Questions tagged [population-genetics]

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

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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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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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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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How do I solve this problem related to specificity and sensitivity?

Consider an autosomal recessive disease with an incidence of 1/10,000 in the general population of 100,000. Your best friend comes to you very upset because he has just taken a screening test for this ...
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234 views

Infinite site model and Watterson's Estimator

Why is it that under migration, the watterson's estimator (theta) is upward biased? What does upward bias means? And why do we have downward bias under exponential growth? Lastly, is it only the ...
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141 views

How to tell if/how allele frequencies change (USABO question)

This is question number 34 from the 2014 USABO Open Exam: Black and white mice live on an island and have allele frequencies of B=0.20, b=0.80. On the continent, there is a much large population of ...
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49 views

What model of epistasis best fit the reality?

In theoretical population genetics, it is very common to have to assume a model of epistatic interaction. The two most common models are the additive model and the multiplicative model. Additive ...
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438 views

How does the introduction of clones would affect population genetics? [closed]

Since the ability to clone animals gives another way to preserve species, this could help for the breeding process. It has been noted that with the ability to clone animals, endangered species can ...
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300 views

Variance in reproductive success and effective population size

Background The effective population size $N_e$ is the size of the Wright-Fisher population that experience the same amount of drift than the population under consideration. The higher the variance ...
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119 views

Efficient algorithm to calculate various population divergence statistics

Intro and description of the data I am simulating the evolution of very long DNA sequences. The model works well, is performant and will output data in the following kind of fasta format ...
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194 views

Falconer & Mackay population mean calculation & genotypic values

I am reading chapter 7 of Falconer and Mackay where they give a formula to calculate the population mean as a deviation from the heterozygote genotypic value. As an example, imagine a one locus two ...
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Analytical Methods for Estimating Probability of Fixation

The probability of fixation $P$ of an allele is an very important measure and there exists several solutions to estimate this probability. Each method has its own assumptions and it is often hard to ...
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177 views

What is the probability of fixation for a mutant under fluctuating selection?

Here is an answer which explains how one can model the frequency of an allele that is under fluctuating selection (the selection that varies through time). Not, thinking about fluctuating selection, ...
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131 views

$F_{ST}$ when considering a multi-allelic locus

Sewall Wright defined the $F_{ST}$ in a metapopulation as being: $$F_{ST} = \frac{\text{Var}(p)}{\bar p (1-\bar p)}$$ , where $p$ is a vector of frequencies of a given allele and $\bar p$ and $\text{...
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80 views

Does anyone know of a study supporting predictions #2 or #9 of the Extended Evolutionary Synthesis?

Regarding the 12 predictions made by the Extended Evolutionary Synthesis (http://extendedevolutionarysynthesis.com/about-ees/), does anyone know of a study that supports #2 or #9? It seems like #1, ...
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3answers
371 views

What fraction of sites are expected to be polymorphic?

Question Consider a very long (eventually infinite) DNA sequence of neutral sites. Consider a panmictic population of constant size $N$ with a per site mutation rate of $\mu$ where all individuals ...
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3answers
606 views

Why is it $q^2$ for the individual count in hardy weinberg?

My understanding: In Hardy-Weinberg problems the frequency of a homozygous recessive genetic occurrence in a population is $q^2$. So if 1 in 100 people in a population have albinism (homozygous ...
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1answer
424 views

Defining: Evolutionary (quantitative) Genetics and Population Genetics

How do we define the fields that are Evolutionary (quantitative) genetics and population genetics. What set these two fields apart? Can you try to provide definitions? To my intuitive understanding, ...
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1answer
26 views

Increase rate of change in coding regions?

If a sequence is under selection will it acquire more changes over time because of faster fixation than if changes were neutral? Is this true or am I missing something?
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1answer
32 views

What percentage of Americans have Native Indian ancestry? [closed]

What percentage of americans have native indian ancestry? I tried to find the answer online and it's difficult to search for.
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2answers
86 views

In marine DNA viral diversity studies, what would “paradigm of rampant mosaicism” refer to?

The recent paper in Cell Marine DNA Viral Macro- and Microdiversity from Pole to Pole describes the (huge) new Global Ocean Viromes 2.0 (GOV 2.0) dataset. In the Results and Discussion section, the ...
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1answer
39 views

Genomic control explanation

I am following the original genomic control article - http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.167.8448&rep=rep1&type=pdf What's the role of $p_i$ in the article? It says that ...
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1answer
91 views

Heritability in population genetics

What is the difference between narrow sense heritability and broad sense heritability? Does heritability in the broad sense refer to the degree of genetic determination? Heritability in the narrow ...
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1answer
213 views

How migration creates Linkage Disquilibrium

I want to know how admixture and migration creates linkage disequilibrium? I am reading about it but I really don't quite get it.
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1answer
66 views

Is it possible to have a random un-mutation of genes?

According to this article: Gene mutations can be classified in two major ways: Hereditary mutations are inherited from a parent and are present throughout a person’s life in virtually every ...
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1answer
497 views

ExAC Browser: What does a “dubious variant annotation” mean? [closed]

I am studying a protein in the ExAC browser. However it is flagged with a "LoF flag". What exactly counts as a "dubious" variant in ExAC. I couldn't find any further information neither at the ...
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432 views

Are heterozygotes always fitter than homozygotes? Can inbreeding be beneficial?

Inbreeding is mostly not very good because when there is a 'disease' in one allele, the other could/would take over the function. But when you have two of the same genes/alleles, do they, or could ...
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1answer
174 views

Statistical genetics: Allele frequencies that follow a Dirichlet distribution

From Foll and Gagiotti (2008) (software BayeScan). They consider a model where several subpopulation are derived from a unique ancestral population. We consider a set of $I$ loci and let $K_i$ be ...
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1answer
124 views

autosomal recessive population numbers

This question is background research for a science fiction / fantasy novel, my knowledge of genetic is very basic. It seems obvious to me that for genetic disorders that are autosomal recessive, if ...
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1answer
4k views

How would cloning affect conservation of rare species?

Many species are at risk of extinction, and cloning could be seen as a relatively quick method to produce large numbers of members of the species to aid in conservation efforts, especially if the ...
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1answer
239 views

Hardy-Weinberg equilibrium generalized to add inbreeding (non-random mating)

Background Quoting from Gillespie's book The level of inbreeding is measured by the inbreeding coefficient, $F_I$, which is the probability that two alleles in an individual are identity by ...
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1answer
1k views

What's the difference between evolution fitness and reproductive success?

What's the difference biological fitness and reproductive success in the biological terminology?
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2answers
2k views

What is the difference between fixation and loss of alleles in a population?

When running a simulation in PopG, with parameters: Population size: 100 AA fitness: 1.0 Aa fitness: 1.0 aa fitness: 1.0 Mutation A to a: 1.0E-6 Mutation a to A: 1.0E-6 Migration rate between ...
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1answer
43 views

Genetics of Hybrids

I'm working on this problem, but I'm not sure I've done it correctly. My initial thought was that the answer was $D$, but I don't see anything in the above graph that indicated the Hybrid species is,...
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1answer
130 views

Coalescent theory - independence of coalescent times

Let $T_i$ be the time to coalesce from $n(t)=i+1$ to $n(t)=i$, where $n(t)$ is the number of sites that have not coalesced yet. In the below example the maximum $n(0)=6$. As I understand it, many ...
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1answer
149 views

Quantitative Traits Genetics

Can someone please help with this question? I'm not so sure whether part A should be 11 inches or something else. Also, is part B correct
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1answer
26 views

Why is the variance of the Wright-Fisher model not equal p(1-p)/(2N)?

I was looking at the properties of the Binomial probability distribution and it says that the variance is np(1-p). In population genetics, n = 2N. So I would expect ...
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1answer
54 views

What proportion of the people who lived 1000 years ago have genetic descendants alive today?

For context, I've been wondering about this for a paper I'm writing (in philosophy). Really, I want to figure out the chances that someone alive today will end up still having descendants 1000 years ...
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1answer
16 views

How to derive the Equilibrium value $\hat F$ equation

In population genetics, there is a relationship between $\hat F$ and $Nm$. $\hat F=\frac{1}{1+4Nm}$ In population genetics textbook, (i.e. Hartl, D. L., and A. G. Clark. 2007. Principles of ...
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1answer
36 views

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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80 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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50 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
461 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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1answer
58 views

Do similar adaptations result in similiar genetic code?

Sometimes organisms within the same species evolve similar adaptations to similar living conditions without interbreeding. Let's say we have two human populations which need to adapt to a colder ...
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1answer
966 views

Question about the consequences of non-random mating and allele frequencies

I just began studying population genetics, and I don't understand something that is written in my lecture: Consequences of non-random mating: More homozygote and less heterozygote ...
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1answer
436 views

How to calculate Fst from AMOVA

I calculated an AMOVA from a genind object, with one hierarchical factor. In the table I obtain there are SSD values (for my grouping factor,"Error" and total) and sigma2 values (for my grouping ...
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1answer
69 views

How can one calculate “probability of possessing a ‘perfect’ profile” from “typical optimal genotype frequencies”?

Can anyone please explain how the "Probability of possessing a ‘perfect’ profile" was calculated from "typical frequency of optimal genotype" in Table 1 in this paper? Paper link here
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33 views

How would you model the evolution of two genotypes across generations?

Say you have a genotype A that produces x offspring and another genotype B that produces y offspring, where x>y. These x offspring are of genotype A but with modest differences in fitness due to ...
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1answer
74 views

Fst Differences Between Mature Trees and Seeds

For a single co-dominant locus in two populations of blue oak, I am given genotype frequency data (genotypes are AA, AB, BB) for adult trees (at least 150 years old) in both populations (pop 1 and pop ...
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251 views

Summary statistic that can distinguish between migration from pop2 to pop1 vs. pop1 to pop2

Given two sister populations that diverged some time ago, say pop2 migrates to pop1 and breeds there, giving offspring with sequence segments similar to those from pop1 but not in pop2. There are ...