strains of rats have two serologically detectable forms that segregate in a Mendelian fashion (allotypes a and b of the RI-I locus). Partial amino-acid sequences from the constant regions of these two forms have been compared. Of the 81 residues of the constant region studied, 10 amino-acid substitutions as well as one size difference (sequence gap) were found. This large number of sequence differences among alternative forms of the kappa allotype raises provocative questions as to the genetic and evolutionary implications of these light chain allotypes. We designate allotypes whose alternative forms differ at multiple residue positions as complex allotypes. There are basically two genetic models that might explain complex allotypes. First, these allotypes are alleles of a single structural gene with an unusual evolutionary history. Second, all rats have genes that code for each of the light chain allotypes and a control mechanism that permits them to be expressed so that they mimic a Mendelian pattern of segregation. We discuss evidence from other immunoglobulin systems that is compatible with this second model.

Alleles↗
PubMed1997

Genetic instability and its possible evolutionary implications on the chromosomal structure of Streptomyces.

Recent progress in the understanding of the chromosomal rearrangements in Streptomyces has allowed us to envisage the possible involvement of genetic instability in the evolution of the chromosomal structure. The characterization of recombinational events in the terminal parts of the S ambofaciens chromosome, as well as the observation by other groups that linear plasmids and chromosomes are able to interact, would provide an explanation for the very high levels of polymorphism seen in the terminal inverted repeats of different strains of Streptomyces.

Chromosomes, Bacterial↗
PubMed2004

Patterns of within population dispersal and mating of the fungus Microbotryum violaceum parasitising the plant Silene latifolia.

This study explores the patterns of dispersal and mating of the anther smut Microbotryum violaceum, a model species in genetics and evolutionary biology. A French metapopulation of the fungus collected from its caryophyllaceous host Silene latifolia was analysed using microsatellites. The genetic diversity was low, populations were strongly differentiated, and there was no pattern of isolation by distance among populations. There was a strong deficit in heterozygotes, confirming the high self-fertilisation rates suggested by previous studies. Within populations there was a strong pattern of isolation by distance, with identical genotypes being highly clustered. This indicates that fungal spores are dispersed mostly between adjacent plants, and such local dispersal is important for understanding the dynamics and evolution of this disease. Local clusters of identical heterozygous genotypes did not contain significantly fewer individuals than did clusters of homozygous genotypes. As selfing between products of independent meiotic events (intertetrad selfing) rapidly reduces heterozygosity, this suggests that intratetrad matings are frequent, which helps to explain the puzzling maintenance of a sex-ratio distortion in M. violaceum.

Founder Effect↗
PubMed2000

A short history of MADS-box genes in plants.

Evolutionary developmental genetics (evodevotics) is a novel scientific endeavor which assumes that changes in developmental control genes are a major aspect of evolutionary changes in morphology. Understanding the phylogeny of developmental control genes may thus help us to understand the evolution of plant and animal form. The principles of evodevotics are exemplified by outlining the role of MADS-box genes in the evolution of plant reproductive structures. In extant eudicotyledonous flowering plants, MADS-box genes act as homeotic selector genes determining floral organ identity and as floral meristem identity genes. By reviewing current knowledge about MADS-box genes in ferns, gymnosperms and different types of angiosperms, we demonstrate that the phylogeny of MADS-box genes was strongly correlated with the origin and evolution of plant reproductive structures such as ovules and flowers. It seems likely, therefore, that changes in MADS-box gene structure, expression and function have been a major cause for innovations in reproductive development during land plant evolution, such as seed, flower and fruit formation.

Animals↗
PubMed2002

Discerning evolutionary processes in patterns of tamarin (genus Saguinus) craniofacial variation.

Quantitative genetic theory specifies evolutionary expectations for morphological diversification by genetic drift in a monophyletic clade. If genetic drift is responsible for the evolutionary morphological diversification of a clade, patterns of within- and between-taxon morphological variance/covariance should be proportional. We tested for proportionality of within- and between-species craniofacial morphological variation in 12 species of tamarins (genus Saguinus). We found that within- and between-taxon morphological variations across the entire genus were not proportional, and hence not likely to be due to genetic drift alone. The primary deviation from proportionality is that size and size-related shape in the cranium is more variable relative to other aspects of cranial morphology than expected under genetic drift, suggesting differential size selection between the two major clades, the small-bodied and large-bodied tamarins. Within each of these major clades, most of the interspecific variation is consistent with the pattern expected under genetic drift, although specific contrasts may indicate the involvement of differential selection. Morphological distances among taxa do not correspond very closely to the phylogeny derived from mtDNA. In particular, S. oedipus and S. geoffroyi are very distinct morphologically from the rest of the tamarins, although they are phylogenetically the sister clade to a clade containing S. midas and S. bicolor. Morphological similarity is not a good guide to phylogenetic affinity in the tamarins, especially with regard to deeper nodes in the phylogenetic tree.

Animals↗
PubMed2003

The constancy of the G matrix through species divergence and the effects of quantitative genetic constraints on phenotypic evolution: a case study in crickets.

Long-term phenotypic evolution can be modeled using the response-to-selection equation of quantitative genetics, which incorporates information about genetic constraints (the G matrix). However, little is known about the evolution of G and about its long-term importance in constraining phenotypic evolution. We first investigated the degree of conservation of the G matrix across three species of crickets and qualitatively compared the pattern of variation of G to the phylogeny of the group. Second, we investigated the effect of G on phenotypic evolution by comparing the direction of greatest quantitative genetic variation within species (g(max)) to the direction of phenotypic divergence between species (Delta(z)). Each species, Gryllus veletis, G. firmus, and G. pennsylvanicus, was reared in the laboratory using a full-sib breeding design to extract quantitative genetic information. Five morphological traits related to size were measured. G matrices were compared using three statistical approaches: the T method, the Flury hierarchy, and the MANOVA method. Results revealed that the differences between matrices were small and mostly caused by differences in the magnitude of the genetic variation, not by differences in principal component structure. This suggested that the G matrix structure of this group of species was preserved, despite significant phenotypic divergence across species. The small observed differences in G matrices across species were qualitatively consistent with genetic distances, whereas ecological information did not provide a good prediction of G matrix variation. The comparison of g(max) and Delta(z) revealed that the angle between these two vectors was small in two of three species comparisons, whereas the larger angle corresponding to the third species comparison was caused in large part by one of the five traits. This suggests that multivariate phenotypic divergence occurred mostly in a direction predicted by the direction of greatest genetic variation, although it was not possible to demonstrate the causal relationship from G to Delta(z). Overall, this study provided some support for the validity of the predictive power of quantitative genetics over evolutionary time scales.

Analysis of Variance↗
PubMed2002

Evolutionary and statistical properties of three genetic distances.

Many genetic distances have been developed to summarize allele frequency differences between populations. I review the evolutionary and statistical properties of three popular genetic distances: DS, DA, and theta;, using computer simulation of two simple evolutionary histories: an isolation model of population divergence and an equilibrium migration model. The effect of effective population size, mutation rate, and mutation mechanism upon the parametric value between pairs of populations in these models explored, and the unique properties of each distance are described. The effect of these evolutionary parameters on study design is also investigated and similar results are found for each genetic distance in each model of evolution: large sample sizes are warranted when populations are relatively genetically similar; and loci with more alleles produce better estimates of genetic distance.

Computer Simulation↗
PubMed1994

Evolutionary algorithms and a fractal inverse problem.

Over the past 30 years, algorithms that model natural evolution have generated robust search methods. These so-called evolutionary algorithms have been successfully applied to a wide range of problems. This paper discusses two types of evolutionary algorithms and their application to a problem in shape representation. Genetic algorithms and evolutionary programming, although both based on evolutionary principles, each place different emphasis on what drives the evolutionary process. While genetic algorithms rely on mimicking specific genotypic transformations, evolutionary programming emphasizes phenotypic adaptation. Results presented show the success of evolutionary programming in solving an example of a fractal inverse problem, but indicate that a genetic algorithm is not as successful. Reasons for this disparity are discussed.

Algorithms↗