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Questions tagged [population-genetics]

Questions related to the study of the distributions and changes of allele frequency in a population.

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Population structure from mtDNA sequence data: A thought experiment

I have 5'-COI sequences for a species of interest, which were downloaded from the Barcode of Life Data (BOLD) systems. Assuming for the moment that the said species was sampled across its entire ...
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For allele frequency determination, is it good to take samples from a college/school or a hospital or any other technique?

I am trying to determine allele frequency of a hla allele. Preliminary analysis shows the prevalence of the allele (homo or heterozygous both) is 3%. The allele is related to a disease (After exposure ...
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Selection coefficient of gorillas

I've been reading about selective sweeps. And I found a case study that talks about drosophila and how their selection coefficient is between 0.0001 and 0.005. I want to know what it'll be like for ...
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Finding specific genotype occurrences given allele frequency

So let's say I have a tetraploid species and I have 4 possible alleles for a particular locus. I have found that I can have 35 total possible genotypes and I know the allele frequencies for each of ...
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Pentaploid genotype frequencies

I know that if I am dealing with a diploid case, and I have 3 alleles, then I can have 6 possible genotypes. I am doing this by adding up all the numbers from 1 to 3. $$1+2+3 = 6$$ But if I want to ...
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What is the distribution of gene polymorphism levels across human genes?

Of the approximately 19,000 human genes, about how many have one allele that occurs with appreciable frequency in the current human population, how many have two alleles, and so on? (By "appreciable ...
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Finding intensity of selection against dominant homozygotes

I was looking at some Olympiad questions and came across the following: If the frequency of a completely recessive allele is $0.2$ and it remains unchanged from generation to generation due to ...
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1answer
33 views

Balancing selection vs introgression?

Balancing selection can maintain polymorphisms in natural populations for extended periods of evolutionary time. However, in this paper, Dannemann et al. 2016 identify three archaic haplotypes in the ...
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32 views

Gene frequency — database/site

Is there any free database when one can check the gene frequency in a healthy population? For example I would like to check it for genes like BIN1, CLU or CR1. On the English Wikipedia I found a gene ...
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Simple interpretation of effective population size?

I'm looking for alternate ways to explain effective populations size, in more conceptual terms. These need not be perfectly accurate "definitions" but should at least be generally accurate in non-edge ...
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What is difference between Incest and Inbreeding? [closed]

Are they the same? As both are related to sexual activity between close relatives.
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36 views

Equation relating probability of fixation and number of generations

I am trying to find an equation that relates the variables of probability of fixation and generations. Or, how does number of generations affect the probability a gene will fix, if population size ...
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What is the population limit that makes consanguinity an issue?

A recent incident brought in the news one of the last uncontacted people - the Sentinelese: the Sentinelese appear to have consistently refused any interaction with the outside world. ...
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How does the new discovery that mitochondrial dna is inherited from both parents change population genetics and other dates?

This new study seem to have pretty much proven that mtDNA is inherited from both parents. I assume that this would lead to most age estimates of ancient human ...
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Offspring of parents with different number of chromosomes

Many papers report that dog-whelks (Nucella lapillus) show a distinct chromosomal polymorphism between populations of 2n = 24 up to 2n = 36. Could somebody please tell me how many chromosomes the F1 ...
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1answer
34 views

Why does the HLA show a high degree of polymorphism?

I know how the HLA undergoes high degree of polymorphism (random genetic rearrangements), but I have not understood why it undergoes rearrangements. What is the advantage offered when HLA shows a high ...
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Can Tajima's D and other population genetic tools be used to copare Arabidopsis ecotypes?

I am currently investigating 2 genes in Arabidopsis taliana that are a product of a recent duplication even (observable from synteny and phylogenetic analysis). In addition to the molecular and ...
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Does consistency in minor allele frequency of a SNP across populations imply selection?

If a particular SNP has very similar MAF value across multiple largely non-overlapping populations, with the assumption of no gene flow between the populations over many generations, would that then ...
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Monohybrid Recombinant Frequency? (three point Gene Linkage)

I am curious to know if it is completely impossible calculate recombinant frequency for monohybrids ( three point link, gene map etc.) Here is an example: Marker 1 xx= 25 xy=100 yy= 20 Marker 2 ...
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Linkage between chromosomal loci and the Hardy-Weinberg principle

Referring to the Hardy-Weinberg principle, which is always stated with respect to a particular locus on the chromosome, if we observe that two different loci are either always together in Hardy-...
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Are mutations a source of genetic variation?

Here is a question from the book SAT II Success Biology E/M (where the SAT is the exam taken by the American high school students): Which of the following statements is true about mutations? (A) ...
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Is it appropriate to say “selection of” or “selection for” an allele that evolves by genetic hitchhiking?

In terms of Sober's selection of/selection for distinction, is it appropriate to say that there was selection of or selection for an allele that evolved by hitchhiking? I am inclined to say selection ...
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1answer
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Population genetics indicates that a billion years are needed for establishment of the millions of genetic differences between human and chimpanzee

Genetic differences between human and chimpanzee include ~50,000 amino acid changes, ~30,000,000 point mutations in non-coding sequences, and millions of insertions, deletions, inversions, genomic ...
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Measuring genetic distance: $F_{ST}$ vs. Nei's distance

As far as I'm aware, Nei's genetic distance is quite old compared to $F_{ST}$. However, I have recently read more papers that utilized Nei's genetic distance alongside with $F_{ST}$. As I'm not very ...
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1answer
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Fst genetic distance: Autosomal vs. mtDNA

As far as I'm aware, mtDNA is only inherited from the mother. Hence, if I compute Fst from autosomal SNPs, then I'll get the actual genetic distance between two human populations. If I compute the ...
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Is there an existing database of mutation rates for mitochondrial loci?

I'm wondering if there exists a database of mutation rates (transitions and transversions) for both mitochondrial loci (such as cytochrome c oxidase subunit I (COI)). Due to the use of COI as a DNA ...
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2answers
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Why the SNPs from the earliest human haplogroups are missing in people outside of Africa if they are infact the descendants of it?

The SNPs M91, P97, M31, P82, M23, M114, P262, M32, M59, P289, P291, P102, M13, M171, M118 from haplogroup A and SNPs M60, M181, P90 from haplogroup B are missing in people without recent African ...
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The concept of high genetic load of disease and non-random segregation of deleterious variants

I'm new in this field. I was reading Shakeel et al. (2018) and came across the below sentences The rate of emergence and distribution of deleterious variants in populations is important in ...
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1answer
120 views

Simulating DNA sequences in R with a given value of $\theta = 4N_{e}\mu$

This might not be the most appropriate site to be asking such a question, but perhaps someone has a solution. My question is: is there an R package or function for simulation of DNA sequences of a ...
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29 views

How to calculate the Marker Index(MI) for a dominant marker such as RAPD and ISSR?

I am working in the genetic diversity analysis of a plant species and have used RAPD and ISSR markers. After scoring the data in a binary matrix, I am trying to find the marker index of the primers. I ...
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Estimating population divergence time with a single mitochondrial marker

Is it possible to estimate population divergence time with a single mitochondrial marker? Here is additional information for my specific case: Mitochondrial marker: Cytochrome Oxidase Subunit 1 (...
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57 views

Which has greater autosomal genetic diversity: East or West Eurasian?

Let's define the two population groups as such: West Eurasian: Northern European, Southern European, Middle Easterner (e.g. Levantine people, Iranian people). Does not include the following mixed ...
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Appropriateness of PCA to visualize clusters in genetic data

In many genetic studies, PCA is often utilized to examine genetic cluster in human populations. Rarely is the % variance reported for the components. With human data it's been my experience that the ...
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Gene flow analysis with a single mitochondrial marker

I am currently studying a mud snail genus called Ecrobia. Several species of this genus occur in both the Mediterranean and Black seas. Therefore, I would like to investigate whether there is: ...
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Is there any data to explore the heterozygosity of the South African lion over the last 18 years?

Background: I need to find data on the heterozygosity of the south African lion over the last 18 years... and I'm struggling: so far I have found a single data point. Question: Where can I find ...
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1answer
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Background selection and hitchhiking effect

As I read the maintenance or removal of an allele from a population is dependent upon the alleles in its linkage group; so, when an advantageous mutation occurs in the population, variation in nearby ...
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1answer
39 views

How to solve these kinds of problems?

16% of people in a population can not roll their tongue .what is the frequency of people which are heterozygous of this character? Please ,any one help and guide me to solve these kind of problems. ...
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1answer
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How much generation of hamster's family it takes to get first bad mutations [closed]

So if I have two humsters and they start to reproduce themselfs then how much generations of hamster's family it takes to get first bad mutations? The info here does not help to find answer https://...
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1answer
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Looking for book or article that derives formula for estimating the “average heterozygosity”

An online lecture I need to watch on population genetics describes a formula for the "average heterozygosity" as follows: ...we can theoretically predict that the average heterozygosity in the ...
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1answer
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Chart of intra-species genetic diversity across species / phyla?

I am looking for information on how genetic diversity within a species (not between species) differs between taxa. In other words: Is the "spread" in the genetic pool, if measured, for instance, in ...
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Easy derivation of Kimura's approximation for the probability of fixation of a mutation

Kimura's approximation for the probability of fixation of a mutation under selection finds recurrent use in population genetics models till date. I am trying to understand the mathematical basis of ...
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Coefficient of relatedness for a locus on the Z chromosome

So i know that the ZW determination system is the equivalent for XY in birds. Moreover, I know that the coefficient of relatedness between siblings for the X chromosome is 0.5 so im guessing that the ...
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How does one go from a couple of DNA sequences to a distance-matrix?

For a project we need to explain the subject of UPGMA. We think we understand thee method itself but I fail to see how you go from a number of DNA-sequences to the distance matrix. I understand ...
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2answers
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What is the conversion between r and FST?

From Schonman (2013): ...allele A can only invade under Hamilton’s condition R=$F_{ST}$ > C/B. From Harpending (2002): The best general definition of the coefficient of relation $R_{XY}$ ...
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What is meant by phenogenotypic disequilibria?

In Invernizzi and Gilman (2015), 5th paragraph of the introduction (see below), I came across the terms phenogenotypic disequilibria and more specifically the terms of positive and negative ...
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What metric(s) is a good proxy for relatedness?

In attempting to seed a simulation, where an individual foregoes resources that go r to same-type individuals and (1-r) to all members (including same-type individuals). What commonly used metrics ...
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Is FST convertible into r?

Would a correct interpretation of Harpending's 2002 article (http://www.humanbiologicaldiversity.com/articles/Harpending,%20Henry.%20%22Kinship%20and%20Population%20Subdivision.%22%20Population%20and%...
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Is there a distinction between linkage phase and haplotype?

Linkage phase- combination of alleles that are coinherited Haplotype- combination of alleles an organism has at different loci. So could an informative meiosis be defined as a meiosis in which a ...
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Calculating heritability, additive variance and total variance from a simulation

I have written a program intending to test a couple of evolutionary strategies and I have calculated heritability for the population (asexual) based on the values recorded during the simulation itself....
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Is there a distinction between the fisherian runaway theory and Fisher's sexy son theory?

In many websites/books they are referred to as part of the same process whereby: "runaway" describing that the process continues even after traits become maladaptive the "sexy son theory" explains ...