scholarly journals Testing for ancient selection using cross-population allele frequency differentiation

2015 ◽  
Author(s):  
Fernando Racimo
Keyword(s):  
Allele Frequency ◽  
Modern Human ◽  
Composite Likelihood ◽  
Likelihood Method ◽  
Population Allele Frequency ◽  
Long Time ◽  
Ancient Times ◽  
Frequency Changes ◽  
Beneficial Allele ◽  
Two Populations

A powerful way to detect selection in a population is by modeling local allele frequency changes in a particular region of the genome under scenarios of selection and neutrality, and finding which model is most compatible with the data. Chen et al. (2010) developed a composite likelihood method called XP-CLR that uses an outgroup population to detect departures from neutrality which could be compatible with hard or soft sweeps, at linked sites near a beneficial allele. However, this method is most sensitive to recent selection and may miss selective events that happened a long time ago. To overcome this, we developed an extension of XP-CLR that jointly models the behavior of a selected allele in a three-population tree. Our method - called 3P-CLR - outperforms XP-CLR when testing for selection that occurred before two populations split from each other, and can distinguish between those events and events that occurred specifically in each of the populations after the split. We applied our new test to population genomic data from the 1000 Genomes Project, to search for selective sweeps that occurred before the split of Yoruba and Eurasians, but after their split from Neanderthals, and that could have led to the spread of modern-human-specific phenotypes. We also searched for sweep events that occurred in East Asians, Europeans and the ancestors of both populations, after their split from Yoruba. In both cases, we are able to confirm a number of regions identified by previous methods, and find several new candidates for selection in recent and ancient times. For some of these, we also find suggestive functional mutations that may have driven the selective events.

scholarly journals Mutation Rate Model Used in the DNA VIEW Program

2020 ◽  
Vol 10 (10) ◽  
pp. 3585 ◽  
Author(s):  
Tomasz Krajka
Keyword(s):  
Computer Simulation ◽  
Allele Frequency ◽  
Mutation Rate ◽  
Allele Frequencies ◽  
Rate Model ◽  
Dna Database ◽  
Mutation Model ◽  
Population Allele Frequency ◽  
Frequency Changes

The first problem considered in this paper is the problem of correctness of a mutation model used in the DNA VIEW program. To this end, we theoretically predict population allele frequency changes in time according to this and similar models (we determine the limit frequencies of alleles—they are uniformly distributed). Furthermore, we evaluate the speed of the above changes using computer simulation applied to our DNA database. Comparing uniformly distributed allele frequencies with these existing in the population (for example, using entropy), we conclude that this mutation model is not correct. The evolution does not follow this direction (direction of uniformly distributed frequencies). The second problem relates to the determination of the extent to which an incorrect mutation model can disturb DNA VIEW program results. We show that in typical computations (simple paternity testing without maternal mutation) this influence is negligible, but in the case of maternal mutation, this should be taken into account. Furthermore, we show that this model is inconsistent from a theoretical viewpoint. Equivalent methods result in different error levels.

scholarly journals Ohana: detecting selection in multiple populations by modelling ancestral admixture components

2019 ◽  
Author(s):  
Jade Yu Cheng ◽  
Fernando Racimo ◽  
Rasmus Nielsen
Keyword(s):  
Native American ◽  
Allele Frequency ◽  
Mexican Americans ◽  
Gaussian Approximation ◽  
Simulated Data ◽  
Fat Distribution ◽  
Likelihood Method ◽  
Multiple Populations ◽  
Frequency Changes ◽  
Candidate Regions

AbstractOne of the most powerful and commonly used methods for detecting local adaptation in the genome is the identification of extreme allele frequency differences between populations. In this paper, we present a new maximum likelihood method for finding regions under positive selection. The method is based on a Gaussian approximation to allele frequency changes and it incorporates admixture between populations. The method can analyze multiple populations simultaneously and retains power to detect selection signatures specific to ancestry components that are not representative of any extant populations. We evaluate the method using simulated data and compare it to related methods based on summary statistics. We also apply it to human genomic data and identify loci with extreme genetic differentiation between major geographic groups. Many of the genes identified are previously known selected loci relating to hair pigmentation and morphology, skin and eye pigmentation. We also identify new candidate regions, including various selected loci in the Native American component of admixed Mexican-Americans. These involve diverse biological functions, like immunity, fat distribution, food intake, vision and hair development.

scholarly journals Online Social Gambling and Its Implications for the Study of Marketing Communications

2015 ◽  
Vol 4 (3) ◽  
pp. 22-50 ◽  
Author(s):  
Wilson Ozuem ◽  
Jason Prasad
Keyword(s):  
Single Case ◽  
Internet Technology ◽  
Marketing Communication ◽  
Single Case Study ◽  
New Approach ◽  
Real Money ◽  
Long Time ◽  
Ancient Times ◽  
Communication Practices

Gambling has been a part of humanity for a long time, and references to it have been found in some of the earliest dated records. Literature on the topic has been accumulating since ancient times. The advent of Internet technology along with its typical subsets provides a new approach to how gambling is conducted in postmodern times. Drawing on qualitative research and utilising a single case study strategy, this study examines online social gambling and real money gambling marketing communication practices as well as offers some insights into the development and implementation of effective marketing communication programmes. In contrast to existing studies, the paper, in part, proposes integrative and higher levels of marketing communication programmes between online social gambling and real money gambling environments.

scholarly journals Using seasonal genomic changes to understand historical adaptation: parallel selection on stickleback in highly-variable estuaries

2020 ◽  
Author(s):  
Alan Garcia-Elfring ◽  
Antoine Paccard ◽  
Timothy J. Thurman ◽  
Ben A. Wasserman ◽  
Eric P. Palkovacs ◽  
...  
Keyword(s):  
Natural Selection ◽  
Allele Frequency ◽  
Calcium Binding ◽  
Gasterosteus Aculeatus ◽  
Environmental Changes ◽  
Threespine Stickleback ◽  
Functional Enrichment ◽  
Genomic Changes ◽  
Parallel Selection ◽  
Frequency Changes

AbstractParallel evolution is considered strong evidence for natural selection. However, few studies have investigated the process of parallel selection as it plays out in real time. The common approach is to study historical signatures of selection in populations already well adapted to different environments. Here, to document selection in action under natural conditions, we study six populations of threespine stickleback (Gasterosteus aculeatus) inhabiting bar-built estuaries that undergo seasonal cycles of environmental changes. Estuaries are periodically isolated from the ocean due to sandbar formation during dry summer months, with concurrent environmental shifts that resemble the long-term changes associated with postglacial colonization of freshwater habitats by marine populations. We used pooled whole-genome sequencing (Pool-WGS) to track seasonal allele frequency changes in these populations and search for signatures of natural selection. We found consistent changes in allele frequency across estuaries, suggesting a potential role for parallel selection. Functional enrichment among candidate genes included transmembrane ion transport and calcium binding, which are important for osmoregulation and ion balance. The genomic changes that occur in threespine stickleback from bar-built estuaries could provide a glimpse into the early stages of adaptation that have occurred in many historical marine to freshwater transitions.

scholarly journals Thol tamil samugathil Palli Sol Keatal

2021 ◽  
Vol 3 (S-1) ◽  
pp. 183-187
Author(s):  
Kalaiselvan P
Keyword(s):  
Tamil Nadu ◽  
Human Life ◽  
Beliefs And Practices ◽  
The Public ◽  
The People ◽  
The World ◽  
Long Time ◽  
Ancient Times

Different beliefs and practices are found in human life from birth to death. These beliefs are created by the people and are followed and protected by the mother’s community. Man has been living with nature since ancient times. Beliefs appeared in natural human life. Hope can be traced back to ancient Tamils and still prevails in Tamil Nadu today. The hope of seeing the omen in it is found all over the world. Proverbs show that people have faith in omens. Our ancestors wrote the book 'Gauli Shastri' because the lizard omen is very important in our society. The word lizard played a major role in Tamil life during the Sangam period. It is possible to know that people have lived by the benefit of the lizard. There is hope from the public that the sound of the lizard will predict what will happen next. The purpose of this article is to illustrate the lizard word that has been around for a long time in folklore.

The Emergence of Bone Technologies at the End of the Pleistocene in Southeast Asia: Regional and Evolutionary Implications

2012 ◽  
Vol 22 (1) ◽  
pp. 37-56 ◽  
Author(s):  
Ryan J. Rabett ◽  
Philip J. Piper
Keyword(s):  
Early Modern ◽  
Large Scale ◽  
Minor Component ◽  
Modern Human ◽  
Small Element ◽  
Adaptive Process ◽  
Long Time ◽  
One Step ◽  
A Minor

For many decades Palaeolithic research viewed the development of early modern human behaviour as largely one of progress down a path towards the ‘modernity’ of the present. The European Palaeolithic sequence — the most extensively studied — was for a long time the yard-stick against which records from other regions were judged. Recent work undertaken in Africa and increasingly Asia, however, now suggests that the European evidence may tell a story that is more parochial and less universal than previously thought. While tracking developments at the large scale (the grand narrative) remains important, there is growing appreciation that to achieve a comprehensive understanding of human behavioural evolution requires an archaeologically regional perspective to balance this.One of the apparent markers of human modernity that has been sought in the global Palaeolithic record, prompted by finds in the European sequence, is innovation in bonebased technologies. As one step in the process of re-evaluating and contextualizing such innovations, in this article we explore the role of prehistoric bone technologies within the Southeast Asian sequence, where they have at least comparable antiquity to Europe and other parts of Asia. We observe a shift in the technological usage of bone — from a minor component to a medium of choice — during the second half of the Last Termination and into the Holocene. We suggest that this is consistent with it becoming a focus of the kinds of inventive behaviour demanded of foraging communities as they adapted to the far-reaching environmental and demographic changes that were reshaping this region at that time. This record represents one small element of a much wider, much longerterm adaptive process, which we would argue is not confined to the earliest instances of a particular technology or behaviour, but which forms part of an on-going story of our behavioural evolution.

scholarly journals НОВЫЙ ПОВЕСТВОВАТЕЛЬНЫЙ МИР В ТВОРЧЕСТВЕ АКИ МОРЧИЛАДЗЕ

2019 ◽  
Vol 2 (8(38)) ◽  
pp. 28-30
Author(s):  
Ната Бердзули
Keyword(s):  
Historical Novel ◽  
Point Of View ◽  
Literary Texts ◽  
Postmodern Literature ◽  
Historical Information ◽  
Narrative Story ◽  
Long Time ◽  
Ancient Times ◽  
The Subject ◽  
Narrative Function

The narrative dates from a long time ago and the subject of its research was to study fundamental principles of narration.It is so old that the ideas of its structure have been developed in the ancient times. The etymology of the term "narrative", is derived from the Latin and its meaning is narration. This term was emerged in the literary studies as a result of novelist works by Roland Bart, Claude Bremann, Cvetan Todorov and others. In the twentieth century, many theories were created about the narrative, and in the same century, the main analytical components of narrative - story, sound, time, point of view, character, role were established.Narrative can be considered as a feature of postmodernism, because narrative sources take special significance in postmodernism.While researching modern literature a significant function is given to the variety of narrative usages. The aim of the theme is to research the narrative function on the basis of comparative analysis of Aka Morchiladze's creative works.Aka Morchiladze's novels are filled with familiar literary or historical motives, acting people, stories, but itcreates a different reality through narrative or literary plays.The author creates a narrative text based on literary texts and "historical information". Historical information that is used in the text does not correspond to reality, and we, the readers, think that we are about to learn “historical novel” and the narrator is a historian,-not a novelist. Finally, we realize that we deal with the "fake history", allusion of writer's fantasy and literary and historical facts. Therefore, with regards of the presented issues, it is necessary to take into consideration the specificity of postmodern literature and peculiarities of realization of this specificity in Georgian reality. Narrative sources are of particular importance in postmodernism, which is one of the most important elements of the study of the text to be analyzed.

On the issue of active therapy for alcoholism

1930 ◽  
Vol 26 (8) ◽  
pp. 844-847
Author(s):  
I. Strelchuk
Keyword(s):  
Vegetarian Diet ◽  
Active Therapy ◽  
Alcohol Education ◽  
Long Time ◽  
Ancient Times ◽  
Work And Life

Along with the prevention of alcoholism, expressed in raising the cultural level of the population, improving work and life, widespread anti-alcohol; propaganda, development of a sufficient network of schools, clubs, libraries, reading rooms, radio, anti-alcohol education of growing youth, etc., we also must not forget about the treatment of the already existing cadre of alcoholics. The treatment of alcoholism has been practiced since ancient times. A galaxy of outstanding minds from different eras were looking for a "philosopher's stone" that could heal alcoholics from their illness; and in spite of disappointment after disappointment, mistake after mistake, the pursuit of the elec- syr of sobriety continues and does not stop for a minute. Treatment of alcoholics simply reached the point of absurdities, for example, several centuries ago, alcoholics were treated with an extract of frog maceria in alcohol, a spoonful 2 times a day. In England, for a long time, some prominent scientists pinned their hopes on cocoa as a means that could replace and supplant alcohol. Some pundits in their time opposed vegetarianism to alcoholism, believing that with a vegetarian diet, alcoholism cannot take place, but we do. we see just the opposite, for the most underpowered strata of the population, by virtue of necessity due to lack of funds, who eat vegetarian food, are the most susceptible to alcoholism.

Genetic and statistical analyses of strong selection on polygenic traits: what, me normal?

Genetics ◽  
1994 ◽  
Vol 138 (3) ◽  
pp. 913-941 ◽  
Author(s):  
M Turelli ◽  
N H Barton
Keyword(s):  
Allele Frequency ◽  
Genetic Variance ◽  
Gaussian Approximation ◽  
Selection Response ◽  
Disruptive Selection ◽  
Breeding Values ◽  
Central Moments ◽  
Linkage Disequilibria ◽  
The Mean ◽  
Frequency Changes

Abstract We develop a general population genetic framework for analyzing selection on many loci, and apply it to strong truncation and disruptive selection on an additive polygenic trait. We first present statistical methods for analyzing the infinitesimal model, in which offspring breeding values are normally distributed around the mean of the parents, with fixed variance. These show that the usual assumption of a Gaussian distribution of breeding values in the population gives remarkably accurate predictions for the mean and the variance, even when disruptive selection generates substantial deviations from normality. We then set out a general genetic analysis of selection and recombination. The population is represented by multilocus cumulants describing the distribution of haploid genotypes, and selection is described by the relation between mean fitness and these cumulants. We provide exact recursions in terms of generating functions for the effects of selection on non-central moments. The effects of recombination are simply calculated as a weighted sum over all the permutations produced by meiosis. Finally, the new cumulants that describe the next generation are computed from the non-central moments. Although this scheme is applied here in detail only to selection on an additive trait, it is quite general. For arbitrary epistasis and linkage, we describe a consistent infinitesimal limit in which the short-term selection response is dominated by infinitesimal allele frequency changes and linkage disequilibria. Numerical multilocus results show that the standard Gaussian approximation gives accurate predictions for the dynamics of the mean and genetic variance in this limit. Even with intense truncation selection, linkage disequilibria of order three and higher never cause much deviation from normality. Thus, the empirical deviations frequently found between predicted and observed responses to artificial selection are not caused by linkage-disequilibrium-induced departures from normality. Disruptive selection can generate substantial four-way disequilibria, and hence kurtosis; but even then, the Gaussian assumption predicts the variance accurately. In contrast to the apparent simplicity of the infinitesimal limit, data suggest that changes in genetic variance after 10 or more generations of selection are likely to be dominated by allele frequency dynamics that depend on genetic details.

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