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

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Your “code of conduct” appears very one-sided [migrated]

You claim that you want a respectful environment where all feel welcome, and yet, as I read through some of the answers provided, I find all kinds of derogatory references towards creationists; ...
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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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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
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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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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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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
29 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
42 views

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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0answers
119 views

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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0answers
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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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1answer
61 views

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 ...
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Is my heritability implementation for an asexual population wrong?

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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0answers
12 views

How common is relatedness significantly positive (say, higher than .05)? (Please see question details.)

How commonly does it occur in natural populations that if an individual were to die, the resources it would have used if it had survived would instead be used with r fraction by same-type individuals ...
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estimate the allele frequencies and test with chi squared

This question is from the 2012 international biology Olympiad theoretical test B. It's not for homework(I wish it were), I'm just preparing for the upcoming IBO. I know other IBO questions have been ...
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How is heritability calculated for an asexual population?

Do I have this calculation correct for the heritability of fitness for an asexual population? (FYI, this is an example of my own, not any sort of a HW question.) One specific concern is, when ...
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How can census population size be smaller than the effective population size in some species? is that possible?

The only way I can think this could happen is through a recent population bottleneck. Can it be possible though ?
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1answer
55 views

Variation of fixation probability over time in Wright-Fisher model

In Wright-Fisher model of population size N and initial mutation frequency of 1/N, how does the fixation probability vary over generations. So, mathematically, what is the function that maps the ...
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0answers
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How does one calculate Rx/a in population genetics?

The ratio of sex-linked to autosome mutation frequencies (R) is Rx/a =(2/3)(2+ α)/(1+ α) for X-linked genes and Ry/a = 2 α /(1+ α) for Y-linked genes. How does one calculate Rx/a, in order to find α?
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What is the coefficient of relatedness between a queen bee and her daughter if the male that mated with the queen was the queen’s own son? [duplicate]

What is the coefficient of relatedness between a queen bee and her daughter if the male that mated with the queen was the queen’s own son? The answer should be 0.75, but I keep getting 1 because 0.5(...
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1answer
101 views

Recommendations for textbooks on statistical and quantitative genetics, and genetic epidemiology

I'm looking for a textbook on statistical genetics, quantitative genetics, association mapping, and genetic epidemiology. My interests include, but are not limited to, complex trait analysis, and the ...
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1answer
109 views

Island model vs. stepping stone model

Wright's Island model and Kimura's stepping stone model are classic explanations for migration/gene flow o individuals between subpopulations within the field of population genetics. My question ...
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1answer
44 views

The total numbers of mutations on different branches of gene tree are independent or not?

I was reading Tajima's 1989 paper on his test for neutrality. Tajima, Fumio. "Statistical method for testing the neutral mutation hypothesis by DNA polymorphism." Genetics 123.3 (1989): 585-595. ...
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1answer
84 views

Practical Question about Evolution, Population Genetics and Speciation

North American cicada male of the genus Magicicada sing depending on the species at different times of the day and attract the females of the corresponding species. The species are very similar, but ...
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1answer
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Low migration rate in Papadopoulou et al. (2008)

In the paper "Speciation and DNA barcodes: testing the effects of dispersal on the formation of discrete sequence clusters" by Papadopoulou et al. (2008), is there an explanation as to why the authors ...
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1answer
106 views

What would be the Hardy-Weinberg equilibrium condition for a population of haploid organism?

What would be the Hardy-Weinberg equilibrium condition for a population of haploid organism? Would it always be in Hardy-Weinberg equilibrium?
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What is a “segregating gene”?

What does the term "segregating" mean in references like the following: "found 42% of a random sample of loci to be segregating" "15 blood group systems are known to be segregating"
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1answer
46 views

Simulating Migration in SimBit Software Program

How is migration incorporated into the SimBit program of Remi Matthey-Doret and Michael Whitlock? Is an island model or stepping stone model assumed?
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1answer
189 views

What is the difference between nucleotide polymorphism (θ) and nucleotide diversity (π)?

In my population genetics book (see reference at bottom) they define them as: Nucleotide polymorphism (θ): proportion of nucleotide sites that are expected to be polymorphic in any sample of size 5 ...
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2answers
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Geographic regions as subpopulations/demes

I am developing a computational simulation for DNA barcoding. One of the parameters in my simulation is the number of subpopulation/demes, which I label as $K$. Most studies that use DNA barcodes tend ...
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1answer
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What is the probability that there are no substitution between an ancestor and a modern individual?

What is the probability that there are no differences if you compare the DNA of the ancient sample to a single DNA sequence from a modern individual? Assuming the individual was diploid and lived T ...
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Please explain this sentence from Hardy-Weinberg principle [duplicate]

Please explain this sentence: The normal frequency of a dominant allele (trait) is 2/3 (p^2 + 2pq) and that of a recessive allele (trait) is 1/3 (q^2). According to my knowledge of allele ...
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1answer
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Limit on the Number of Facial Phenotype [closed]

Individuals of each species all have unique facial structure variations (shape of nose, position of chin etc) from humans to birds and fish etc. We humans don't seem to be reaching mathematical limit ...