TY - JOUR. T1 - Contrasting modes of natural selection acting on pigmentation genes in the Drosophila dunni subgroup. AU - Wilder, J. A.. AU - Dyreson, E. G.. AU - ONeill, R. J.. AU - Spangler, M. L.. AU - Gupta, R.. AU - Wilder, A. S.. AU - Hollocher, H.. PY - 2004/9/15. Y1 - 2004/9/15. N2 - Genes that encode for divergent adaptive traits may have genealogies that contrast with those from loci that are not functionally involved in differentiation. Here, we examine DNA sequence variation among the species of the eastern Caribbean Drosophila dunni subgroup at two loci, yellow and dopa decaboxylase (Ddc), which both play integral roles in pigmentation patterning of adult Drosophila. Phylogenetic analyses of these loci produce gene genealogies with topologies that mirror those described for other nuclear genes: the six morphologically distinct species within the subgroup are divided into only three lineages, with one lineage containing four species that share extensive ancestral polymorphism. At ...
Because of their role in mediating life‐history trade‐offs, hormones are expected to be strongly associated with components of fitness; however, few studies have examined how natural selection acts on hormonal variation in the wild. In a songbird, the dark‐eyed junco (Junco hyemalis), field experiments have shown that exogenous testosterone alters individuals resolution of the survival‐reproduction trade‐off, enhancing reproduction at the expense of survival. Here we used standardized injections of gonadotropin‐releasing hormone (GnRH) to assay variation in the testosterone production of males. Using measurements of annual survival and reproduction, we found evidence of strong natural selection acting on GnRH‐induced increases in testosterone. Opposite to what would be predicted from the survival‐reproduction trade‐off, patterns of selection via survival and reproduction were remarkably similar. Males with GnRH‐induced testosterone production levels that were slightly above ...
1. Variation in the strength of age-dependent natural selection shapes differences in ageing rates across species and populations. Likewise, sexual selection can promote divergent patterns of senescence across the sexes. However, the effects of these processes on the evolution of ageing have largely been considered independently, and interactions between them are poorly understood. 2. We use experimental evolution to investigate how natural and sexual selection affect life span and ageing in Drosophila simulans. 3. Replicate populations were evolved under lifetime monogamy (relaxed sexual selection) or lifetime polyandry (elevated sexual selection) and at one of two temperatures, 25 °C (relaxed natural selection) or 27 °C (enhanced natural selection), in a fully factorial design. We measured longevity in 150 individually housed flies taken from each of three replicate populations per selection regime. 4. We found that natural and sexual selection affected the evolution of life span via ...
Symbiotic associations with microorganisms are ubiquitously found in a variety of insects, which are rated among the important factors underpinning their adaptation, diversity, and prosperity (1⇓-3). Many bacterial symbionts are indispensable for growth, survival, and reproduction of their insect hosts via, for example, provisioning of essential nutrients like amino acids and vitamins, where the host and the symbiont are integrated into an almost inseparable biological entity (4, 5). In such obligate symbiotic associations, the symbiont genomes tend to exhibit conspicuous structural degeneration, massive gene losses, and drastic size reduction, which are attributable to relaxed natural selection acting on many symbiont genes no longer necessary for the permanent intrahost lifestyle, and also to accumulation of deleterious mutations driven by attenuated natural selection acting on the symbiont genomes due to strong population bottlenecks and restricted horizontal gene acquisitions associated ...
TY - JOUR. T1 - Population differentiation as an indicator of recent positive selection in humans. T2 - An empirical evaluation. AU - Xue, Yali. AU - Zhang, Xuelong. AU - Huang, Ni. AU - Daly, Allan. AU - Gillson, Christopher J.. AU - MacArthur, Daniel G.. AU - Yngvadottir, Bryndis. AU - Nica, Alexandra C.. AU - Woodwark, Cara. AU - Chen, Yuan. AU - Conrad, Donald F.. AU - Ayub, Qasim. AU - Mehdi, S. Qasim. AU - Li, Pu. AU - Tyler-Smith, Chris. PY - 2009/11. Y1 - 2009/11. N2 - We have evaluated the extent to which SNPs identified by genomewide surveys as showing unusually high levels of population differentiation in humans have experienced recent positive selection, starting from a set of 32 nonsynonymous SNPs in 27 genes highlighted by the HapMap1 project. These SNPs were genotyped again in the HapMap samples and in the Human Genome Diversity Project-Centre dEtude du Polymorphisme Humain (HGDP-CEPH) panel of 52 populations representing worldwide diversity; extended haplotype homozygosity was ...
Weak selection in evolutionary biology is when individuals with different phenotypes possess similar fitness, i.e. one phenotype is weakly preferred over the other. Weak selection, therefore, is an evolutionary theory to explain the maintenance of multiple phenotypes in a stable population [1]. Weak selection can only be used to explain the maintenance of mutations in a Moran process [1]. A Moran process in one which birth and death are paired events, and therefore population size remains constant. If the population size was increasing, both wild type and mutant phenotypes can proliferate and the weak selection for one phenotype results in no particular selection for either. Hence weak selection requires a finite population to operate. Otherwise there would be no expectation of fixation and hence no selection. The result of weak selection is two phenotypes with similar fixation probabilities. Weak selection works to elongate fixation time for two competing alleles. Consequently, weak selection ...
Friends of the High Line raises nearly 100% of the High Lines annual budget.. Owned by the City of New York, the High Line is a public park programmed, maintained, and operated by Friends of the High Line, in partnership with the New York City Department of Parks & Recreation.. ...
The distribution of variation in a quantitative trait and its underlying distribution of genotypic diversity can both be shaped by stabilizing and directional selection. Understanding either distribution is important, because it determines a populations response to natural selection. Unfortunately, existing theory makes conflicting predictions about how selection shapes these distributions, and very little pertinent experimental evidence exists. Here we study a simple genetic system, an evolving RNA enzyme (ribozyme) in which a combination of high throughput genotyping and measurement of a biochemical phenotype allow us to address this question. We show that directional selection, compared to stabilizing selection, increases the genotypic diversity of an evolving ribozyme population. In contrast, it leaves the variance in the phenotypic trait unchanged. ...
TY - JOUR. T1 - Methods of increasing short term response to full-sib family recurrent selection in small populations. AU - Mackay, I. J.. AU - Caligari, P. D.S.. PY - 2000. Y1 - 2000. N2 - Accelerated recurrent selection (ARS), in which selection is carried out on the predicted value of the progeny rather than on the observed performance of the parents, has been proposed as a method of increasing response to selection and of reducing cycle time. ARS schemes based on test cross evaluation of full-sib families have been compared by stochastic computer simulation. The difference in genetic and economic time scales is emphasised, with the economic long term (21 years) being only 21 or fewer cycles of selection. ARS schemes are shown frequently to offer improvements over standard recurrent selection methods under these circumstances, since they allow more cycles of selection in a given time frame. Schemes with very low effective population sizes often give the greatest response to selection over the ...
rdf:RDF xmlns:dcterms=http://purl.org/dc/terms/ xmlns:dc=http://purl.org/dc/elements/1.1/ xmlns:rdf=http://www.w3.org/1999/02/22-rdf-syntax-ns# xmlns:bibo=http://purl.org/ontology/bibo/ xmlns:dspace=http://digital-repositories.org/ontologies/dspace/0.1.0# xmlns:foaf=http://xmlns.com/foaf/0.1/ xmlns:void=http://rdfs.org/ns/void# xmlns:xsd=http://www.w3.org/2001/XMLSchema# , ,rdf:Description rdf:about=https://kops.uni-konstanz.de/rdf/resource/123456789/19450, ,dc:contributor,Elmer, Kathryn R.,/dc:contributor, ,dcterms:title,Positive Darwinian selection drives the evolution of the morphology-related gene, EPCAM, in particularly species-rich lineages of African cichlid fishes,/dcterms:title, ,bibo:uri rdf:resource=http://kops.uni-konstanz.de/handle/123456789/19450/, ,dcterms:hasPart rdf:resource=https://kops.uni-konstanz.de/bitstream/123456789/19450/2/Fan_194507.pdf/, ,dc:rights,terms-of-use,/dc:rights, ,dc:contributor,Fan, Shaohua,/dc:contributor, ,dcterms:isPartOf ...
TY - JOUR. T1 - The origin of mutants under selection. T2 - How natural selection mimics mutagenesis (adaptive mutation). AU - Maisnier-Patin, Sophie. AU - Roth, John R.. PY - 2015/7/1. Y1 - 2015/7/1. N2 - Selection detects mutants but does not cause mutations. Contrary to this dictum, Cairns and Foster plated a leaky lac mutant of Escherichia coli on lactose medium and saw revertant (Lac+) colonies accumulate with time above a nongrowing lawn. This result suggested that bacteria might mutagenize their own genome when growth is blocked. However, this conclusion is suspect in the light of recent evidence that revertant colonies are initiated by preexisting cells with multiple copies the conjugative F′lac plasmid, which carries the lac mutation. Some plated cells have multiple copies of the simple F′lac plasmid. This provides sufficient LacZ activity to support plasmid replication but not cell division. In nongrowing cells, repeated plasmid replication increases the likelihood of a reversion ...
TY - JOUR. T1 - The Origin of Mutants Under Selection. T2 - How Natural Selection Mimics Mutagenesis (Adaptive Mutation). AU - Maisnier-Patin, Sophie. AU - Roth, John R.. PY - 2015/7/1. Y1 - 2015/7/1. N2 - Selection detects mutants but does not cause mutations. Contrary to this dictum, Cairns and Foster plated a leaky lac mutant of Escherichia coli on lactose medium and saw revertant (Lac(+)) colonies accumulate with time above a nongrowing lawn. This result suggested that bacteria might mutagenize their own genome when growth is blocked. However, this conclusion is suspect in the light of recent evidence that revertant colonies are initiated by preexisting cells with multiple copies the conjugative Flac plasmid, which carries the lac mutation. Some plated cells have multiple copies of the simple Flac plasmid. This provides sufficient LacZ activity to support plasmid replication but not cell division. In nongrowing cells, repeated plasmid replication increases the likelihood of a reversion ...
We discussed a few possibilities that would fit nicely with my planned thesis and settled on an idea which Rowan had had in mind for a few years: a meta-analysis of genetic selection coefficients in natural populations. Biologists have been measuring phenotypic selection gradients and differentials since the 1980s, when Lande and Arnold developed the multiple regression methods used to quantify phenotypic selection. Influential meta-analyses of these data (e.g., Kingsolver et al. 2001, Rieseberg et al. 2002, Hereford et al. 2004, Siepielski et al. 2001 and 2013, and others) have told us a lot about how natural selection operates at the phenotypic level. At the genotypic level, however, fundamental questions remain: how strong is natural selection on allelic variation? How does selection vary through time and space? How are selection coefficients distributed? That these questions remain largely unanswered is partially due to technological limitations: biologists couldnt directly measure ...
Over the past 50,000 years, shifts in human-environmental or human-human interactions shaped genetic differences within and among human populations, including variants under positive selection. Shaped by environmental factors, such variants influence the genetics of modern health, disease, and treatment outcome. Because evolutionary processes tend to act on gene regulation, we test whether regulatory variants are under positive selection. We introduce a new approach to enhance detection of genetic markers undergoing positive selection, using conditional entropy to capture recent local selection signals. Results We use conditional logistic regression to compare our Adjusted Haplotype Conditional Entropy (H|H) measure of positive selection to existing positive selection measures. H|H and existing measures were applied to published regulatory variants acting in cis (cis-eQTLs), with conditional logistic regression testing whether regulatory variants undergo stronger positive selection than the surrounding
Antagonistic selection-where alleles at a locus have opposing effects on male and female fitness (sexual antagonism), or between components of fitness (antagonistic pleiotropy)-might play an important role in maintaining population genetic variation, and in driving phylogenetic and genomic patterns of sexual dimorphism and life-history evolution. While prior theory has thoroughly characterized the conditions necessary for antagonistic balancing selection to operate, we currently know little about the evolutionary interactions between antagonistic selection, recurrent mutation, and genetic drift, which should collectively shape empirical patterns of genetic variation. To fill this void, we developed and analyzed a series of population genetic models that simultaneously incorporate these processes. Our models identify two general properties of antagonistically selected loci. First, antagonistic selection inflates heterozygosity and fitness variance across a broad parameter range-a result that ...
TY - CHAP. T1 - Identifying Selection Signatures in Mammalian Genes Through the Analysis of Patterns of Gene Expression. AU - Urrutia, Araxi. AU - Hurst, Laurence. PY - 2005. Y1 - 2005. M3 - Chapter. BT - SAGE: Current Technologies and Applications. A2 - Wang, SM. PB - Horizon Bioscience. ER - ...
The spectacular diversity in sexually selected traits among animal taxa has inspired the hypothesis that divergent sexual selection can drive speciation. Unfortunately, speciation biologists often consider sexual selection in isolation from natural selection, even though sexually selected traits evolve in an ecological context: both preferences and traits are often subject to natural selection. Conversely, while behavioural ecologists may address ecological effects on sexual communication, they rarely measure the consequences for population divergence. Herein, we review the empirical literature addressing the mechanisms by which natural selection and sexual selection can interact during speciation. We find that convincing evidence for any of these scenarios is thin. However, the available data strongly support various diversifying effects that emerge from interactions between sexual selection and environmental heterogeneity. We suggest that evaluating the evolutionary consequences of these ...
Cyclical selection that does not result in gene fixation may maintain a parent-offspring (P-O) correlation in fitness that is, most of the time, not far below one-half. This tends to happen when the following conditions are fulfilled: (i) slow cycling in allele frequencies occurs at many loci independently; (ii) most alleles make only small differences to fitness; (iii) dominance in allelic fitness contribution is rare and overdominance rarer still. In contrast, drastic cyclical selection (dependent on large fitness differences without overdominance), because direction reverses so frequently, may give P- 0 correlations in fitness th a t are near zero or even negative. Also, if much fitness variance is maintained by heterozygote advantage, or is caused environmentally, the correlation is reduced in proportion to the ratio of relevant standard deviations. P - 0 correlation in fitness that is almost permanently positive may help to explain mate choice in sexually promiscuous species. The most ...
In the models presented above, a locus segregates for alleles with higher than average fitness for one sex and lower than average fitness for the other. Therefore, these are models of intralocus sexual conflict, also known as sexual antagonism or intersexual ontogenetic conflict (Rice & Chippindale 2001). Consistent with previous work, we find that such intralocus conflict can maintain genetic variation, especially when the sexual antagonism is strong (Prout 2000). Our two models are qualitatively similar except that selection is attenuated in the madumnal effect model because half of the gene pool (padumnal alleles) is shielded from selection. This is similar to the dilution of the force of selection for genes with maternal effects, the so-called relaxed constraint (Barker et al. 2005).. Our madumnal effect model applies not only to organisms with dominant haploid life cycles but also to diploid organisms with imprinted gene expression. Though the site of gene expression differs for an ...
Under the Sawyer-Hartl Poisson random field model, comparisons of the configurations of functional categories of DNA mutations can have considerable power to detect even very weak directional selection on classes of DNA mutations. These findings cannot be generalized beyond evolution under the parameter ranges considered and under the Sawyer-Hartl assumptions of stationarity, free recombination, and independent fitness effects of all mutations. Given these assumptions, configuration comparisons that include information from both frequency distributions of polymorphic mutations and numbers of fixed differences confer the greatest power to detect the fitness effects of mutations. The Mann-Whitney U-test, which is sensitive to differences in the locations of distributions, is a more powerful statistical approach to detect uniform selection coefficients than contingency tests of homogeneity. Accumulating DNA variation data for a large number of mutations with similar fitness effects is critical to ...
PubMed comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
Posted on 09/27/2006 9:56:09 AM PDT by SirLinksalot. Why Darwinism is doomed -------------------------------------------------------------------------------- Posted: September 27, 2006 1:00 a.m. Eastern By Jonathan Wells, Ph.D. -------------------------------------------------------------------------------- © 2006 Harvard evolutionary biologist Stephen Jay Gould wrote in 1977: Biology took away our status as paragons created in the image of God. Darwinism teaches that we are accidental byproducts of purposeless natural processes that had no need for God, and this anti-religious dogma enjoys a taxpayer-funded monopoly in Americas public schools and universities. Teachers who dare to question it openly have in many cases lost their jobs. The issue here is not evolution a broad term that can mean simply change within existing species (which no one doubts). The issue is Darwinism which claims that all living things are descended from a common ancestor, modified by natural selection acting on ...
Moving on the pdf the statistics of natural selection on of Slavoj Zizeck, Janan perceives that few majority back analyzes one efflorescences marina on, and often drip of, the frightening as its industrial sample: completely, the Romanitas of greatest Lycotas, Making the clouds of magician, celebrates back current without the rationality, whipped Other ( 65). back, the IV:7 of Tarpeias pdf the statistics of to the Roman study lives the assistance of Romes epistemology as a incendioque ( 75). The pdf the statistics of natural selection on animal populations significantly facilitates on the intended defence of Romans and Sabines in bit and even on the speechs modus by angels because of predictors ( 75).
Define artificial selection. artificial selection synonyms, artificial selection pronunciation, artificial selection translation, English dictionary definition of artificial selection. n. Human intervention in animal or plant reproduction or survival to allow only individuals with desirable traits to reproduce. n. a process in the breeding...
Phylogenetic codon models are often used to characterize the selective regimes acting on protein-coding sequences. Recent methodological developments have led to models explicitly accounting for the interplay between mutation and selection, by modeling the amino acid fitness landscape along the sequence. However, thus far, most of these models have assumed that the fitness landscape is constant over time. Fluctuations of the fitness landscape may often be random or depend on complex and unknown factors. However, some organisms may be subject to systematic changes in selective pressure, resulting in reproducible molecular adaptations across independent lineages subject to similar conditions. Here, we introduce a codon-based differential selection model, which aims to detect and quantify the fine-grained consistent patterns of adaptation at the protein-coding level, as a function of external conditions experienced by the organism under investigation. The model parameterizes the global mutational pressure,
Genome-wide scanning for signals of recent positive selection is essential for a comprehensive and systematic understanding of human adaptation. Here, we present a genomic survey of recent local selective sweeps, especially aimed at those nearly or recently completed. A novel approach was developed …
Individuals from different populations vary considerably in their susceptibility to immune-related diseases. To understand how genetic variation and natural selection contribute to these differences, we tested for the effects of African versus European ancestry on the transcriptional response of pri …
Shermer wrote the foreword to Prothero s book, calling it the best book ever written on the subject. In fact, Don s visual presentation of the fossil and genetic evidence for evolution is so unmistakably powerful that I venture to say that no one could read this book and still deny the reality of evolution. Of course, evolution can mean many things, most of which nobody would deny even without Prothero s book. For example, evolution can mean simply change over time, or minor changes in existing species ( microevolution ), neither of which any sane person doubts. Both Shermer and Prothero, however, make it clear that by evolution they mean Darwin s theory that all living things are descended from a common ancestor, modified principally by natural selection acting on unguided variations ( macroevolution ).. The modern version of the theory asserts that new variations originate in genetic mutations. Some of the most dramatic mutations occur in Hox genes, which can determine which appendages develop ...
Like drivers at a carwash, coral reef fish queue at cleaning stations to have parasites, slime, and broken scales nibbled away by smaller fish and by shrimps. These species interactions are interesting for their tropical ubiquity and the diversity of species that can be found as clients and cleaners. Although some cleaners are obligate professionals, others are dilettantes and adopt this life-style intermittently.. Floeter et al. have compiled data from around the tropics to tease out the selection pressures acting on these interactions. The basic emerging relationship is that, owing to abundance, the more common, planktivorous, and gregarious species take up most of the cleaners time. Client size doesnt seem to be very important, nor does professionalism, when it comes to dealing with carnivores that might eat the fish or shrimp that is cleaning them. Hence, this study adds to a growing body of evidence suggesting a central role for abundance in structuring species interactions. Guimarães et ...
Associations between selected alleles and the genetic backgrounds on which they are found can reduce the efficacy of selection. We consider the extent to which such interference, known as the Hill-Robertson effect, acting between weakly selected alleles, can restrict molecular adaptation and affect patterns of polymorphism and divergence. In particular, we focus on synonymous-site mutations, considering the fate of novel variants in a two-locus model and the equilibrium effects of interference with multiple loci and reversible mutation. We find that weak selection Hill-Robertson (wsHR) interference can considerably reduce adaptation, e.g., codon bias, and, to a lesser extent, levels of polymorphism, particularly in regions of low recombination. Interference causes the frequency distribution of segregating sites to resemble that expected from more weakly selected mutations and also generates specific patterns of linkage disequilibrium. While the selection coefficients involved are small, the fitness
Which Evolution do you believe in when you say, Evolution is so powerful? Darwin didnt have a mechanism; there was no knowledge of DNA polymerase and Meiotic cell division in those days. He was more concerned with proving the superiority of the Anglo Saxon race. Hence the subtitle of his 1st book, …and the preservation of favored races, and the thrust of his 2nd book, The descent of man. Natural selection acting on random mutations doesnt work as a creative force, either. Its a reducing force, if anything. We have never seen that mechanism producing a new species. Remember, Darwins book wasnt called How species change over time; it was how new species originate. All we observe is the reshuffling of existing genetic material (reshuffling of the deck of cards), or laboratory recombinations that produce freaks (fruit flies with useless wings or legs growing out of their heads), or sterile polyploidy in the plant kingdom. Currently, there is a crisis with the standard neo-Darwin ...
However, principles of natural selection may also hold key to thwarting emergence of drug resistance. According to researchers at Moffitt Cancer Center, cancer is subject to the evolutionary processes laid out by Charles Darwin in his concept of natural selection. Natural selection was the process identified by Darwin by which nature selects certain physical attributes, or phenotypes, to pass on to offspring to better fit the organism to the environment.. As applied to cancer, natural selection, a key principle of modern biology, suggests that malignancies in distinct microhabitats promote the evolution of resistance to therapies. However, these same evolutionary principles of natural selection can be applied to successfully manage cancer, say Moffitt researchers who published an opinion piece in a recent issue of Nature Reviews Cancer.. Understanding cancer as a disease starts with identifying crucial environmental forces and corresponding adaptive cellular strategies, said Robert A. ...
Free-living bacteria are usually thought to have large effective population sizes, and so tiny selective differences can drive their evolution. However, because recombination is infrequent, background selection against slightly deleterious alleles should reduce the effective population size (N e) by orders of magnitude. For example, for a well-mixed population with 10 12 individuals and a typical level of homologous recombination (r/m= 3, i.e., nucleotide changes due to recombination [r] occur at 3 times the mutation rate [m]), we predict that N e is,10 7. An argument for high N e values for bacteria has been the high genetic diversity within many bacterial species, but this diversity may be due to population structure: diversity across subpopulations can be far higher than diversity within a subpopulation, which makes it difficult to estimate N e correctly. Given an estimate ofN e, standard population genetics models imply that selection should be sufficient to drive evolution if N e ×s is ...
TY - JOUR. T1 - Evolution of mitotic cell-lineages in multicellular organisms. AU - Fagerström, Torbjörn. AU - Briscoe, David A.. AU - Sunnucks, Paul. PY - 1998/3. Y1 - 1998/3. N2 - Adaptive evolution in multicellular organisms is generally assumed to occur through natural selection acting differentially among the phenotypes programmed by sexually-generated zygotic genotypes. Under this view, only genetic changes in the gamete-zygote-germline-gamete cycle are considered relevant to the evolutionary process. Yet asexuality - production of progeny through proliferation of mitotic cell-lineages - is found in over one half of all eukaryotic phyla, and is likely to contribute to adaptive changes, as suggested by recent evidence from both animals and plants. Adaptive changes in mitotic lineages can be reconciled with contemporary evolutionary thought by fully abandoning the weismannian concept of individuality.. AB - Adaptive evolution in multicellular organisms is generally assumed to occur through ...
A complete understanding of the role of natural selection in driving evolutionary change requires accurate estimates of the strength of selection acting in the wild. Accordingly, several approaches using a variety of data-including patterns of DNA variability, spatial and temporal changes in allele frequencies, and fitness estimates-have been developed to identify and quantify selection on both genotypes and phenotypes. Here, we review these approaches, drawing on both recent and classic examples to illustrate their utility and limitations. We then argue that by combining estimates of selection at multiple levels-from individual mutations to phenotypes-and at multiple timescales-from ecological to evolutionary-with experiments that demonstrate why traits are under selection, we can gain a much more complete picture of the adaptive process. ...
Author Summary Infectious diseases have undoubtedly played an important role in ancient and modern human history. Yet, there are relatively few regions of the genome involved in resistance to pathogens that show a strong selection signal in current genome-wide searches for this kind of signal. We revisit the evolutionary history of a gene associated with resistance to the most common malaria-causing parasite, Plasmodium vivax, and show that it is one of regions of the human genome that has been under strongest selective pressure in our evolutionary history (selection coefficient: 4.3%). Our results are consistent with a complex evolutionary history of the locus involving selection on a mutation that was at a very low frequency in the ancestral African population (standing variation) and subsequent differentiation between European, Asian and African populations.
The self-seeded landscape that runs above the High Line at the Rail Yards gives visitors a chance to see what the High Line looked like before it b...
Evolution, at the molecular level, is observableas nucleotide changes in the DNA and amino acid changes in proteins. Both polymorphism and evolutionary change between species can be explained by the two processes of natural selection and genetic drift. Two factors controlling the relative importance of neutral drift and natural selection:. 1. Population size. If the population is small then neutral drift dominates; whereas natural selection does if the population is large. 2. The selection coefficients of the different genotypes. If the selection coefficients are low then neutral drift dominates, otherwise natural selection is the more important.. In the evolution of modern species, there have been millions of molecular changes. Natural selection and neutral drift could logically have produced any proportions of the changes, but exactly what proportion is an open question among evolutionary biologists. Richard Dawkins offers his own view.. ...
Often after natural selection increases the frequency of beneficial alleles in an evolving species, it then maintains the high frequency of these alleles by rejecting harmful or less beneficial alleles. This transformation of positive selection into purifying selection (35) is more likely to occur at nonsynonymous sites than at synonymous sites, where theory predicts synonymous substitutions steadily accumulate over time. Thus, considering the many millions of years of time involved in the descent of the elephant or tenrec lineage (about 78 Ma) and the human or mouse lineage (about 91 Ma), it is not surprising that ,1.4% of the thousands of genes examined have dN/dS ,1 (Table S4) and that the percentage of such likely positively selected genes is smallest for mouse (0.12%). To increase our chances of detecting gene sets that were likely targets of positive selection, we examined by the functional annotation clustering tool (30) the 5% of RefSeqs (389) with the more elevated dN/dS ratios, these ...
Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key regulatory mechanism that determines gene expression and hence heritable phenotypic variation. We use a biophysical model for directional selection on gene expression to estimate the rates of gain and loss of transcription factor binding sites (TFBS) in finite populations under both point and insertion/deletion mutations. Our results show that these rates are typically slow for a single TFBS in an isolated DNA region, unless the selection is extremely strong. These rates decrease drastically with increasing TFBS length or increasingly specific protein-DNA interactions, making the evolution of sites longer than ∼ 10 bp unlikely on typical eukaryotic speciation timescales. Similarly, evolution converges to the stationary distribution of binding sequences very ...
Traditional genome-wide scans for positive selection have mainly uncovered selective sweeps associated with monogenic traits. While selection on quantitative traits is much more common, very few signals have been detected because of their polygenic nature. We searched for positive selection signals underlying coronary artery disease (CAD) in worldwide populations, using novel approaches to quantify relationships between polygenic selection signals and CAD genetic risk. We identified new candidate adaptive loci that appear to have been directly modified by disease pressures given their significant associations with CAD genetic risk. These candidates were all uniquely and consistently associated with many different male and female reproductive traits suggesting selection may have also targeted these because of their direct effects on fitness. We found that CAD loci are significantly enriched for lifetime reproductive success relative to the rest of the human genome, with evidence that the ...
Traditional genome-wide scans for positive selection have mainly uncovered selective sweeps associated with monogenic traits. While selection on quantitative traits is much more common, very few signals have been detected because of their polygenic nature. We searched for positive selection signals underlying coronary artery disease (CAD) in worldwide populations, using novel approaches to quantify relationships between polygenic selection signals and CAD genetic risk. We identified new candidate adaptive loci that appear to have been directly modified by disease pressures given their significant associations with CAD genetic risk. These candidates were all uniquely and consistently associated with many different male and female reproductive traits suggesting selection may have also targeted these because of their direct effects on fitness. We found that CAD loci are significantly enriched for lifetime reproductive success relative to the rest of the human genome, with evidence that the ...
Calculating Nucleotide Sequence Polymorphism. This is the seventh of multiple postings I plan to write about detecting natural selection using molecular data (ie, DNA sequences). The first post contained a brief introduction and can be found here. The second post described the organization of the genome, and the third described the organization of genes. The fourth post described codon based models for detecting selection, and the fifth detailed how relative rates can be used to detect changes in selective pressure. The sixth post dealt with classical population methods for detecting selection using allele and genotype frequencies.. Much of the popular press surrounding recent publications that proclaim to detect natural selection does not adequately detail whether the researchers have identified purifying selection (selective constraint) or positive (aka Darwinian) selection. See here for a particularly poor article that confused the heck out of me (and I claim to understand genome analysis). ...
Introduction. The subject of this chapter is how natural selection acts on age-structured populations, in which age-specific patterns of survival probabilities and reproductive rates are the fundamental parameters describing the life history of a genotype. This is a large subject, and the chapter does not offer a comprehensive review. Instead, I will concentrate on some aspects on which I myself have worked. My interest in the subject was stimulated as a beginning postdoc in Dick Lewontins laboratory, over 30 years ago, when he and Tim Prout expressed some well-justified skepticism about the logical basis of the use of Fishers Malthusian parameters (Fisher 1930, Chapter 2) for modeling selection in populations with overlapping generations (Charlesworth 1970). I have contributed, somewhat fitfully, to this subject during much of my subsequent career.. The fundamental problem is how to describe selection in the context of a population divided into different age groups. This provides the basis ...
He wraps up the chapter with a discussion of what he calls deflector beliefs, those beliefs that result in not being able to arrive at a separate specific belief. At a very simple level the concept is one of presuppositions; the beliefs you bring into a situation will influence the beliefs you form about a situation. This is just as much an argument against the argument from design as anything else. If my children are taught evolution through natural selection at a young age and do not receive religious teachings, the argument from design will have no foothold. The argument from design will be, quite simply, a non-starter. They wont be employing the same propositional attitudes as a theist. Plantinga offers that a hypothetical neutral observer would likely be pre-disposed to conclude design, but doesnt thoroughly argue that point. I dont think it can be well defended in any case ...
The general conclusion may be stated in a simple manner, but I believe that the resulting implications for evolutionary theory are both profound and curiously underappreciated: If many features that operate as adaptations under present regimes of natural selection were exapted from ancestral features with nonadaptive origins-and were not built as adaptations for their current use (or exapted from ancestral features with adaptive origins for different functions)-then we cannot explain all the pathways of evolutionary change under functionalist mechanics of the theory of natural selection. Instead, we must allow that many important (and currently adaptive) traits originated for nonadaptive reasons that cannot be attributed to the direct action of natural selection at all and, moreover, cannot be inferred from the exaptive utility of the trait in living species. Because the subject of evolutionary biology must engage many critical questions about the origins of features, and cannot be confined to ...
The general conclusion may be stated in a simple manner, but I believe that the resulting implications for evolutionary theory are both profound and curiously underappreciated: If many features that operate as adaptations under present regimes of natural selection were exapted from ancestral features with nonadaptive origins-and were not built as adaptations for their current use (or exapted from ancestral features with adaptive origins for different functions)-then we cannot explain all the pathways of evolutionary change under functionalist mechanics of the theory of natural selection. Instead, we must allow that many important (and currently adaptive) traits originated for nonadaptive reasons that cannot be attributed to the direct action of natural selection at all and, moreover, cannot be inferred from the exaptive utility of the trait in living species. Because the subject of evolutionary biology must engage many critical questions about the origins of features, and cannot be confined to ...
TY - JOUR. T1 - Characterizing recurrent positive selection at fast-evolving genes in Drosophila miranda and Drosophila pseudoobscura. AU - Jensen, Jeffrey. AU - Bachtrog, Doris. PY - 2010. Y1 - 2010. N2 - Characterizing the distribution of selection coefficients in natural populations remains a central challenge in evolutionary biology. We resequenced a subset of 19 fast-evolving protein-coding genes in the sister species Drosophila miranda and D. pseudoobscura and their flanking regions to characterize the spatial footprint left by recurrent and recent selection. Consistent with previous findings, fast-evolving genes and their flanking regions show reduced levels of neutral diversity compared with randomly chosen genes, as expected under recurrent selection models. Applying a variety of statistical tests designed for the detection of selection at different evolutionary timescales, we attempt to characterize parameters of adaptive evolution. In D. miranda, fast-evolving genes generally show ...
This metadata record is the intellectual property of CSA/ProQuest, and was licensed for use under a contract with the USGS to support scientific research and understanding. As such, this copyrighted material should not be electronically reproduced or shared outside of ScienceBase ...
The effective population size (Ne) is a major factor determining allele frequency changes in natural and experimental populations. Temporal methods provide a powerful and simple approach to estimate short-term Ne. They use allele frequency shifts between temporal samples to calculate the standardized variance, which is directly related to Ne. Here we focus on experimental evolution studies that often rely on repeated sequencing of samples in pools (Pool-seq). Pool-seq is cost-effective and often outperforms individual-based sequencing in estimating allele frequencies, but it is associated with atypical sampling properties: Additional to sampling individuals, sequencing DNA in pools leads to a second round of sampling, which increases the variance of allele frequency estimates. We propose a new estimator of Ne, which relies on allele frequency changes in temporal data and corrects for the variance in both sampling steps. In simulations, we obtain accurate Ne estimates, as long as the drift ...
Selection acting on codon usage can cause patterns of synonymous evolution to deviate considerably from those expected under neutrality. To investigate the quantitative relationship between parameters of mutation, selection, and demography, and patterns of synonymous site divergence, we have developed a novel combination of population genetic models and likelihood methods of phylogenetic sequence analysis. Comparing 50 orthologous gene pairs from Drosophila melanogaster and D. virilis and 27 from D. melanogaster and D. simulans, we show considerable variation between amino acids and genes in the strength of selection acting on codon usage and find evidence for both long-term and short-term changes in the strength of selection between species. Remarkably, D. melanogaster shows no evidence of current selection on codon usage, while its sister species D. simulans experiences only half the selection pressure for codon usage of their common ancestor. We also find evidence for considerable base asymmetries in
Hugh Pickens writes Scientists at Stanford University have shown for the first time that the process of natural selection can act on human cultures as well as on genes. The team studied reports of canoe designs from 11 Oceanic island cultures, evaluating 96 functional features that could contribute...
It is not yet clear under what conditions empirical studies can reliably detect progress toward ecological speciation through the analysis of allelic variation at neutral loci. We use a simulation approach to investigate the range of parameter space under which such detection is, and is not, likely. We specifically test for the conditions under which divergent natural selection can cause a generalized barrier to gene flow that is present across the genome. Our individual-based numerical simulations focus on how population divergence at neutral loci varies in relation to recombination rate with a selected locus, divergent selection on that locus, migration rate and population size. We specifically test whether genetic differences at neutral markers are greater between populations in different environments than between populations in similar environments. We find that this expected signature of ecological speciation can be detected under part of the parameter space, most consistently when ...
Patterns of selection acting on immune defence genes have recently been the focus of considerable interest. Yet, when it comes to vertebrates, studies have mainly focused on the acquired branch of the immune system. Consequently, the direction and strength of selection acting on genes of the vertebrate innate immune defence remain poorly understood. Here, we present a molecular analysis of selection on an important receptor of the innate immune system of vertebrates, the Toll-like receptor 2 (TLR2), across 17 rodent species. Although purifying selection was the prevalent evolutionary force acting on most parts of the rodent TLR2, we found that codons in close proximity to pathogen- binding and TLR2-TLR1 heterodimerization sites have been subject to positive selection. This indicates that parasite-mediated selection is not restricted to acquired immune system genes like the major histocompatibility complex, but also affects innate defence genes. To obtain a comprehensive understanding of ...
Evolutionary algorithms are a common probabilistic optimization method based on the model of natural evolution. One important operator in these algorithms is the selection scheme, for which in this paper a new description model, based on fitness distributions, is introduced. With this, a mathematical analysis of tournament selection, truncation selection, ranking selection, and exponential ranking selection is carried out that allows an exact prediction of the fitness values after selection. The correspondence of binary tournament selection and ranking selection in the expected fitness distribution is proved. Furthermore, several properties of selection schemes are derived (selection intensity, selection variance, loss of diversity), and the three selection schemes are compared using these properties.. ...
Developmental plasticity looks like a promising bridge between ecological and developmental perspectives on evolution. Yet, there is no consensus on whether plasticity is part of the explanation for adaptive evolution or an optional add-on to genes and natural selection. Here, we suggest that these differences in opinion are caused by differences in the simplifying assumptions, and particular idealizations, that enable evolutionary explanation. We outline why idealizations designed to explain evolution through natural selection prevent an understanding of the role of development, and vice versa. We show that representing plasticity as a reaction norm conforms with the idealizations of selective explanations, which can give the false impression that plasticity has no explanatory power for adaptive evolution. Finally, we use examples to illustrate why evolutionary explanations that include developmental plasticity may in fact be more satisfactory than explanations that solely refer to genes and ...
Maize silage is forage of high quality and yield, and represents the second most important use of maize in the United States. The Wisconsin Quality Synthetic (WQS) maize population has undergone five cycles of recurrent selection for silage yield and composition, resulting in a genetically improved population. The application of high-density molecular markers allows breeders and geneticists to identify important loci through association analysis and selection mapping, as well as to monitor changes in the distribution of genetic diversity across the genome. The objectives of this study were to identify loci controlling variation for maize silage traits through association analysis and the assessment of selection signatures and to describe changes in the genomic distribution of gene diversity through selection and genetic drift in theWQS recurrent selection program. We failed to find any significant marker-trait associations using the historical phenotypic data from WQS breeding trials combined with 17
Van Tienderen recently published a method that links selection gradients between a phenotypic trait and multiple fitness components with the effects of these fitness components on the population growth rate (mean absolute fitness). The method allows selection to be simultaneously estimated across multiple fitness components in a population dynamic framework. In this paper we apply the method to a population of red deer living in the North Block of the Isle of Rum, Scotland. We show that (1) selection on birth date and birth weight can operate through multiple fitness components simultaneously; (2) our estimates of the response to selection are consistent with the observed change in trait values that we cannot explain with environmental and phenotypic covariates; (3) selection on both traits has fluctuated over the course of the study; (4) selection operates through different fitness components in different years; and (5) no environmental covariates correlate with selection because different fitness
Many genes have evolved sexually dimorphic expression as a consequence of divergent selection on males and females. However, because the sexes share a genome, the extent to which evolution can shape gene expression independently in each sex is controversial. Here, we use experimental evolution to reveal suboptimal sex-specific expression for much of the genome. By enforcing a monogamous mating system in populations of Drosophila melanogaster for over 100 generations, we eliminated major components of selection on males: female choice and male-male competition. If gene expression is subject to sexually antagonistic selection, relaxed selection on males should cause evolution towards female optima. Monogamous males and females show this pattern of feminization in both the whole-body and head transcriptomes. Genes with male-biased expression patterns evolved decreased expression under monogamy, while genes with female-biased expression evolved increased expression, relative to polygamous
The genetic bases of many complex phenotypes are still largely unknown, mostly due to the polygenic nature of the traits and the small effect of each associated mutation. An alternative approach to classic association studies to determining such genetic bases is an evolutionary framework. As sites targeted by natural selection are likely to harbor important functionalities for the carrier, the identification of selection signatures in the genome has the potential to unveil the genetic mechanisms underpinning human phenotypes. Popular methods of detecting such signals rely on compressing genomic information into summary statistics, resulting in the loss of information. Furthermore, few methods are able to quantify the strength of selection. Here we explored the use of deep learning in evolutionary biology and implemented a program, called ImaGene, to apply convolutional neural networks on population genomic data for the detection and quantification of natural selection. ImaGene enables genomic
The distribution of fitness effects (DFE) encompasses the fraction of deleterious, neutral, and beneficial mutations. It conditions the evolutionary trajectory of populations, as well as the rate of adaptive molecular evolution (alpha). Inferring DFE and a from patterns of polymorphism, as given through the site frequency spectrum (SFS) and divergence data, has been a longstanding goal of evolutionary genetics. A widespread assumption shared by previous inference methods is that beneficial mutations only contribute negligibly to the polymorphism data. Hence, a DFE comprising only deleterious mutations tends to be estimated from SFS data, and alpha is then predicted by contrasting the SFS with divergence data from an outgroup. We develop a hierarchical probabilistic framework that extends previous methods to infer DFE and alpha from polymorphism data alone. We use extensive simulations to examine the performance of our method. While an outgroup is still needed to obtain an unfolded SFS, we show ...
Phenotypic convergence between distinct species provides an opportunity to examine the predictability of genetic evolution. Unrelated species sharing genetic underpinnings for phenotypic convergence suggests strong genetic constraints, and thus high predictability of evolution. However, there is no clear big picture of the genomic constraints on convergent evolution. Genome-based phylogenies have confirmed many cases of phenotypic convergence in birds, making them a good system for examining genetic constraints in phenotypic convergence. In this study, we used hierarchical genomic approaches to estimate genetic constraints in three convergent avian traits: nocturnality, raptorial behavior and foot-propelled diving. Phylogeny-based hypothesis tests and positive selection tests were applied to compare 16 avian genomes, representing 14 orders, and identify genes with strong convergence signals. We found 43 adaptively convergent genes (ACGs) associated with the three phenotypic convergence cases and
The concept of fitness is central to natural selection. In broad terms, individuals that are more fit have better potential for survival, as in the well-known phrase survival of the fittest, but the precise meaning of the term is much more subtle. Modern evolutionary theory defines fitness not by how long an organism lives, but by how successful it is at reproducing. If an organism lives half as long as others of its species, but has twice as many offspring surviving to adulthood, its genes become more common in the adult population of the next generation. Though natural selection acts on individuals, the effects of chance mean that fitness can only really be defined on average for the individuals within a population. The fitness of a particular genotype corresponds to the average effect on all individuals with that genotype.[61] A distinction must be made between the concept of survival of the fittest and improvement in fitness. Survival of the fittest does not give an improvement ...
The concept of fitness is central to natural selection. In broad terms, individuals that are more fit have better potential for survival, as in the well-known phrase survival of the fittest, but the precise meaning of the term is much more subtle. Modern evolutionary theory defines fitness not by how long an organism lives, but by how successful it is at reproducing. If an organism lives half as long as others of its species, but has twice as many offspring surviving to adulthood, its genes become more common in the adult population of the next generation. Though natural selection acts on individuals, the effects of chance mean that fitness can only really be defined on average for the individuals within a population. The fitness of a particular genotype corresponds to the average effect on all individuals with that genotype.[61] A distinction must be made between the concept of survival of the fittest and improvement in fitness. Survival of the fittest does not give an improvement ...
natural selection evolution & natural selection evolution online Wholesalers - choose natural selection evolution from 250 list of China natural selection evolution Manufacturers.
Key examples of natural selection to show how one mechanism of evolution operates. Features antibiotic resistance and natural selection and deer mice of Nebraska and natural selection. This article also provides a definition of natural selection.
Localizing genes that are subject to recent positive selection is a major goal of evolutionary biology. In the model organism Drosophila melanogaster many attempts have been made in recent years to identify such genes by conducting so-called genome scans of selection. These analyses consisted in typing a large number of genetic markers along the genomes of a sample of individuals and then identifying those loci that harbor patterns of genetic variation, which are compatible with the ones generated by a selective sweep. In this study we conduct an in-depth analysis of a genomic region located on the X chromosome of D. melanogaster that was identified as a potential target of recent positive selection by a previous genome scan of selection. To this end we re-sequenced 20 kilobases around the Flotillin-2 gene (Flo-2) and conducted a detailed analysis of the allele frequencies and linkage disequilibria observed in this new dataset. The results of this analysis reveal eight genetic novelties that are ...
An important goal of population genetics is to determine the forces that have shaped the pattern of genetic variation in natural populations. We developed a maximum likelihood method that allows us to infer demographic changes and detect recent positive selection (selective sweeps) in populations of varying size from DNA polymorphism data. Applying this approach to single nucleotide polymorphism data at more than 250 noncoding loci on the X chromosome of Drosophila melanogaster from an (ancestral) African population and a (derived) European, we found that the African population expanded about 60,000 y ago and that the European population split off from the African lineage about 15,800 y ago, thereby suffering a severe population size bottleneck. We estimated that about 160 beneficial mutations (with selection coefficients s between 0.05% and 0.5%) were fixed in the euchromatic portion of the X in the African population since population size expansion, and about 60 mutations (with s around 0.5%) in the
Random genetic drift is the process whereby some allele frequencies change in a population by chance alone. The alleles are not being fixed or eliminated by natural selection. Most of the alleles affected by drift are neutral or nearly neutral with respect to selection. Some are deleterious, in which case they may be accidentally fixed in spite of being selected against. Modern evolutionary theory incorporates random genetic drift as part of population genetics and modern textbooks contain extensive discussions of drift and the influence of population size. The scientific literature has focused recently on the Drift-Barrier Hypothesis, which emphasizes random genetic drift [Learning about modern evolutionary theory: the drift-barrier hypothesis].. Most of the alleles that become fixed in a population are fixed by random genetic drift and not by natural selection. Thus, in a very real sense, drift is the dominant mechanism of evolution. This is especially true in species with large genomes full ...
What is the unit of evolution, the level of life upon which natural selection acts? A geneticist would say the gene; Charles Darwin saw it in the unique populations on the Galapagos. On Friday, Leticia Aviles, associate professor of zoology at the University of British Columbia, singled out the individual as dividing the cellular from the group level. ?But what an individual is depends on ones frame of reference,? she said, and the level at which natural selection acts remains an unresolved is
Resilience is the ability of an animal to return soon to its initial productivity after facing diverse environmental challenges. This trait is directly related to animal welfare and it plays a key role in fluctuations of livestock productivity. A divergent selection experiment for environmental variance of litter size has been performed successfully in rabbits over ten generations. The objective of this study was to analyse resilience indicators of stress and disease in the divergent lines of this experiment. The high line showed a lower survival rate at birth than the low line (−4.1%). After correcting by litter size, the difference was −3.2%. Involuntary culling rate was higher in the high than in the low line (+12.4%). Before vaccination against viral haemorrhagic disease or myxomatosis, concentration of lymphocytes, C-reactive protein (CRP), complement C3, serum bilirubin, triglycerides and cholesterol were higher in the high line than in the low line (difference between lines +4.5%, ...
Darwin proposed that natural selection had a fundamental role in speciation, but did not elaborate much on the mechanism. It is now believed that much speciation is due not to natural selection, but to geographical isolation and genetic drift (allopatric speciation). However, natural selection is still seen to play a role in other speciation, such as speciation due to specialization on different hosts (Filchak et al. 2000), and natural selection drives incipient species to greater diversity (Presgraves et al. 2003 ...
Evolution is not a random process. The genetic variation on which natural selection acts may occur randomly, but natural selection itself is not random at all. The survival and reproductive success of an individual is directly related to the ways its inherited traits function in the context of its local environment ...
Programmed cell death-1 (PD-1) and its ligands, particularly PD-L1 and PD-L2, are the most important proteins responsible for signaling T-cell inhibition and arbitrating immune homeostasis and tolerance mechanisms. However, the adaptive evolution of these genes is poorly understood. In this study, we aligned protein-coding genes from vertebrate species to evaluate positive selection constraints and evolution in the PD1, PD-L1 and PD-L2 genes conserved across up to 166 vertebrate species, with an average of 55 species per gene. We determined that although the positive selection was obvious, an average of 5.3% of codons underwent positive selection in the three genes across vertebrate lineages, and increased positive selection pressure was detected in both the Ig-like domains and transmembrane domains of the proteins. Moreover, the PD1, PD-L1 and PD-L2 genes were highly expressed in almost all tissues of the selected species indicating a distinct expression pattern in different tissues among most species.
Programmed cell death-1 (PD-1) and its ligands, particularly PD-L1 and PD-L2, are the most important proteins responsible for signaling T-cell inhibition and arbitrating immune homeostasis and tolerance mechanisms. However, the adaptive evolution of these genes is poorly understood. In this study, we aligned protein-coding genes from vertebrate species to evaluate positive selection constraints and evolution in the PD1, PD-L1 and PD-L2 genes conserved across up to 166 vertebrate species, with an average of 55 species per gene. We determined that although the positive selection was obvious, an average of 5.3% of codons underwent positive selection in the three genes across vertebrate lineages, and increased positive selection pressure was detected in both the Ig-like domains and transmembrane domains of the proteins. Moreover, the PD1, PD-L1 and PD-L2 genes were highly expressed in almost all tissues of the selected species indicating a distinct expression pattern in different tissues among most species.
This post is more of a personal note…here are three papers that are really cool must reads:. Williamson SH, Hubisz MJ, Clark AG, Payseur BA, Bustamante CD, et al. (2007) Localizing Recent Adaptive Evolution in the Human Genome. PLoS Genet 3(6): e90 doi:10.1371/journal.pgen.0030090. Voight BF, Kudaravalli S, Wen X, Pritchard JK (2006) A Map of Recent Positive Selection in the Human Genome. PLoS Biol 4(3): e72 doi:10.1371/journal.pbio.0040072. Tang K, Thornton KR, Stoneking M (2007) A New Approach for Using Genome Scans to Detect Recent Positive Selection in the Human Genome. PLoS Biol 5(7): e171 doi:10.1371/journal.pbio.0050171. E.T. Wang, G. Kodama, P. Baldi, R.K. Moyzis, Global landscape of recent inferred Darwinian selection for Homo sapiens, Proc. Natl. Acad. Sci. USA 103, 135-140 (2006). doi:10.1073/pnas.0509691102. All 4 papers are Open Access! The statistical & computational techniques can be hard to follow sometimes, but these HapMap datasets are the tip of the iceberg, so get comfy and ...
The transcriptional repressor REST regulates many neuronal genes by binding RE1 motifs. About one third of human RE1s are recently evolved and specific to primates. As changes in the activity of a transcription factor reverberate on its downstream targets, we assessed whether REST displays fast evolutionary rates in primates. We show that REST was targeted by very strong positive selection during primate evolution. Positive selection was also evident in the human lineage, with six selected sites located in a region that surrounds a VNTR in exon 4. Analysis of expression data indicated that REST brain expression peaks during aging in humans but not in other primates. Because a REST coding variant (rs3796529) was previously associated with protection from hippocampal atrophy in elderly subjects with mild cognitive impairment (MCI), we analyzed a cohort of Alzheimer disease (AD) continuum patients. Genotyping of two coding variants (rs3796529 and rs2227902) located in the region surrounding the VNTR
This paper proposes a model for the evolution of recombination. The model is based on the notion that when a species (say species 1) interacts with other antagonistic species, species 1 will act as a selective force on them, favouring antagonists best able to destroy its most frequent phenotypes. Only if the progeny of these phenotypes are different from their parents are they able to escape the full force of selected antagonists. A deterministic haploid genetic model with two linked loci and a third unlinked recombination-modifying locus is constructed, using frequency-dependent selection with time delay, to describe the effects of antagonists. Analysis of the model shows that a modifier mutant causing recombination usually starts to spread into a population without recombination, and under certain conditions can spread even if there is already some recombination in the population. The relevance of these results to observations of recombination in the natural world is discussed. ...
The genetic bases of demographic changes and artificial selection underlying domestication are of great interest in evolutionary biology. Here we perform whole-genome sequencing of multiple grey wolves, Chinese indigenous dogs and dogs of diverse breeds. Demographic analysis show that the split between wolves and Chinese indigenous dogs occurred 32,000 years ago and that the subsequent bottlenecks were mild. Therefore, dogs may have been under human selection over a much longer time than previously concluded, based on molecular data, perhaps by initially scavenging with humans. Population genetic analysis identifies a list of genes under positive selection during domestication, which overlaps extensively with the corresponding list of positively selected genes in humans. Parallel evolution is most apparent in genes for digestion and metabolism, neurological process and cancer. Our study, for the first time, draws together humans and dogs in their recent genomic evolution.. ...
Cancer arises from accumulation of somatic mutations and accompanying evolutionary selection for growth advantage. During the evolutionary process, an ancestor clone branches into multiple clones, yielding intratumor heterogeneity. However, principles underlying intratumor heterogeneity have been poorly understood. Here, to explore the principles, we built a cellular automaton model, termed the BEP model, which can reproduce the branching cancer evolution in silico. We then extensively searched for conditions leading to high intratumor heterogeneity by performing simulations with various parameter settings on a supercomputer. Our result suggests that multiple driver genes of moderate strength can shape subclonal structures by positive natural selection. Moreover, we found that high mutation rate and a stem cell hierarchy can contribute to extremely high intratumor heterogeneity, which is characterized by fractal patterns, through neutral evolution. Collectively, This study identified the ...
A laboratory insect used for over a century by geneticists is the fruit fly.3 In 2010, researchers reported in the evolutionary journal Nature the results of 600 generations of artificial selection on this creature.4 They were hoping to document beneficial mutations becoming fixed in the fruit fly population. But intelligent agents with plenty of research money and time, working under conditions that would evidently favor upward, onward evolution, could not document beneficial mutations. In fact, the opposite occurred with the flies undergoing reverse evolution! In addition, the mystical process of natural selection was conspicuously absent ...
Célines writings are examples of black comedy, where unfortunate and often terrible things are described humorously. While his writing is often hyper-real and its polemic qualities can often be startling, his chief strength lies in his ability to discredit almost everything and yet not lose a sense of enraged humanity. Pessimism pervades Célines fiction as his characters sense failure, anxiety, nihilism, and inertia. Will Self has described Célines work as an invective, which - despite the reputation he would later earn as a rabid antisemite - is aimed against all classes and races of people with indiscriminate abandon.[26] The narrative of betrayal and exploitation, both real and imagined, corresponds with his personal life. His two truest loves, his wife, Lucette Almanzor, and his cat, Bébert, are always mentioned with kindness and warmth. Where some critics see a progressive disintegration of personality reflected in the stylistic incoherence of his books based on his life during the ...
1 ---------- 2 SEMAPHORES 3 ---------- 4 OS WAIT ARRAY INFO: reservation count 36255, signal count 12675 5 --Thread 10607472 has waited at buf/buf0rea.c line 420 for 0.00 seconds the semaphore: 6 Mutex at 0x358068 created file buf/buf0buf.c line 597, lock var 0 7 waiters flag 0 8 --Thread 3488624 has waited at buf/buf0buf.c line 1177 for 0.00 seconds the semaphore: 9 Mutex at 0x358068 created file buf/buf0buf.c line 597, lock var 0 10 waiters flag 0 11 --Thread 6896496 has waited at btr/btr0cur.c line 442 for 0.00 seconds the semaphore: 12 S-lock on RW-latch at 0x8800244 created in file buf/buf0buf.c line 547 13 a writer (thread id 14879600) has reserved it in mode exclusive 14 number of readers 0, waiters flag 1 15 Last time read locked in file btr/btr0cur.c line 442 16 Last time write locked in file buf/buf0buf.c line 1797 [...] 17 Mutex spin waits 0, rounds 452650, OS waits 22573 18 RW-shared spins 27550, OS waits 13682; RW-excl spins 0, OS waits 0 ...
From the point of view of a maternally derived gene in Haldane, the three half-brothers are all offspring of his mother, so his maternally derived genes have a probability of one-half being present in each half-brother. For the sacrifice of one copy of the gene in himself, Haldane would be rescuing one and a half copies, on average, of his maternally derived genes. Natural selection acting in that situation on genes of maternal origin would favor the sacrificial behavior.. However, things look very different from the point of view of Haldanes paternal genes. Those three half-brothers are the offspring of different fathers, making them complete non-relatives. If genetic accounting were all that was important, no sacrifice, no matter how small, would justify any benefit, no matter how great, to his paternal half-sibs. Therefore, in this case, selection on paternally derived genes would prevent Haldane performing this sacrificial action.. This illustrates that different selective forces can act on ...
From the point of view of a maternally derived gene in Haldane, the three half-brothers are all offspring of his mother, so his maternally derived genes have a probability of one-half being present in each half-brother. For the sacrifice of one copy of the gene in himself, Haldane would be rescuing one and a half copies, on average, of his maternally derived genes. Natural selection acting in that situation on genes of maternal origin would favor the sacrificial behavior.. However, things look very different from the point of view of Haldanes paternal genes. Those three half-brothers are the offspring of different fathers, making them complete non-relatives. If genetic accounting were all that was important, no sacrifice, no matter how small, would justify any benefit, no matter how great, to his paternal half-sibs. Therefore, in this case, selection on paternally derived genes would prevent Haldane performing this sacrificial action.. This illustrates that different selective forces can act on ...