Questions tagged [population-genetics]
Questions related to the study of the distributions and changes of allele frequency in a population.
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Hardy-Weinberg Equilibrium Test Result for Merged Genotypes
I was curious if two populations are in Hardy-Weinberg Equilibrium (HWE), and if they are merged, then what happens? To find out, I considered populations from the 1000 genome project data. For ...
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Calculate expected heterozygocity using Wright's F statistics (here, FIS)
I try to better understand Wright's F statistics. In general, there are many derivations and many interpretations, and in books, the parameters are called differently, that's why I am struggling.
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Do multiple alleles undergo crossover?
For a reference, point 3 of this article: https://www.biologydiscussion.com/genetics/multiple-alleles/multiple-alleles-meaning-characteristics-and-examples-genes/35452
According to google Bard and ...
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Are there two different senses of the word 'heritability' in use?
Target Height as Predicted by Parental Heights in a Population-Based Study states:
The heritability value was taken as the regression coefficient between
final height and midparental height
Is this ...
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Expected number of SNPs in a sample of size `k`
Consider a Wright-Fisher population of constant size $N$. We sample $k$ haplotypes in this population. What is the expected number of SNPs?
I think the answer should be in Watterson (1975) but it ...
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Datasets for Genetic Diversity of Species Across Geographical Distribution
I'm carrying out some research on applying machine learning methods to ecology and conservation. I'd like to know: are there some datasets on genetic diversity across geographical positions? ...
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Initial population when I count backwards?
My question deals with the number of ancestors it took to produce me:
--> To produce me, it took 2 people (my parents) = ($2^1$) people = 2
--> One generation further included = ($2^1 + 2^2$) ...
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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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Understanding ancestry testing mathematically
Forgive me if this question has been asked here before, because it is something which should be very easy to find, but I can't seem to find an answer no matter where I search.
The question is simply ...
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Is there a term for a sequence of genomes for a family?
Suppose that I am following how a "familial" genome changes throughout generations. That is, I have the genome of a grandmother, father, and daughter, and my objective is to see how the ...
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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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Why is linkage disequilibrium high on either side of a beneficial mutation, but not between sites across the mutation, during a selective sweep?
I was reading the paper "A survey of methods and tools to detect recent and strong positive selection" (2017) and came across this:
Upon fixation of the beneficial mutation, elevated levels ...
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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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Saving a Maize Landrace from Inbreeding Depression
I have 10 seeds of a rare corn landrace. I probably won't be able to acquire more and the cultigen's long term fate is unknown. So, I want to do my best to preserve it for future generations.
Corn is ...
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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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Ways to distinguish between purifying selection and selective sweep
When looking a population genomic data, regions of low diversity (lower than expected; such as in a region of high recombination) can indicate either purifying selection of deleterious mutations or a ...
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How exactly do mutations cause genetic variation in bilaterians?
I am trying to understand how mutations cause genetic variance, and I'm stuck on one issue that I'm going to try my best to explain.
(I am specifically talking about mutations that cause a ...
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How do you convert mtDNA sequences in FASTA to FSTAT format?
I've got control region sequence data from a population of shark and I'm looking to convert this from FASTA to FSTAT in order to calculated the effective population size of females. The software I ...
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Disease-causing allele frequency and modern medicine
I was thinking about what the impact modern medicine might have on human evolution based on a couple assumptions.
If we assume that:
modern medicine has massively cushioned the selection pressure ...
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What exactly is extreme heterozygosity and how does it work?
What does the concept of "extreme heterozygosity" mean?
I first encountered this concept in "The Drunken Botanist". They describe that when planting a seed from, say, a 'red ...
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Effective population size formula in haploid populations undergoing serial bottlenecks
This classic Lenski paper computes the effective population size of an evolving E. coli population subjected to daily population bottlenecks as $N_e = N_0 * g$, where $N_e$ is the effective population ...
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How is a haploblock defined with only one SNP location?
I am reading Impact of estrogen receptor gene polymorphisms and mRNA levels on obesity and lipolysis – a cohort study and am looking at Figure 1. I understand that haplotypes are associated with ...
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Average and lowest degrees of kinship/consanguinity among humans?
I would appreciate insight into the average, median, RMS or any similar measure of relatedness among the current world population - and perhaps something about how rapidly this may be changing. 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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Balancing selection vs introgression? [closed]
Balancing selection can maintain polymorphisms in natural populations for extended periods of evolutionary time. However, in this paper, Dannemann et al. 2016 identify three archaic haplotypes in the ...
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Really having problem comprehending this Hardy-Weinberg example from biology textbook
Genetic equilibrium is a hypothetical state, but it is often used as a benchmark. Consider how the Hardy–Weinberg equations were used in early studies of an allele that causes hereditary ...
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How can I find/simulate mixed-ancestry DNA data?
Some collaborators and I are building an ancestral inference tool, and we're having trouble obtaining reliable ground-truth data for samples of mixed ancestry. All the ground-truth DNA datasets we're ...
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Making sense of infinite-sites mutation but finite-sites recombination coalescent simulator
Hudson (1983) introduced a coalescent simulator with infinite-sites mutations and finite-sites recombination. This seems paradoxical because the documentation of the simulator (section on crossing ...
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What are the considerations for studying population genetics of bacterial pan-genomes?
I am beginning to work in the field of human gut microbiome, and wondering how (and if) the concepts of population genetics could be applied there.
Considering the competition between the species ...
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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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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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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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Why isn't speciation a negative feedback loop?
To rephrase my question more articulately:
Speciation begins when two groups within a species starts to become reproductively isolated, and is complete when the two groups can't interbreed (for the ...
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Ancestral inference from demographic data
The question is inspired by this one, in the History community:
We consider a population, whereas the data we have the number of migrants arriving every year, as well as the initial and the current ...
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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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What are the Genes/Enzymes responsible for the supposedly stark between-individual differences in lethargy after eating starches?
Andrew Huberman claims in one if his podcasts episodes that:
[...] because starches cause the release of serotonin in the brain and lend themselves to a state of sleepiness.
Now, I should mention ...
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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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Method of determining base values of traits in isolated populations
Prelude: I came across a discussion about the correct formula for calculating the average IQ of offspring, which goes something like the following
$$ 100 + \frac35 \left( \left(\text{father's IQ} + \...
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Genetic evolution without crossover
Can someone please point me to the origin of the system of coupled differential equations (1) in Section 2 of Shahshahani's book$^\star$?
$$ \dot{x}_i = x_i \sum_{j=1}^n m_{ij} \frac{x_j}{|x|} $$
...
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Do humans have enough biological differences to be grouped into races or subspecies?
After my online research on the subject, I learnt that, biologically speaking, many scientists believe that there is no such thing as a race. Homo sapiens as a species is only 200,000 years old, which ...
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Viruses in human history
How much do we know about ancient viruses and the viral evolution throughout the human history?
To my knowledge the HIV history has been rather well documented for about hundred years back (e.g., see ...
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How to confirm pure-breeding parents
I was reading Genetic Analysis (Sanders, Bowman) and saw the following figure summarizing the 1909 work of Herman Nilsson-Ehle in describing the genetic control of kernel color in wheat:
How did ...
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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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If crossing over can cause formation of new allele, can it affect Hardy-Weinberg equilibrium?
I was reading about Hardy-Wienberg equilibrium on Wikipedia and there are seven assumptions underlying HW
It is mentioned that sexual reproduction one of the assumption and is a must for HW, but ...
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Do mutations that cause the loss of a complex trait occur more often than mutations causing gain of a complex traits?
The Wiki entry on the evolution of biological complexity states that "[m]utations causing loss of a complex trait occur more often than mutations causing gain of a complex trait". There is ...
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What is the methodogy used to determine the exact genetic flow from one area to another and the times in which it flowed?
For example, I take the instance of Central Asian migration into India.
Say geneticists studied a) ancient bones in CA b) ancient bones in India c) living people in Central Asia d) living people in ...
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What would cause red-haired people to become fewer?
There is this misconception that red-haired people are going to die out. This person on the Internet ("howstuffworks") also connected it to a marketing campaign of a hair dyer company. But I'...
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Nonlinear (Quadratic) selection gradients formula
Under scenarios of stabilizing or disruptive selection, we can add a quadratic component to our model of phenotype and fitness like so.
Specifically, I am not clear on where the 1/2 comes from nor do ...
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Can a trait be too successful? Wouldn't overwhelmingly successful traits limit variability, which is one of the requirements of NS? [closed]
Can a trait be too successful? Wouldn't an overwhelmingly successful trait soon limit the gene pool, and if so, how would the process of natural selection react to that? If an individual is born ...
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Will Fst (inbreeding coefficient) always be a value close or at 0 in asexual populations?
FST is the average inbreeding coefficient of a total population. The equation is:
$F_{ST} = \frac{Var(S)}{Var(T)} $
$Var(S)$ = variance in the frequency of the allele between different subpopulations, ...
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