Questions tagged [population-genetics]
Questions related to the study of the distributions and changes of allele frequency in a population.
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Models of evolution by positive versus negative selection
I am making a program for simulating natural selection. Now, I have discovered an interesting difference between positive selection and negative selection.
Positive selection occurs when the ...
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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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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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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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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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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 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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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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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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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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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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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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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 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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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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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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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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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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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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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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Population Genetics Using WGS: How do I know when I have enough individuals?
I am having a difficult time finding information about a minimum threshold for number of individuals to use in wgs pop gen analyses. Are there software or formulas/theory available to determine what ...
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Are the "cocaine hippos" suffering from noticeable inbreeding depression? [duplicate]
Colombia has a population of about 100 "cocaine hippos" founded from a group of one male and three females, which escaped from a drug kingpin's private zoo; it's even estimated that this ...
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Why didn't Escobar's hippos introduced in a single event die out due to inbreeding
Today I read a BBC Report about how Pablo Escobar had once imported 4 hippos (1 male, 3 female) into his estate in Colombia for his private zoo. After his downfall, while other species were shipped ...
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Blood and plucked-feather sample storage
This next field season I will be collecting both blood and feather samples and I wondered how best to store the samples. The blood samples will be used for microsatellite and/or SNP analysis. The ...
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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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Deviation from Hardy Weinberg equilibrium (HWE)
I have a set of 10 genes, each gene contains around 15 SNPs. I have tested the deviation from Hardy Weinberg equilibrium (HWE) for all SNPs. All of the SNPs didn't deviate from HWE, except 5 SNPs in ...
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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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Can the mutation rate vary for individuals of the same species, growing in similar environments?
Suppose we consider several populations who originally inherited their genome from the same ancestor, and that we put for a few thousands generations in similar environments.
Could the mutation rate ...
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'Big ideas' behind constrained selective breeding (optimization)
I'm looking for help in finding the 'big ideas' behind a project I'm beginning and want to make sure I'm not missing anything since I wasn't trained in Biology.
My idea is investigating constrained ...
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Hardy-Weinberg principle
The following paragraph on Wikipedia about the Hardy-Weinberg principle is bothering me.
It should be mentioned that the genotype frequencies after the first generation need not equal the genotype ...
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Inbreeding of selfing and outcrossing plant
I am reading John H. Gillespie's Population Genetics A Concise Guide Section 4.3 Inbreeding. I do not understand these two paragraphs quoted below concerning selfing and outcrossing.
The first ...
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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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Estimates of historical human population size
What are the estimates of minimum historical human population size, and how are they obtained from the current human genetic diversity?
I seem to recall a Scientific American article from over 30 ...
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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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Rigorous definition of the kinship coefficient and proof of a recursion thereof
I am reading Section 5.2, Kinship and Inbreeding Coefficients, of Kenneth Lange, Mathematical and Statistical Methods for Genetic Analysis. There the kinship coefficient $\Phi_{i,j}$ is defined for ...
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What are the long term consequences of settling an isolated territory with an extremely limited gene pool?
I remember reading about a discredited theory - I'm afraid that, despite some frantic Googling, I've been unable to track down a link - which stated that Australia was first settled by a woman, ...
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The significance of haplotype blocks
I looked up haplotype blocks in Google Scholar, and the results returned seemed to show that almost all the relevant articles were published between 2001 and 2009, with almost nothing since 2010.
Why ...
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Why is selection less effective in small populations than in larger?
I can understand that the genetic drift has a higher impact on smaller populations, but what does it mean for the selection to be less effective in small populations than higher?
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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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