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*  Estimating the effective population size from temporal allele frequency changes in experimental evolution
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 ...
https://research-repository.st-andrews.ac.uk/handle/10023/10250
*  Warburg's Lens: A Mathematical oncology pre-print discussion forum: Allele Frequency Spectrum in a Cancer Cell Population
A cancer grows from a single cell, thereby constituting a large cell population. In this work, we are interested in how mutations accumulate in a cancer cell population. We provide a theoretical framework of the stochastic process in a cancer cell population and obtain near exact expressions of allele frequency spectrum or AFS (only continuous approximation is involved) from both forward and backward treatments under a simple setting; all cells undergo cell division and die at constant rates, b and d, respectively, such that the entire population grows exponentially. This setting means that once a parental cancer cell is established, in the following growth phase, all mutations are assumed to have no effect on b or d (i.e., neutral or passengers). Our theoretical results show that the difference from organismal population genetics is mainly in the coalescent time scale, and the mutation rate is defined per cell division, not per time unit (e.g., generation). ...
http://mathematicaloncology.blogspot.ch/2017/01/allele-frequency-spectrum-in-cancer.html
*  Dienekes' Anthropology Blog: Rare and common genetic variants in humans
One of the longest running debates in evolutionary biology concerns the kind of genetic variation that is primarily responsible for phenotypic variation in species. Here, we address this question for humans specifically from the perspective of population allele frequency of variants across the complete genome, including both coding and noncoding regions. We establish simple criteria to assess the likelihood that variants are functional based on their genomic locations and then use whole-genome sequence data from 29 subjects of European origin to assess the relationship between the functional properties of variants and their population allele frequencies. We find that for all criteria used to assess the likelihood that a variant is functional, the rarer variants are significantly more likely to be functional than the more common variants. Strikingly, these patterns disappear when we focus on only those variants in which the major alleles are derived. These analyses indicate ...
https://dienekes.blogspot.com/2011/04/rare-and-common-genetic-variants-in.html
*  Identifying consistent allele frequency differences in studies of stratified populations
1. With increasing application of pooled-sequencing approaches to population genomics robust methods are needed to accurately quantify allele frequency differences between populations. Identifying consistent differences across stratified populations can allow us to detect genomic regions under selection and that differ between populations with different histories or attributes. Current popular statistical tests are easily implemented in widely available software tools which make them simple for researchers to apply. However, there are potential problems with the way such tests are used,which means that underlying assumptions about the data are frequently violated. 2. These problems are highlighted by simulation of simple but realistic population genetic models of neutral evolution and the performance of different tests are assessed. We present alternative tests (including GLMs with quasibinomial error structure) with attractive properties for the analysis of allele ...
https://research-repository.st-andrews.ac.uk/handle/10023/11003
*  Hardy-Weinberg equilibrium | definition of Hardy-Weinberg equilibrium by Medical dictionary
Looking for online definition of Hardy-Weinberg equilibrium in the Medical Dictionary? Hardy-Weinberg equilibrium explanation free. What is Hardy-Weinberg equilibrium? Meaning of Hardy-Weinberg equilibrium medical term. What does Hardy-Weinberg equilibrium mean?
http://medical-dictionary.thefreedictionary.com/Hardy-Weinberg+equilibrium
*  "Cultural Barriers and Gene Frequencies . . ." by Guido Barbujani, Paolo Vian et al.
Analysis of geographic variation for eight red cell markers in Italy shows significant spatial structure for most alleles. Effective population sizes estimated from FST values at these loci are much smaller than those predicted from data on consanguineous marriage, suggesting the presence of factors (presumably barriers) that have reduced gene flow and enhanced the evolutionary weight of genetic drift. Most regions of sharp gene frequency change correspond to geographic and linguistic barriers. Two allele frequencies are significantly correlated with measures of linguistic differentiation but not with indexes describing broad religious and social attitudes. The similarity between patterns of genetic and linguistic variation in Italy, also observed in a previous study, suggests that in specific areas linguistic diversity has acted as a biological barrier constraining mating, dispersal, or both. There is no evidence for a ...
http://digitalcommons.wayne.edu/humbiol/vol64/iss4/1/
*  Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates | Haldane's Sieve
Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates mathieu gautier doi: http://dx.doi.org/10.1101/023721 In population genomics studies, accounting for the neutral covariance structure across population allele frequencies is critical to improve the robustness of genome-wide scan approaches. Elaborating on the BayEnv model, this study investigates several modeling extensions i) to improve the estimation accuracy…
https://haldanessieve.org/2015/08/03/genome-wide-scan-for-adaptive-divergence-and-association-with-population-specific-covariates/
*  MATH IN GENETICS AND GENOMICS | Department of Mathematics
Introduction to basic mathematical methods in genetics and genomics: Mendelian segregation, population allele frequencies, sex-linked traits, genetic recombination, sequence analysis, phylogenetic trees. Necessary background in elementary probability, statistics, and matrix algebra will be provided. Instructor: Staff. ...
http://math.duke.edu/math-genetics-and-genomics
*  conflictos interfamiliares wayuu: Topics by Science.gov
Further data on the microsatellite locus D12S67 in worldwide populations: an unusual distribution of D12S67 alleles in Native Americans.. PubMed. Mitchell, R J; Federle, L; Sofro, A S; Papiha, S S; Briceno, I; Bernal, J E. 2000-08-01. We report the frequencies of alleles at the microsatellite locus D12S67 in 2 widely separated ethnic groups of the world: 2 populations from Sulawesi, an island in the Indonesian archipelago, and 5 Native American tribes of Colombia, South America. The allele frequencies in the Minihasans and Torajans of Sulawesi are similar to each other (but the modal class allele is different) and in general agreement with those reported in mainland Asian groups, but different from both Europeans and Chinese Han of Taiwan. The 5 Native American tribes (Arsario, Kogui, Ijka, Wayuu, and Coreguaje) display different allele frequencies from those seen in Sulawesi populations, in other groups from Europe and mainland Asia, and in Chinese Han of Taiwan. Native Americans exhibit a ...
https://www.science.gov/topicpages/c/conflictos+interfamiliares+wayuu.html
*  Evolution and the Genetics of Populations, Volume 2: The Theory of Gene Frequencies: Sewall Wright | NHBS Book Shop
Buy Evolution and the Genetics of Populations, Volume 2 (9780226910390) (9780226910505): The Theory of Gene Frequencies: NHBS - Sewall Wright, University of Chicago Press
https://www.nhbs.com/evolution-and-the-genetics-of-populations-volume-2-book
*  Hardy-Weinberg Tutorial | Sophia Learning
To discuss the conditions for a population to be in hardy-weinberg equilibrium To use mathematical equations to examine how changes in allele frequency change a population. This is a lesson from the evolution unit that teaches about the hardy-weinberg equilbrium. It exams how changes in allele frequency can alter a population over time.
https://www.sophia.org/tutorials/hardy-weinberg
*  Genetics PPT
What is population? What is the role of Population in Evolution? What is population genetics? What is Mendelian population? What is gene pool? What is gene frequency? What is genotypic frequency? What is Hardy-Weinberg Equilibrium? What are the Evolutionary Forces in a Population? What are the significance of hardy-Weinberg Equilibrium? What is the relationship between Hardy-Weinberg Equilibrium and Evolution?. Learn more: Hardy Weinberg's Equilibrium. You can DOWNLOAD the PPT by clicking on the download link below the preview…. ...
http://www.easybiologyclass.com/category/biology-ppt/genetics-ppt/
*  Gene Frequency - Biology-Online
Two separate populations of equal size are in equilibrium for the same pair of alleles because of random mating within each. In population I, pA=0.6, while in population II, pA=0.2, with q=1-p in each population. If a random sample of females from one population is crossed to a random sample of males from the other population, what would be the progeny genotype frequncies? If these progeny are then allowed to mate at random, what would be the expected gene and genotypic frequencies in the next generation? What happens to the heterozygote frequencies between F1 and F2 ...
https://www.biology-online.org/biology-forum/viewtopic.php?p=144848
*  Biology-Online • View topic - The Colin Leslie Dean species paradox
Could it be you are almost there? Yes, the population could be made up of millions of individuals, or more often, thousands or hundreds of individuals. Individuals reproduce, but populations evolve. Evolution is a change in gene frequency over time... individuals do not change in gene frequency, that is why they do not evolve. The size of the population does not preclude evolution. If a gene confers a benefit to fitness, it will increase in the population... this is simple statistics. Studies have shown even a small benefit is sufficient. Thus, there does not need to be multiple mutations all at the same time. One is enough, assuming a mutation is part of the preocess, which is not even necessary. This is where you may have been misinformed... mutations are not required for a given speciation event, though they may be invovled. I told you before that polygenic traits can vary widely without any new mutations, but you ...
http://www.biology-online.org/biology-forum/post-113615.html
*  Review of allele and genotypic frequencies
Genotypic frequency is given by \[ f(AA) = P = \frac{\text{No. of } AA \text{ individuals}}{\text{Total no. individuals}} \\ f(Aa) = H = \frac{\text{No. of } Aa \text{ individuals}}{\text{Total no. individuals}} \\ f(aa) = Q = \frac{\text{No. of } aa \text{ individuals}}{\text{Total no. individuals}}. \\ \]. ...
http://morotalab.org/asci431-2017/day05/day05.html
*  Sandwalk: September 2016
If a population is finite in size (as all populations are) and if a given pair of parents have only a small number of offspring, then even in the absence of all selective forces, the frequency of a gene will not be exactly reproduced in the next generation because of sampling error. If in a population of 1000 individuals the frequency of 'a' is 0.5 in one generation, then it may by chance be 0.493 or 0.505 in the next generation because of the chance production of a few more or less progeny of each genotype. In the second generation, there is another sampling error based on the new gene frequency, so the frequency of 'a' may go from 0.505 to 0.501 or back to 0.498. This process of random fluctuation continues generation after generation, with no force pushing the frequency back to its ...
http://sandwalk.blogspot.com/2016/09/
*  Sandwalk: 2016
If a population is finite in size (as all populations are) and if a given pair of parents have only a small number of offspring, then even in the absence of all selective forces, the frequency of a gene will not be exactly reproduced in the next generation because of sampling error. If in a population of 1000 individuals the frequency of 'a' is 0.5 in one generation, then it may by chance be 0.493 or 0.505 in the next generation because of the chance production of a few more or less progeny of each genotype. In the second generation, there is another sampling error based on the new gene frequency, so the frequency of 'a' may go from 0.505 to 0.501 or back to 0.498. This process of random fluctuation continues generation after generation, with no force pushing the frequency back to its ...
http://sandwalk.blogspot.de/2016/
*  Sandwalk: September 2016
If a population is finite in size (as all populations are) and if a given pair of parents have only a small number of offspring, then even in the absence of all selective forces, the frequency of a gene will not be exactly reproduced in the next generation because of sampling error. If in a population of 1000 individuals the frequency of 'a' is 0.5 in one generation, then it may by chance be 0.493 or 0.505 in the next generation because of the chance production of a few more or less progeny of each genotype. In the second generation, there is another sampling error based on the new gene frequency, so the frequency of 'a' may go from 0.505 to 0.501 or back to 0.498. This process of random fluctuation continues generation after generation, with no force pushing the frequency back to its ...
http://sandwalk.blogspot.de/2016/09/
*  R-Forge: Software Map
1. Evolution simulation and classification - After measuring gene frequencies of modern populations that have a common ancestor, we estimate ancestral allele frequency and selection state for each gene. A bayesian model is used and verified using the included simulator ...
https://r-forge.r-project.org/softwaremap/trove_list.php?form_cat=276&discrim=314
*  R-Forge: Software Map
1. Evolution simulation and classification - After measuring gene frequencies of modern populations that have a common ancestor, we estimate ancestral allele frequency and selection state for each gene. A bayesian model is used and verified using the included simulator ...
https://r-forge.r-project.org/softwaremap/trove_list.php?form_cat=306&discrim=307,314
*  Define how to make a histogram and a frequency distribution, Basic Statistics
Basic Statistics Assignment Help, Define how to make a histogram and a frequency distribution, 1. Describe two graphs/tables and how they are used to examine data. 2. Why are graphs and tables useful when examining data? 3. Describe how to make a histogram and a frequency distribution.
http://www.expertsmind.com/questions/define-how-to-make-a-histogram-and-a-frequency-distribution-30140399.aspx
*  Table 2
... : Genotype /Allele frequency distribution of CDKN2A/2B rs10811661(C/T) variant among control subjects and type 2 diabetes patients and their Odds Ratio (OR ...
https://www.omicsonline.org/articles-images/2155-6156-3-227-t002.html
*  Constructing Frequency Tables | Frequency Distribution
A frequency table is a way of summarizing a set of data. It is a record of the each value of the variable in data/question. Constructing Frequency Tables
http://itfeature.com/statistics/constructing-frequency-tables
*  Frequency distribution
271 363 159 76 227 337 295 319 250 279 205 279 266 198 117 162 232 303 192 181 321 309 246 278 50 41 335 116 100 151 240 474 297 170 188 320 429 294 570 342 279 235 434 123 325 How many classes would you recommend? What.
https://brainmass.com/business/accounting/frequency-distribution-66817
*  Rife Frequency Research
Rife was a researcher who studied viruses and bacteria. Rife discovered that when increasing the intensity of the frequency at which a microbe resonates, it disintegrates from structural stresses. He designed frequency generating equipment and discovered the mortal oscillatory rates for many viruses.
http://www.essense-of-life.com/healthtopics/A-709/rife-frequency-research.html