Hitchhiking and Selective Sweeps

2018 ◽  
Author(s):  
Bruce Walsh ◽  
Michael Lynch
Keyword(s):  
Codon Bias ◽  
Common Ancestor ◽  
Selective Sweep ◽  
Favorable Allele ◽  
Effective Population ◽  
Different Types ◽  
History Of ◽  
Genomic Regions ◽  
Considerable Body ◽  
New Mutations

When a favorable allele increases in frequency, it alters the coalescent structure (the pattern of times back to a common ancestor) at linked sites relative to that under drift. This creates patterns of sequence polymorphism than can be used to potentially detect ongoing, or very recent, selection. This idea of a neutral allele hitchhiking up to high frequency when coupled to a favorable allele is the notion of a selective sweep, and this chapter reviews the considerable body of associated population-genetics theory on sweeps. Different types of sweeps leave different signatures, resulting in the very diverse collection of tests of selection discussed in Chapter 9. Either a history of recurrent sweeps, or of background selection, results in linked genomic regions of reduced effective population size. This implies that more mutations in sich regions are efficiently neutral, which can result in increased substitution rates and lower codon bias. Finally, the chapter examines the theory for when response is expected to start from existing variation, as opposed to waiting for the appearance of new mutations.

The Genetic Effective Size of a Population

2018 ◽  
Author(s):  
Bruce Walsh ◽  
Michael Lynch
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Genome Structure ◽  
Population Subdivision ◽  
Effective Population ◽  
Entire Genome ◽  
History Of ◽  
A Site ◽  
The Hill ◽  
New Mutations

The effects of genetic drift usually assume an idealized population of constant size. This chapter shows how the population size for such an idealized population can be replaced with an effective population size for populations with age structure, unequal sex ratios, a history of expansion or contraction, inbreeding, and population subdivision. These demographic features impact the entire genome more or less equally. A relatively recent understanding is that selection at a site can dramatically reduce the local effective population size experienced by nearby linked sites (the Hill-Robertson effect). This can arise from background selection to remove deleterious new mutations or from selective sweeps wherein favorable new mutations are driven toward fixation. The Hill-Robertson effect is a general way to describe the fact that selection at a site makes selection are other linked sites less efficient, and, therefore, more neutral. This chapter discusses the implications of this finding for genome structure.

A Microsatellite-Based Multilocus Screen for the Identification of Local Selective Sweeps

Genetics ◽  
2002 ◽  
Vol 160 (2) ◽  
pp. 753-763 ◽  
Author(s):  
Christian Schlötterer
Keyword(s):  
Microsatellite Loci ◽  
Selective Sweep ◽  
Demographic History ◽  
Human Populations ◽  
Selective Sweeps ◽  
Test Statistic ◽  
Data Set ◽  
History Of ◽  
Microsatellite Mutation ◽  
Genomic Regions

AbstractWith the availability of completely sequenced genomes, multilocus scans of natural variability have become a feasible approach for the identification of genomic regions subjected to natural and artificial selection. Here, I introduce a new multilocus test statistic, ln RV, which is based on the ratio of observed variances in repeat number at a set of microsatellite loci in two groups of populations. The distribution of ln RV values captures demographic history of the populations as well as variation in microsatellite mutation among loci. Given that microsatellite loci associated with a recent selective sweep differ from the remainder of the genome, they are expected to fall outside of the distribution of neutral ln RV values. The ln RV test statistic is applied to a data set of 94 loci typed in eight non-African and two African human populations.

scholarly journals Population, Evolutionary and Genomic Consequences of Interference Selection

Genetics ◽  
2002 ◽  
Vol 161 (1) ◽  
pp. 389-410 ◽  
Author(s):  
Josep M Comeron ◽  
Martin Kreitman
Keyword(s):  
Codon Bias ◽  
Temporal Dynamics ◽  
Low Frequency ◽  
Coding Region ◽  
Effective Population ◽  
Intergenic Regions ◽  
Study Population ◽  
Neutral Mutations ◽  
Genomic Regions ◽  
Evolutionary Consequences

AbstractWeakly selected mutations are most likely to be physically clustered across genomes and, when sufficiently linked, they alter each others’ fixation probability, a process we call interference selection (IS). Here we study population genetics and evolutionary consequences of IS on the selected mutations themselves and on adjacent selectively neutral variation. We show that IS reduces levels of polymorphism and increases low-frequency variants and linkage disequilibrium, in both selected and adjacent neutral mutations. IS can account for several well-documented patterns of variation and composition in genomic regions with low rates of crossing over in Drosophila. IS cannot be described simply as a reduction in the efficacy of selection and effective population size in standard models of selection and drift. Rather, IS can be better understood with models that incorporate a constant “traffic” of competing alleles. Our simulations also allow us to make genome-wide predictions that are specific to IS. We show that IS will be more severe at sites in the center of a region containing weakly selected mutations than at sites located close to the edge of the region. Drosophila melanogaster genomic data strongly support this prediction, with genes without introns showing significantly reduced codon bias in the center of coding regions. As expected, if introns relieve IS, genes with centrally located introns do not show reduced codon bias in the center of the coding region. We also show that reasonably small differences in the length of intermediate “neutral” sequences embedded in a region under selection increase the effectiveness of selection on the adjacent selected sequences. Hence, the presence and length of sequences such as introns or intergenic regions can be a trait subject to selection in recombining genomes. In support of this prediction, intron presence is positively correlated with a gene’s codon bias in D. melanogaster. Finally, the study of temporal dynamics of IS after a change of recombination rate shows that nonequilibrium codon usage may be the norm rather than the exception.

GENERAL CHARACTERISTIC OF TEA IN THE MARKETS OF TURKESTAN IN THE XIX-XX CENTURIES

2019 ◽  
Vol 16 (2) ◽  
pp. 55-60
Author(s):  
Maxfuza Mamatova ◽  
Keyword(s):  
General Characteristic ◽  
General Description ◽  
Different Types ◽  
History Of

This article deals with the general description of tea in the markets of Turkestan,provides an overview of the history of our country in the XIX-XX centuries, which based on archival materials and sources. This article tells about the types and varieties of tea consumed by our people, about the different types of tea that replace tea, where they were brought from, the meanings of their historical names and the consumption that was loved by our people.

Zum Einsatz von Definitionen in Pädagogik und Erziehungswissenschaft

2019 ◽  
Vol 95 (2) ◽  
pp. 145-161
Author(s):  
Thomas Mikhail
Keyword(s):  
Historical Research ◽  
Educational Science ◽  
Different Types ◽  
History Of ◽  
Academic Genre

Abstract On the Use of Definitions in Pedagogy and Educational Science. A Historical Journey with Systematic Intent In the academic genre of pedagogy and educational science, definitions were used from the very beginning. The question is if it is possible to differentiate between types of definitions within the history of these sciences. To answer this question the paper revives two different types of traditional definitions in order to generate a typology of definition usage. The typology can be used as a heuristic instrument for further systematic and historical research.

scholarly journals Low Nucleotide Diversity in Chimpanzees and Bonobos

Genetics ◽  
2003 ◽  
Vol 164 (4) ◽  
pp. 1511-1518 ◽  
Author(s):  
Ning Yu ◽  
Michael I Jensen-Seaman ◽  
Leona Chemnick ◽  
Judith R Kidd ◽  
Amos S Deinard ◽  
...  
Keyword(s):  
Nucleotide Diversity ◽  
Nuclear Dna ◽  
Demographic History ◽  
Nuclear Genome ◽  
Limited Data ◽  
Effective Population ◽  
East Central ◽  
Dna Diversity ◽  
History Of ◽  
Mtdna Diversity

Abstract Comparison of the levels of nucleotide diversity in humans and apes may provide much insight into the mechanisms of maintenance of DNA polymorphism and the demographic history of these organisms. In the past, abundant mitochondrial DNA (mtDNA) polymorphism data indicated that nucleotide diversity (π) is more than threefold higher in chimpanzees than in humans. Furthermore, it has recently been claimed, on the basis of limited data, that this is also true for nuclear DNA. In this study we sequenced 50 noncoding, nonrepetitive DNA segments randomly chosen from the nuclear genome in 9 bonobos and 17 chimpanzees. Surprisingly, the π value for bonobos is only 0.078%, even somewhat lower than that (0.088%) for humans for the same 50 segments. The π values are 0.092, 0.130, and 0.082% for East, Central, and West African chimpanzees, respectively, and 0.132% for all chimpanzees. These values are similar to or at most only 1.5 times higher than that for humans. The much larger difference in mtDNA diversity than in nuclear DNA diversity between humans and chimpanzees is puzzling. We speculate that it is due mainly to a reduction in effective population size (Ne) in the human lineage after the human-chimpanzee divergence, because a reduction in Ne has a stronger effect on mtDNA diversity than on nuclear DNA diversity.

Adverse Childhood Experiences and Prevalence of Cigarette and E-Cigarette Use Among Adolescents in Bangkok, Thailand

2020 ◽  
Vol 32 (8) ◽  
pp. 398-405
Author(s):  
Takuma Ofuchi ◽  
Aye Myat Myat Zaw ◽  
Bang-on Thepthien
Keyword(s):  
Adverse Childhood Experiences ◽  
Multinomial Logistic Regression ◽  
Tobacco Product ◽  
Dual Use ◽  
Childhood Experiences ◽  
Adverse Childhood ◽  
Different Types ◽  
History Of ◽  
The Relationship ◽  
Score Range

Currently, e-cigarettes are the most popular tobacco product among adolescents. The purpose of this study was to explore the relationship between exposure to adverse childhood experiences (ACEs) and use of cigarettes, e-cigarettes, and dual use in a sample of adolescents in Bangkok, Thailand. The sample comprises 6167 students from 48 schools (grades 9, 11, and vocational year 2) who participated in the 2019 round of the Behavior Surveillance Survey. History of 11 ACEs was used to calculate a cumulative ACE score (range 0-11). Multinomial logistic regression was used to assess the relationship between history of ACEs and smoking. In the sample, 7.0% reported using e-cigarettes only and 9.5% used e-cigarettes and cigarettes (dual use). After controlling for sociodemographic characteristics, history of ACEs was associated with increased odds of dual use. The odds of cigarette, e-cigarette, and dual use was significantly greater if the adolescent had a history of ≥4 ACEs. Special attention is needed to prevent smoking of different types among those with a history of ACEs.

scholarly journals Nucleotide Variation at theCHALCONE ISOMERASELocus inArabidopsis thaliana

Genetics ◽  
2000 ◽  
Vol 155 (2) ◽  
pp. 863-872 ◽  
Author(s):  
Helmi Kuittinen ◽  
Montserrat Aguadé
Keyword(s):  
Nucleotide Diversity ◽  
Direct Relationship ◽  
Selective Sweep ◽  
Balancing Selection ◽  
Neutral Theory ◽  
Low Frequency ◽  
The Other ◽  
Nucleotide Variation ◽  
Rapid Population Growth ◽  
History Of

AbstractAn ~1.9-kb region encompassing the CHI gene, which encodes chalcone isomerase, was sequenced in 24 worldwide ecotypes of Arabidopsis thaliana (L.) Heynh. and in 1 ecotype of A. lyrata ssp. petraea. There was no evidence for dimorphism at the CHI region. A minimum of three recombination events was inferred in the history of the sampled ecotypes of the highly selfing A. thaliana. The estimated nucleotide diversity (θTOTAL = 0.004, θSIL = 0.005) was on the lower part of the range of the corresponding estimates for other gene regions. The skewness of the frequency spectrum toward an excess of low-frequency polymorphisms, together with the bell-shaped distribution of pairwise nucleotide differences at CHI, suggests that A. thaliana has recently experienced a rapid population growth. Although this pattern could also be explained by a recent selective sweep at the studied region, results from the other studied loci and from an AFLP survey seem to support the expansion hypothesis. Comparison of silent polymorphism and divergence at the CHI region and at the Adh1 and ChiA revealed in some cases a significant deviation of the direct relationship predicted by the neutral theory, which would be compatible with balancing selection acting at the latter regions.

Memory impairment induced by amphetamine derivatives in laboratory animals and in humans: a review

2012 ◽  
Vol 3 (1) ◽  
pp. 1-12 ◽  
Author(s):  
Jordi Camarasa ◽  
Teresa Rodrigo ◽  
David Pubill ◽  
Elena Escubedo
Keyword(s):  
Illicit Drugs ◽  
Molecular Mechanisms ◽  
Memory Performance ◽  
Laboratory Animals ◽  
Club Drugs ◽  
Synthetic Drugs ◽  
History Of ◽  
Amphetamine Derivatives ◽  
Considerable Body

AbstractThe 20th century brought with it the so-called club drugs (the most notorious being amphetamine derivatives), which are used by young adults at all-night dance parties. Methamphet­amine and 3,4-methylenedioxymethamphetamine (MDMA or ecstasy) are synthetic drugs with stimulant and psychoactive properties that belong to the amphetamine family. Here, we have reviewed the literature about the cognitive impairment induced by these two amphetamine derivatives and the preclinical and clinical outcomes. Although there is controversial evidence about the effect of methamphetamine and MDMA on learning and memory in laboratory animals, results from published papers demonstrate that amphetamines cause long-term impairment of cognitive functions. A large number of pharmacological receptors have been studied and screened as targets of amphetamine-induced cognitive dysfunction, and extensive research efforts have been invested to provide evidence about the molecular mechanisms behind these cognitive deficits. In humans, there is a considerable body of evidence indicating that methamphetamine and MDMA seriously disrupt memory and learning processes. Although an association between the impairments of memory performance and a history of recreational amphetamine ingestion has also been corroborated, a number of methodological difficulties continue to hamper research in this field, the most important being the concomitant use of other illicit drugs.

scholarly journals Elucidation of Early Evolution of HIV-1 Group M in the Congo Basin Using Computational Methods

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 517
Author(s):  
Marcel Tongo ◽  
Darren P. Martin ◽  
Jeffrey R. Dorfman
Keyword(s):  
Genetic Relatedness ◽  
Early Evolution ◽  
Congo Basin ◽  
Global Epidemic ◽  
The Past ◽  
History Of ◽  
Cold Spots ◽  
Genomic Regions ◽  
Basin Region ◽  
Hiv 1

The Congo Basin region is believed to be the site of the cross-species transmission event that yielded HIV-1 group M (HIV-1M). It is thus likely that the virus has been present and evolving in the region since that cross-species transmission. As HIV-1M was only discovered in the early 1980s, our directly observed record of the epidemic is largely limited to the past four decades. Nevertheless, by exploiting the genetic relatedness of contemporary HIV-1M sequences, phylogenetic methods provide a powerful framework for investigating simultaneously the evolutionary and epidemiologic history of the virus. Such an approach has been taken to find that the currently classified HIV-1 M subtypes and Circulating Recombinant Forms (CRFs) do not give a complete view of HIV-1 diversity. In addition, the currently identified major HIV-1M subtypes were likely genetically predisposed to becoming a major component of the present epidemic, even before the events that resulted in the global epidemic. Further efforts have identified statistically significant hot- and cold-spots of HIV-1M subtypes sequence inheritance in genomic regions of recombinant forms. In this review we provide ours and others recent findings on the emergence and spread of HIV-1M variants in the region, which have provided insights into the early evolution of this virus.

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