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 does the population fitness change after a change in mutation rate?
The mean population fitness as given by mutation load theory depends only on the genome-wide mutation rate ($U$). My question is: How many generations is needed to reach a new mutation load ...
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Is there a term for fixation OR loss of an allele?
I remember reading a paper which used a term to describe either fixation OR loss of an allele via drift. Its definition is basically "the removal/fixation of a polymorphism in a population due to ...
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ABO allele frequencies: Why use the EM algorithm?
In textbooks and lecture notes and slides posted online, determining allele frequencies using blood type information (ABO), under the assumption of Hardy-Weinberg equilibrium, is accomplished using ...
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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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Mutation-Selection-Drift Equilibrium
mutation-selection-drift equilibrium is one of the most important concept of population genetics. I could easily find the calculations for mutation-secltion equilibrium and for mutation-drift ...
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Inbreeding Coefficient and Coefficient of Relationship
Wikipedia gives the following formula to calculate a "path of coefficient of relationship" between an ancestor $A$ and an offspring $O$:
$$\rho_{AO} = 2^{-n} \left( \frac{1+f_A}{1+f_O} \right)^{1/2} =...
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Why is Fst/1-Fst used when calculating isolation by distance?
In population genetics a common analysis when considering the genetic structure of a population is to examine isolation by distance - the relationship between the genetic difference and the geographic ...
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Is Panmixia very rare?
I'm reading the wikipidia page on Panmixia.
Panmixia (or panmixis) means random mating. A panmictic population is one where all individuals are potential partners. This assumes that there are no ...
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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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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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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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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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What is the effective population size of a simple two deme metapopulation?
I am confused as to how to compute the effective population size $N_e$ of a theoretical structured population. Let's consider here a simple case study.
Imagine a 2-deme metapopulation. Each deme is ...
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Population size and genetic drift - What are the evidences?
Wright-Fisher model
From the Wright-Fisher model of genetic drift, the random sampling of allele from one generation to the next is taken from a binomial distribution with parameters $2N$ and $p$, ...
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Runs of homozygosity - degree of inbreeding and disease associations
Been reading recently about methods to determine how inbred a particular person is by measuring their "runs of homozygosity." Loosly, these are defined as regions of the genome (typically >1Mb) where ...
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Is $F_{ST}$ a probability and a correlation coefficient?
$F_{ST}$ is one of the most famous and most important statistics of all of evolutionary biology. Yet, many people misunderstand it or misuse the classical results from the literature on $F_{ST}$ (...
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How should one interpret heritability? Is it related to $R^2$?
From Wikipedia:
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. ...
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How to understand relatedness in an infinite island model?
My understanding is that the relatedness coefficient in kin selection models measures positive assortment. That is, altruism is more likely to evolve if altruists tend to interact with other altruists....
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Bottleneck in population that is already experiencing inbreeding depression
What would be the result when a population experiences a bottleneck, while already manifesting inbreeding depression?
I only found this article and it suggests that the inbreeding depression would ...
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How does an engineered supressive Lethal (when present in 2 copies) gene drive spread through a population until causing population extinction?
I understand that at the molecular level a CRISPR mediated gene drive works by copying the altered gene (and the drive containing CAS enzyme, and guide RNA) into the other chromosome containing the ...
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Genetic evolution without crossover
Can someone please point me to the origin of the system of coupled differential equations (1) in Section 2 of Shahshahani's book$^\star$?
$$ \dot{x}_i = x_i \sum_{j=1}^n m_{ij} \frac{x_j}{|x|} $$
...
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What the "due to" means in the definition of heritability?
According to Wray and Visscher,
heritability is formally defined as the proportion of phenotypic variation (VP) that is due to variation in genetic values (VG).
My question is, what does “due to” ...
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what is the difference between homozygous and heterozygous duplication?
In a genetic test result it's written
homozygous duplication
or
heterozygous duplication
Does it mean four copies of the ...
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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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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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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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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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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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Ecological specialization and relative abundance
I am reading Evolution in Changing Environments by R. Levin but have a hard time.
Claim
At page 25, Levin says as a conclusion
The more efficient a caste at meeting the contingency for which it ...
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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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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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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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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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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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What precisely is the pairwise Fst calculated in GenAlEx 6.5?
A professor of population genetics informed me that there is not a unique notion of pairwise Fst scores in the literature. This information has made me more cautious about what may be implemented by a ...
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Why is $H_{S}$ divided by $H_{T}$ in Wright's $F_{st}$ equation?
$F_{st} = H_{t}-\frac{H_{s}}{H_{T}}$, where $H_{T}$ stands for expected average heterozygosity in the meta population and $H_{S}$ stands for expected average heterozygosity in the sub-population.
As I ...
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Probabilities in calculating the kinship coefficient
I've been reading up to try to understand how the kinship coefficient (or coefficient of coancestry) is calculated. https://brainder.org/2015/06/13/genetic-resemblance-between-relatives/ this is the ...
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What are the differences between internal organs between sub-saharan Africans and Northern Europeans
Lets take as examples a typical Norwegian and a typical Nigerian.
In terms of human anatonomy the outer differences are more obvious e.g. (on average)
White skin vs dark skin
Pointy nose vs broad ...
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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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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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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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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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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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