Questions tagged [population-genetics]
Questions related to the study of the distributions and changes of allele frequency in a population.
295
questions
4
votes
1answer
43 views
Neisseria meningitidis transformation into a pathogen
I read the wikipedia article about Neisseria meningitidis, and it says that
N. meningitidis is a part of the normal nonpathogenic flora in the nasopharynx of up to 5–15% of adults
In some cases ...
1
vote
1answer
32 views
What percentage of Americans have Native Indian ancestry? [closed]
What percentage of americans have native indian ancestry?
I tried to find the answer online and it's difficult to search for.
2
votes
1answer
22 views
If number of children born were spread more evenly among all parents, would our species' genetics have more variability?
Instead of some parents having lots of kids, if the number of kids were spread more evenly to parents having few kids and people who have no children, would it introduce more genetic variability in ...
0
votes
0answers
34 views
What are the consequences of less DARC expression as a result of a Duffy weak allele?
According to codegen.eu I'm a carrier of a Duffy weak allele. For SNP rs34599082 I have alleles C and T. T is a rare allele that found is less thatn ~1% of the population.
Codegen.eu directs me to ...
1
vote
1answer
25 views
Why is the variance of the Wright-Fisher model not equal p(1-p)/(2N)?
I was looking at the properties of the Binomial probability distribution and it says that the variance is np(1-p). In population genetics, n = 2N. So I would expect ...
0
votes
1answer
29 views
What does the MAF/MinorAlleleCount mean?
I'm not sure why reporting the second most frequent allele is helpful?
what is the Major allele?
0
votes
0answers
13 views
Finding genotype/allele frequencies of second generation in Hardy-Weinberg equilibrium given that the recessive allele is deleterious [duplicate]
A population in Hardy-Weinberg equilibrium has p=0.6 and q=0.4, and allele q (recessive) is deleterious. If 25% of heterozygous individuals and 50% of homozygous recessive individuals die before ...
2
votes
0answers
38 views
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” ...
1
vote
1answer
54 views
What proportion of the people who lived 1000 years ago have genetic descendants alive today?
For context, I've been wondering about this for a paper I'm writing (in philosophy). Really, I want to figure out the chances that someone alive today will end up still having descendants 1000 years ...
0
votes
0answers
18 views
How can I calculate Fst, Gst, and Nei diversity index?
I got different polymorphisms of Cucumber mosaic virus in different regions of its genome from different libraries of RNAseq.
This virus have two coding regions which are 3A and CP regions.
I have ...
0
votes
2answers
43 views
What's the difference between reaction norms and phenotypic plasticity?
I'm trying to understand better these two concepts, but I cannot see a clear difference yet.
Reaction norm: "set of phenotypes that can be produced by an individual genotype when exposed to different ...
-1
votes
1answer
27 views
difference between population genetics and genomics
I don't have a biological question therefore, this might be be quite basic. But I want to know does genomics entail population genetics or these are completely different fields?
1
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1answer
42 views
What is the cause of “imbalanced” linkage disequilibrium?
With perfect linkage disequilibrium ($D' = 1, R^2 = 1$), you might have the following table of counts for the alleles:
B b
A 100 0
a 0 100
With "...
1
vote
2answers
84 views
In marine DNA viral diversity studies, what would “paradigm of rampant mosaicism” refer to?
The recent paper in Cell Marine DNA Viral Macro- and Microdiversity from Pole to Pole describes the (huge) new Global Ocean Viromes 2.0 (GOV 2.0) dataset.
In the Results and Discussion section, the ...
1
vote
1answer
26 views
Increase rate of change in coding regions?
If a sequence is under selection will it acquire more changes over time because of faster fixation than if changes were neutral? Is this true or am I missing something?
1
vote
1answer
16 views
How to derive the Equilibrium value $\hat F$ equation
In population genetics, there is a relationship between $\hat F$ and $Nm$.
$\hat F=\frac{1}{1+4Nm}$
In population genetics textbook, (i.e. Hartl, D. L., and A. G. Clark. 2007. Principles of ...
1
vote
1answer
25 views
Repopullation after a mass extinction [duplicate]
Is it possible to restart the whole human species with less than 10 individual.
let say that the whole human species was wipe out of the surface of the earth by a catastrophe only 8 different couple ...
0
votes
1answer
51 views
Is it trivial to assume a version of Hamilton's rule that applies for numerous generations?
Is it trivial to assume that a version of Hamilton's rule that applies to numerous generations is:
C > rB
C = lineage fitness lost by an actor,
B = lineage fitness gained from the act, and
r = ...
2
votes
0answers
106 views
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 ...
0
votes
0answers
19 views
Population structure from mtDNA sequence data: A thought experiment
I have 5'-COI sequences for a species of interest, which were downloaded from the Barcode of Life Data (BOLD) systems.
Assuming for the moment that the said species was sampled across its entire ...
0
votes
1answer
30 views
For allele frequency determination, is it good to take samples from a college/school or a hospital or any other technique?
I am trying to determine allele frequency of a hla allele. Preliminary analysis shows the prevalence of the allele (homo or heterozygous both) is 3%. The allele is related to a disease (After exposure ...
0
votes
0answers
26 views
Selection coefficient of gorillas
I've been reading about selective sweeps. And I found a case study that talks about drosophila and how their selection coefficient is between 0.0001 and 0.005.
I want to know what it'll be like for ...
0
votes
1answer
23 views
Finding specific genotype occurrences given allele frequency
So let's say I have a tetraploid species and I have 4 possible alleles for a particular locus. I have found that I can have 35 total possible genotypes and I know the allele frequencies for each of ...
0
votes
1answer
21 views
Pentaploid genotype frequencies
I know that if I am dealing with a diploid case, and I have 3 alleles, then I can have 6 possible genotypes. I am doing this by adding up all the numbers from 1 to 3. $$1+2+3 = 6$$
But if I want to ...
1
vote
0answers
25 views
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 ...
1
vote
0answers
27 views
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 ...
1
vote
1answer
51 views
Balancing selection vs introgression?
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 ...
0
votes
1answer
44 views
Gene frequency — database/site
Is there any free database when one can check the gene frequency in a healthy population? For example I would like to check it for genes like BIN1, CLU or CR1. On the English Wikipedia I found a gene ...
0
votes
1answer
32 views
Simple interpretation of effective population size?
I'm looking for alternate ways to explain effective populations size, in more conceptual terms. These need not be perfectly accurate "definitions" but should at least be generally accurate in non-edge ...
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votes
2answers
1k views
What is difference between Incest and Inbreeding? [closed]
Are they the same? As both are related to sexual activity between close relatives.
0
votes
2answers
52 views
Equation relating probability of fixation and number of generations
I am trying to find an equation that relates the variables of probability of fixation and generations. Or, how does number of generations affect the probability a gene will fix, if population size ...
0
votes
1answer
55 views
What is the population limit that makes consanguinity an issue?
A recent incident brought in the news one of the last uncontacted people - the Sentinelese:
the Sentinelese appear to have consistently refused any interaction
with the outside world.
...
4
votes
0answers
102 views
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 ...
3
votes
0answers
46 views
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 ...
0
votes
1answer
46 views
Why does the HLA show a high degree of polymorphism?
I know how the HLA undergoes high degree of polymorphism (random genetic rearrangements), but I have not understood why it undergoes rearrangements. What is the advantage offered when HLA shows a high ...
1
vote
0answers
33 views
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 ...
1
vote
0answers
25 views
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 ...
1
vote
0answers
46 views
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
...
2
votes
1answer
47 views
Linkage between chromosomal loci and the Hardy-Weinberg principle
Referring to the Hardy-Weinberg principle, which is always stated with respect to a particular locus on the chromosome, if we observe that two different loci are either always together in Hardy-...
20
votes
4answers
4k views
Are mutations a source of genetic variation?
Here is a question from the book SAT II Success Biology E/M (where the SAT is the exam taken by the American high school students):
Which of the following statements is true about mutations?
(A) ...
1
vote
1answer
36 views
Is it appropriate to say “selection of” or “selection for” an allele that evolves by genetic hitchhiking?
In terms of Sober's selection of/selection for distinction, is it appropriate to say that there was selection of or selection for an allele that evolved by hitchhiking? I am inclined to say selection ...
11
votes
1answer
139 views
Discrepancy in time for genetic differences between human and chimpanzee to accumulate
Genetic differences between human and chimpanzee include ~50,000 amino acid changes, ~30,000,000 point mutations in non-coding sequences, and millions of insertions, deletions, inversions, genomic ...
1
vote
0answers
33 views
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 ...
2
votes
1answer
150 views
Fst genetic distance: Autosomal vs. mtDNA
As far as I'm aware, mtDNA is only inherited from the mother. Hence, if I compute Fst from autosomal SNPs, then I'll get the actual genetic distance between two human populations.
If I compute the ...
2
votes
0answers
18 views
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 ...
-1
votes
2answers
142 views
Why the SNPs from the earliest human haplogroups are missing in people outside of Africa if they are infact the descendants of it?
The SNPs M91, P97, M31, P82, M23, M114, P262, M32, M59, P289, P291, P102, M13, M171, M118 from haplogroup A and SNPs M60, M181, P90 from haplogroup B are missing in people without recent African ...
1
vote
0answers
30 views
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 ...
5
votes
1answer
221 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
0answers
29 views
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 (...
2
votes
0answers
48 views
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 ...
