Questions tagged [population-genetics]
Questions related to the study of the distributions and changes of allele frequency in a population.
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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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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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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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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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Background (null) distribution for higher observed frequency of an allele [closed]
I am testing the hypothesis that being heterozygote at a certain gene locus, say X, increases the chances of having the good allele of X compared to being homozygote. I have data of more than 6000 ...
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How can someone share 50% of their DNA with their parents yet all humans share 99.9%?
I have heard that humans share 99.9% of their DNA with other humans. I have also heard that a child shares 50% of their DNA with their parents. How do I resolve this apparent contradiction? It has ...
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Is it mostly true that predators or parasites traverse wider spatial areas than their prey or hosts?
Does it tend to be true that as you go up the food chain, the species tend to cover wider areas? I am basically asking whether a population's prey varies spatially more than a population's predators ...
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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 individuals in the ...
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Why aren't there more Ash-Red pigeons?
My favorite color pigeon is Ash-Red, but I don't see a lot of them. I figured it must be a recessive phenotype, but when I googled it, I found out it's dominant. So why aren't there more Ash-Red ...
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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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How is "selection" best defined?
There is natural selection but there is also sexual selection which some regard as a category of natural selection. There is also artificial selection (by humans). The question is, what is a most ...
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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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What is Hamilton's rule for multiple generations?
What is Hamilton's rule as it applies to multiple generations? Is it that the lineage success given up by the actor must be exceeded by the lineage success acquired times the relatedness between ...
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Isn't heritability more important to genic capture than just genetic variance?
Rowe & Houle (1996) give two criteria for the selection of costly female choice:
Condition dependence of sexually selected traits
High genetic variance in condition
Regarding heritability, ...
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How EGDS (endurance genetic distance score) is calculated?
Can anybody please make me understand how EGDS5 has been calculated to 40.8 in this paper at page#31?
The formula has been described in this paper but when i tried the same, I am not getting the same ...
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Polymorphism in number of chromosomes?
The answer to this question, saying that Down Syndrome - a trisomy of human chromosome 21 - is caused by de novo mutation (rather than resulting from standing variation) made me think about ...
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Down syndrome in subsaharan populations
What is the rate of occurrences of Down syndrome in subsaharan African populations? Is it the same as in white European populations?
An interesting hypothesis came to my mind:
Could it be that Down ...
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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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Can the value of heritability be greater than 1?
Heritability defined as genetic variance divided by total variance seems to be bounded between 0 and 1. However, I see a way of calculating heritability on this page (http://www.radford.edu/~rsheehy/...
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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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Dominance coefficient
I am trying to understand the meaning of the dominance coefficient. I'll be more specific to what I don't understand, in a moment.
Let $A_{11}$, $A_{12}$ and $A_{22}$ be genotypes with fitnesses $1$, $...
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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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Why does my simulation not support the idea that inbreeding is bad?
After reading this post, I wrote some code to simulate inbreeding.
We have a population of $N$ creatures. Each creature has two genes, which come in two forms: recessive (a) and dominant (A). The ...
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What are the consequences of inbreeding?
Inbreeding increases the risk of getting two identical recessive genes, alleles, that cause a disease which wouldn't have been activated with mixed genes. That's how I understand it anyway. But I ...
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Assumptions of Hardy-Weinberg rule
The post Solving Hardy Weinberg problems offers an easy explanation of Hardy-Weinberg rule. The current top answer explicitly does not talk about the assumptions of Hardy-Weinberg. A model makes sense ...
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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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How Can Homosexuality be Genetic? [duplicate]
I hold no strong opinions towards homosexuality one way or the other; I'll personally refrain, but don't apply my personal tastes to the rest of the world.
I remember seeing some articles a while ...
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Example of code with pypgen (python)
I have a VCF file and wish to calculate a few indices of population divergence over a sliding window.
I consider using pypgen but the documentation is currently very limited. Can you please give me ...
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On the selection coefficient
I'm reading Williams' Adaptation and Natural Selection:
A Critique of Some Current Evolutionary Thought.
In this book the author talks about selection coefficients which, if I understand it ...
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Are epicanthic folds a dominant trait?
My state (Tripura) originally had a mostly mongoloid-feature-possessing population (ethnic group: Tripuri). Recently a large number of non-mongoloid people (ethnic group: Bengali) have migrated to ...
user15816
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Hardy Weinberg principle
The principle is that sum total of all allelic frequencies is 1.
Individual frequencies for example can be named p,q.In a diploid cell , p and q represent the frequency of allele A and a respectively ...
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Is this formula describing the loss of unfixed genes from a population accurate?
In the 1954 science fiction novel Search the Sky by Frederick Pohl and Cyril M. Kornbluth, a formula is featured that "quantitatively describes the loss of unfixed genes from a population".
$$L_T=L_0 ...
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Need clarification on HKA test
I understand that HKA test tests for neutrality. And under neutrality we say that "ratio of segregating sites with species (S1) and fixed differences between locus (F1)" (S1/F2) at one locus is equal ...
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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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Need clarification on Coalescent with Recombination
I've been reading about recombination with coalescent. The link to that file is as follows:
http://www.stats.ox.ac.uk/__data/assets/pdf_file/0008/4688/Reading_for_Recombination.pdf
I get the part ...
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Is inbreeding really efficient at producing homozygosity?
Inbreeding results in homozygosity.
I've come across this concept many times and there's a question that comes to my mind every time I read it.
Let us suppose the character we are trying to ...
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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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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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How to distinguish between a genetic bottleneck and directional selection?
Genetic bottlenecks and directional selection should have relatively similar genetic signals: reduced heterozygosity and greater genetic divergence (Fst?) in contemporary populations compared to the ...
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How does Genetic drift and selection affect fixation of an allele?
I want to know how does genetic drift, and selection coefficient (s) together affect the fixation of an allele? For example, if there is a neutral allele (s=0), will only genetic drift cause the ...
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Linkage disequilibrium
I want to know what ranges of value can D' in linkage disequilibrium take? Because I read in my book (An introduction to population genetics by Nielsen and Slatkin) that D' is guaranteed to be between ...
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How to predict future generations from heritability
The heritability of human intelligence is estimated to be around 0.5. There are of course various estimates, some lower, some higher. But let's work with this value of 0.5 for the moment.
I wanted ...
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Genotype frequencies and fitness values in haploid population with clonal growth
I found a small problem, and I am not sure at all about my answers. If someone could correct it, that would be awesome.
Consider a heterogeneous population with the following genotype frequencies ...
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How to determine the probability that a mutation is lost / fixed?
I have a question about how to determine the probability that a mutation is lost or fixed after 1 or 2 generations in population genetics.
Let's say we have a randomly mixing population, with N ...
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Interpretation of table on analysis of genetic diversity between groups
I am very confused about how to interpret Table 8.3 in Smith's Evolutionary Genetics.
Is the GST in the table the same as the G,ST (with the comma), which is defined (pg. 156; Box 8.3) as "the ...
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Lethal gene and population genetics
In the European population, about 1 in 2500 people suffers from Cystic Fibrosis, a genetically determined (descared), autosomal disease. Healthy parents have a child suffering from Cystic Fibrosis. ...
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How to determine whether changes of an allele's frequency are due to genetic drift or selection?
Given that both natural/artifical selection and genetic drift are evolutionary mechanisms that influence how allele frequencies shift in a population:
Are there ways to determine whether a frequency ...
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Does covariance and phenotypic variance have to be for the same trait to calculate narrow-sense heritability?
I'm working on a problem where I'm given that the phenotypic variance of the parent, $p$, for trait $A$ is $175.2$ and the phenotypic variance of the offspring, $o$, for trait $A$ is $146.1$. However, ...
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What is a typical value of the selection coefficient s?
I am trying to gain an understanding of the real world effects of natural selection from the equations, especially comparing it with drift. However I have been unable to find any examples which give ...
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Mixed-mating plants: is the number of mixed mating plants supposed to be trivial?
I am referring to Winn et al. 2011
Last sentence of the first paragraph is
Although sampling bias against both selfing and highly outcrossing species may inflate the frequency of mixed-mating ...
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