Questions tagged [population-genetics]

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

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1 answer
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Interpretation of arrow-sense heritability over one (using R/S = h^2)

Here is my data: Mean height score of the total parental population: 5.2 Mean height score of selected parents (those chosen for breeding due to their higher height): 6.4 Mean height score of the ...
1 vote
1 answer
111 views

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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1 answer
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Can DNA reveal an approximate chronological generation of a person?

Given complete nuclear and mitochondrial DNA from an individual, would it be possible to approximate in what generation they were born? For example, imagine DNA from someone who lived circa 200 to 700 ...
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Is there a program that demonstrates overall fitness will increase in a population overtime?

Of course this will not always be the case with environmental factors, but generally speaking. I'm searching for a program that shows evolution works from a statistical standpoint.
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3 answers
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Have there ever been "half-twins" who were halfway between siblings and twins?

Have there ever been two human siblings who were 75% or more genetically related?
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Why is the expected time to coalesce the same as the ploidy times inbreeding effective population size?

The expected time to coalesce, in generations, is the same as the ploidy (e.g., 2 for humans) times Nef, the inbreeding effective population size, under coalescent theory. Why? Both ploidy * Nef and ...
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Coefficient of fraternity between grandparent and grandchild from full-sib parents

I have the following pedigree and I would like to calculate the coefficient of fraternity between individual 1 and 5. R/AGHmatrix::Amatrix gives a coefficient of 0 for this pair. Shouldn't it be non-...
8 votes
2 answers
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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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1 answer
101 views

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. More ...
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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 ...
1 vote
1 answer
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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 ...
2 votes
1 answer
102 views

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 ...
1 vote
1 answer
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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? ...
5 votes
3 answers
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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 = ($2^1 + 2^2$) ...
2 votes
0 answers
43 views

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 ...
5 votes
2 answers
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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 ...
0 votes
1 answer
48 views

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 ...
2 votes
0 answers
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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 ...
4 votes
2 answers
47 views

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 ...
3 votes
2 answers
3k views

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 $1$, $...
5 votes
1 answer
124 views

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 ...
1 vote
0 answers
254 views

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 ...
5 votes
1 answer
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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 ...
5 votes
1 answer
134 views

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 ...
1 vote
1 answer
907 views

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 ...
0 votes
1 answer
134 views

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 ...
3 votes
3 answers
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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 ...
3 votes
1 answer
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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 ...
3 votes
1 answer
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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 ...
6 votes
2 answers
578 views

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 ...
1 vote
0 answers
52 views

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 ...
1 vote
1 answer
122 views

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 ...
2 votes
2 answers
97 views

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 ...
7 votes
1 answer
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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 ...
2 votes
1 answer
63 views

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 ...
2 votes
2 answers
251 views

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 ...
3 votes
0 answers
637 views

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. ...
4 votes
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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 ...
11 votes
5 answers
6k views

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 ...
2 votes
2 answers
179 views

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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1 answer
65 views

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 ...
3 votes
0 answers
580 views

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 ...
5 votes
1 answer
279 views

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 ...
5 votes
1 answer
298 views

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 ...
2 votes
0 answers
63 views

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$^\star$? $$ \dot{x}_i = x_i \sum_{j=1}^n m_{ij} \frac{x_j}{|x|} $$ ...
42 votes
6 answers
55k views

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 ...
6 votes
1 answer
105 views

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 ...
2 votes
2 answers
4k views

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 ...
2 votes
1 answer
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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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