Darwinism; an exposition of the theory of natural selection, with some of its applications,

Mode of access: Internet.

Darwinism: an exposition of the theory of natural selection, with some of its applications.

Mode of access: Internet.

Darwinism; an exposition of the theory of natural selection, with some of its applications.

Mode of access: Internet.

Detecting the signature of natural selection with microsatellites

Natural selection is one of the major factors in the evolution of all organisms. Detecting the signature of natural selection has been a central theme in evolutionary genetics. With the availability of microsatellite data, it is of interest to study how natural selection can be detected with microsatellites. ^ The overall aim of this research is to detect signatures of natural selection with data on genetic variation at microsatellite loci. The null hypothesis to be tested is the neutral mutation theory of molecular evolution, which states that different alleles at a locus have equivalent effects on fitness. Currently used tests of this hypothesis based on data on genetic polymorphism in natural populations presume that mutations at the loci follow the infinite allele/site models (IAM, ISM), in the sense that at each site at most only one mutation event is recorded, and each mutation leads to an allele not seen before in the population. Microsatellite loci, which are abundant in the genome, do not obey these mutation models, since the new alleles at such loci can be created either by contraction or expansion of tandem repeat sizes of core motifs. Since the current genome map is mainly composed of microsatellite loci and this class of loci is still most commonly studied in the context of human genome diversity, this research explores how the current test procedures for testing the neutral mutation hypothesis should be modified to take into account a generalized model of forward-backward stepwise mutations. In addition, recent literature also suggested that past demographic history of populations, presence of population substructure, and varying rates of mutations across loci all have confounding effects for detecting signatures of natural selection. ^ The effects of the stepwise mutation model and other confounding factors on detecting signature of natural selection are the main results of the research. ^

Approximate theory of natural-convection with small grashof number

To gain some insight into the behaviour of low-gravity flows in the material processing in space, an approximate theory has been developed for the convective motion of fluids with a small Grashof number Gr. The expansion of the variables into a series of Gr reduces the Boussinesq equation to a system of weakly coupled linearly inhomogeneous equations. Moreover, the analogy concept is proposed and utilized in the study of the plate bending problems in solid mechanics. Two examples are investigated in detail, i. e. the 2-dimensional steady flows in either circular or square infinite closed cylinder, which is horizontally imposed at a specified temperature of linear distribution on the boundaries. The results for stream function ψ, velocity u and temperature T are provided. The analysis of the influences of some parameters such as the Grashof number Gr and the Prandtl number Pr, on motions will lead to several interesting conclusions. The theory seems to be useful for seeking for an analytical solutions. At least, it will greatly simplify the complicated problems originally governed by the Navier-Stokes equation including buoyancy. It is our hope that the theory might be applicable to unsteady or 3-dimensional cases in future.

The spatial pattern of natural selection when selection depends upon experience

Apostatic (frequency‐ or density‐dependent) selection, aposematic signals, and mate choice behavior generally require that the mean prey or potential mate density m value be high enough (above a threshold T) to result in sufficient encounter rates for the searcher to learn or retain the association between conspicuous signals and prey unprofitability, to forage apostatically, or to choose among mates. This assumes that all searchers experience , which implicitly assumes an even dispersion of targets among searcher territories. Uneven dispersion generates new phenomena. If , then only territories with local density x values that are greater than T favor experience‐based behavior, leading to spatially variable frequency‐ or density‐dependent selection intensity. As aggregation increases, the increase in percentage of targets in favorable territories ( ) is greater than the increase in the percentage of territories that are favorable. The relationship is reversed when . In both cases, because as few as 10% of the territories can contain 80% of the targets, only a few territory holders may account for most of the selection on most of the target population; accidents of experience in only a few searchers can have unexpectedly large effects on the target population. This also provides an explanation for high searcher behavior variation (personalities) : individuals from favorable territories will behave differently in behavioral experiments than those from unfavorable territories, at least with respect to similar kinds of targets. These effects will generate spatial heterogeneity in natural and sexual selection in what are otherwise uniform environments.

Genetic diversity of the HLA-G coding region in Amerindian populations from the Brazilian Amazon: a possible role of natural selection

HLA-G has an important role in the modulation of the maternal immune system during pregnancy, and evidence that balancing selection acts in the promoter and 3′UTR regions has been previously reported. To determine whether selection acts on the HLA-G coding region in the Amazon Rainforest, exons 2, 3 and 4 were analyzed in a sample of 142 Amerindians from nine villages of five isolated tribes that inhabit the Central Amazon. Six previously described single-nucleotide polymorphisms (SNPs) were identified and the Expectation-Maximization (EM) and PHASE algorithms were used to computationally reconstruct SNP haplotypes (HLA-G alleles). A new HLA-G allele, which originated in Amerindian populations by a crossing-over event between two widespread HLA-G alleles, was identified in 18 individuals. Neutrality tests evidenced that natural selection has a complex part in the HLA-G coding region. Although balancing selection is the type of selection that shapes variability at a local level (Native American populations), we have also shown that purifying selection may occur on a worldwide scale. Moreover, the balancing selection does not seem to act on the coding region as strongly as it acts on the flanking regulatory regions, and such coding signature may actually reflect a hitchhiking effect.Genes and Immunity advance online publication, 3 October 2013; doi:10.1038/gene.2013.47.

Balancing immunity and tolerance: genetic footprint of natural selection in the transcriptional regulatory region of HLA-G

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Network-based analysis of genome-wide scans of natural selection

The genomic era brought by recent advances in the next-generation sequencing technology makes the genome-wide scans of natural selection a reality. Currently, almost all the statistical tests and analytical methods for identifying genes under selection was performed on the individual gene basis. Although these methods have the power of identifying gene subject to strong selection, they have limited power in discovering genes targeted by moderate or weak selection forces, which are crucial for understanding the molecular mechanisms of complex phenotypes and diseases. Recent availability and rapid completeness of many gene network and protein-protein interaction databases accompanying the genomic era open the avenues of exploring the possibility of enhancing the power of discovering genes under natural selection. The aim of the thesis is to explore and develop normal mixture model based methods for leveraging gene network information to enhance the power of natural selection target gene discovery. The results show that the developed statistical method, which combines the posterior log odds of the standard normal mixture model and the Guilt-By-Association score of the gene network in a naïve Bayes framework, has the power to discover moderate/weak selection gene which bridges the genes under strong selection and it helps our understanding the biology under complex diseases and related natural selection phenotypes.^

DNA variation at the Sod locus of Drosophila melanogaster: An unfolding story of natural selection

Patterns of variation at the Sod locus of Drosophila melanogaster suggest that the protein polymorphism at this locus has very recently arisen. In addition, it appears that a previously rare DNA variant has been recently and rapidly driven to intermediate frequency. From the size of the region (>20 kb) that has been swept along with this rare variant, and patterns of linkage disequilibrium in the region, it is inferred that strength of selection was large (s > 0.01) and that the sweep occurred more than 25,000 generations ago. In addition, there are striking similarities to patterns of variation observed at the Est6 and Est-P loci, which are located approximately 1,000 kb from Sod.

On the origin of species by means of natural selection; or The preservation of favored races in the struggle for life.

"First edition 1859; 6th ed. 1872."

Where Darwin erred, or the fallacy of natural selection.

Mode of access: Internet.

A Theory of Natural Addiction

Economic theories of rational addiction aim to describe consumer behavior in the presence of habit-forming goods. We provide a biological foundation for this body of work by formally specifying conditions under which it is optimal to form a habit. We demonstrate the empirical validity of our thesis with an in-depth review and synthesis of the biomedical literature concerning the action of opiates in the mammalian brain and their eects on behavior. Our results lend credence to many of the unconventional behavioral assumptions employed by theories of rational addiction, including adjacent complementarity and the importance of cues, attention, and self-control in determining the behavior of addicts. We oer evidence for the special case of the opiates that "harmful" addiction is the manifestation of a mismatch between behavioral algorithms encoded in the human genome and the expanded menu of choices faced by consumers in the modern world.

Analysis of Sequence Periodicity in E. coli Proteins: Empirical Investigation of the ?Duplication and Divergence? Theory of Protein Evolution

Gatherer, D., and McEwan, N.R. (2003). Analysis of sequence periodicity in E. coli proteins: empirical investigation of the 'duplication and divergence' theory of protein evolution. Journal of Molecular Evolution 57, 149-158. RAE2008

The roles of natural and sexual selection during adaptation to a novel environment

The net effect of sexual selection on nonsexual fitness is controversial. On one side, elaborate display traits and preferences for them can be costly, reducing the nonsexual fitness of individuals possessing them, as well as their offspring, In contrast, sexual selection may reinforce nonsexual fitness if an individual's attractiveness and quality are genetically correlated. According to recent models, such good-genes mate choice should increase both the extent and rate of adaptation. We evolved 12 replicate populations of Drosophila serrata in a powerful two-way factorial experimental design to test the separate and combined contributions of natural and sexual selection to adaptation to a novel larval food resource. Populations evolving in the presence of natural selection had significantly higher mean nonsexual fitness when measured over three generations (13-15) during the course of experimental evolution (16-23% increase). The effect of natural selection was even more substantial when measured in a standardized, monogamous mating environment at the end of the experiment (generation 16; 52% increase). In contrast, and despite strong sexual selection on display traits, there was no evidence from any of the four replicate fitness measures that sexual selection promoted adaptation. In addition, a comparison of fitness measures conducted under different mating environments demonstrated a significant direct cost of sexual selection to females, likely arising from some form of male-induced harm. Indirect benefits of sexual selection in promoting adaptation to this novel resource environment therefore appear to be absent in this species, despite prior evidence suggesting the operation of good-genes mate choice in their ancestral environment. How novel environments affect the operation of good-genes mate choice is a fundamental question for future sexual selection research.