Questions tagged [population-genetics]

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

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30 views

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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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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1answer
44 views

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
285 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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471 views

How should one interpret heritability? Is it related to $R^2$?

From Wiki: Heritability estimates are often misinterpreted if it is not understood that they refer to the proportion of variation between individuals on a trait that is due to genetic factors. It ...
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1answer
138 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
58 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
29 views

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
485 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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168 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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1answer
42 views

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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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
84 views

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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33 views

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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1answer
6k views

Why are the genomes of Humans 99.5% the same?

Human's DNA sequence is said to be roughly 99.5% equal. As far as I understand, this means that if I walked up to you and compared our DNA, the sequence of base pairs would be 99.5% the same. My ...
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1answer
824 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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71 views

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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2answers
441 views

Disease causing variants and Hardy-Weinberg Equilibrium

Is it true that many disease causing variants/mutations do not follow Hardy Weinberg Equilibrium? If so, then please elaborate on why this may be true (or not) and provide examples. I am interested ...
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1answer
998 views

Why does the slope of parent-offspring regression equals the heritability in the narrow sense?

Background ---- Notations and assumptions ---- let $W_{ij}$ be the fitness associated to the genotype $AiAj$. $x$ is the frequency of the allele $A1$ in the population. The frequency of the allele $...
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175 views

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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30 views

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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427 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
54 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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2answers
7k views

How to interpret the breeders equation?

The univariate breeders equation is defined as, $\ R = h^2 s$ where $\ R $ is the response, $\ h^2 $ is the heritability (additive genetic variation), $\ s $ is the selection differential. The ...
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1answer
115 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
654 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
194 views

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
64 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
78 views

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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2answers
66 views

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
169 views

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 ...
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1answer
186 views

Question on the concept of mitochondrial Eve [closed]

My question is about the very definition of this common ancestor. Why shouldn't be the mother of mitocondrial Eve the real Eva m (and so on to grand grand ...mother)? All I know on the subject comes ...
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1answer
170 views

Correct migration rate expression in infinite island model

In Sewall Wright's infinite island model, where all demes exchange migrants each generation, I have seen the migration rate stated variously as $m$ or $\frac{m}{d - 1}$ (as in Matthew B. Hamilton's ...
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2answers
118 views

“50% of the variance in antisocial phenotypes is the result of genetic factors” means what?

How can i understand the following sentence: Overall, the conclusions reached by these studies have been highly consistent in showing that approximately 50% of the variance in antisocial phenotypes ...
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3answers
5k views

Do men have a higher genetic variance than women?

I've heard that with the distribution of our genome women have less variation on the bell curve than men. Is there any basis for this? It was my understanding that women have more genetic variation ...
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1answer
785 views

Does the term “fitness advantage” or “fitness disadvantage” make sense?

Same for the terms "selective advantage" and "selective disadvantage" which I intend to use synonymously. There are usages of each on Google Scholar, but do evolutionary biologists understand what is ...
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1answer
65 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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2answers
1k views

Are mutations random?

The following claim Mutations are random or just the use of the expression Random mutations are very common among lay people. The claim is very common among lay people. The claim is often ...
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1answer
94 views

About lack of selective pressure

In [1] it is stated that: the frequency of comutations in FGFR3 and KRAS or PIK3CA and KRAS was lower than predicted by chance, suggesting ... a lack of selective pressure for both mutations to ...
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3answers
972 views

Human genetic diversity in Africa in comparison with the rest of the world

Background The claim ... Most of the genetic diversity in humans is in Africa ... is quite common. On Biology.SE, it is easy to find posts that make this claim. Consider for example: Do humans ...
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1answer
162 views

Can we estimate effective population size from DNA sequence data (CR or cytB sequence)? [closed]

I have DNA sequence data (control region) of two population of a species. Can anybody suggest me any software to calculate effective population size? Is it possible and meaningful?
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1answer
71 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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4answers
2k views

How is it possible for the absolute fitness to be more than 1?

The wikipedia definition of Absolute fitness is "the ratio between the number of individuals with that genotype after selection to those before selection. It is calculated for a single generation and ...
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0answers
85 views

How to choose the most appropriate measure of genetic distance

I am conducting a phylogeography study of a fish species and am trying to construct a phylogenetic tree to describe population structure and ancestry. I have constructed trees using various measures ...
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42 views

Use numbers or algebra when introducing an evolutionary biology concept?

I'm working on an (approximately 20 pg) evolutionary biology paper for submission to a journal. The paper introduces a couple of strategies (I use "strategies" loosely; they can be carried out by ...
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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
194 views

Text Book Recommendation: Organic Evolution

I was wondering if anyone could point me in the direction of any text books on organic evolution? I have recently become interested in the subject and would like to know more. I think an undergrad ...
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0answers
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Replication cohorts in microbial GWAS

Replication in an independent cohort is of course the gold standard in GWAS studies, and many high profile journals will now (quite rightly) not accept finding indicating a phenotype genotype ...

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