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Questions tagged [population-genetics]

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

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Calculating F_IS, F_IT on ancient DNA

I am trying to calculate genetic diversity within a handful of ancient communities. I have 1240K genotype data (made pseudohaploid), and I need to generate statistics to estimate the levels of genetic ...
dnv89's user avatar
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Why might allele frequencies change over many generations at neutral loci?

Lets say that a research team is looking at natural insect populations (e.g. beetle), and they find that allele frequencies at a locus in the genome have changed over the past few generations even ...
BananaGrams's user avatar
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What does it mean when observed genotype frequency is different from expected genotype frequency in Hardy-Weinberg equilibrium?

As I understand it, if a population is at Hardy-Weinberg equilibrium, then the genotype frequencies should be $$p^2 + 2pq + q^2 = 1,$$ given the allele frequencies of $p$ and $q$, which you can figure ...
geneticscodingnoob's user avatar
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In the context of GWAS we have an alternate allele and a reference allele. Why do we only have one possible alternate instead of three?

I recently started analyzing a GWAS summary dataset. It has a column for the reference allele in which it mentions the base in the reference genome. There is another column for the alternate allele (...
hgz's user avatar
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3 answers
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If you want to understand evolution from a genetics standpoint what are some must reads be it books or textbooks? [closed]

The question basically sums it up. I'm looking for books/textbooks that explain evolution from a genetic perspective.
Shannon T's user avatar
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Interpretation of narrow-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 ...
BigMistake's user avatar
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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.
Shannon T's user avatar
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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 ...
CXJ's user avatar
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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 ...
BigMistake's user avatar
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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?
BigMistake's user avatar
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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-...
jnolen's user avatar
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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 ...
statm's user avatar
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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 ...
OnLeRo's user avatar
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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 ...
abhijaat's user avatar
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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 ...
Mohan's user avatar
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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? ...
Shiran Yuan's user avatar
2 votes
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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 ...
ARGYROU MINAS's user avatar
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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 ...
Ron Snow's user avatar
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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 ...
Sanjay Biswas's user avatar
4 votes
2 answers
50 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 ...
arara's user avatar
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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 ...
Galen's user avatar
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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 ...
Luke B's user avatar
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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 ...
neurosciencecalc's user avatar
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1 answer
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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 ...
AnethOthbo's user avatar
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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 ...
Bionoob's user avatar
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1 answer
70 views

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 ...
Dahlai's user avatar
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2 votes
2 answers
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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 ...
geneticscodingnoob's user avatar
7 votes
1 answer
117 views

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 ...
Jeff's user avatar
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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 ...
Till Hoffmann's user avatar
4 votes
0 answers
43 views

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 ...
Nick O'Brien's user avatar
6 votes
2 answers
792 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 ...
cTen's user avatar
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3 votes
2 answers
184 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 ...
AnethOthbo's user avatar
3 votes
0 answers
731 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 ...
rainbird's user avatar
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5 votes
1 answer
286 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 ...
Florian Magin's user avatar
1 vote
1 answer
123 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(\frac{\text{father's IQ ...
Maximilian's user avatar
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$^\star$? $$ \dot{x}_i = x_i \sum_{j=1}^n m_{ij} \frac{x_j}{|x|} $$ ...
DavideL's user avatar
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5 votes
1 answer
144 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 ...
JOhnny's user avatar
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6 votes
1 answer
106 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 ...
Roger V.'s user avatar
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0 votes
1 answer
68 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 ...
Roger V.'s user avatar
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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 ...
Samardeep singh's user avatar
1 vote
1 answer
85 views

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 ...
alghazali's user avatar
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0 answers
70 views

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 ...
user1194497's user avatar
19 votes
1 answer
4k views

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'...
akraf's user avatar
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3 votes
1 answer
73 views

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 ...
user6817734's user avatar
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1 answer
105 views

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 ...
BentonB's user avatar
1 vote
1 answer
60 views

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 ...
Apis_delorean's user avatar
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1 answer
806 views

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 ...
got trolled too much this week's user avatar
34 votes
6 answers
7k views

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 ...
RedBaron's user avatar
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1 vote
0 answers
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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 ...
Quinn's user avatar
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2 votes
1 answer
137 views

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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