Questions tagged [population-genetics]

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

Filter by
Sorted by
Tagged with
0
votes
0answers
5 views

What software can I use to develop a population haplotype network? [migrated]

I want to prepare a haplotype network using Co1 mitochondrial sequence data to study population structure in Anopheles mosquitoes.
0
votes
0answers
18 views

Genetic diversity from meeting an isolated tribe?

Assume we make contact to a tribe we did not know existed. We understand the value of genetic diversity for our species. And as we had no contact for a long time, we can assume that the tribe adds to ...
4
votes
1answer
44 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
2answers
40 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
35 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
26 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
31 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
39 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
55 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
19 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
44 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
28 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
vote
1answer
43 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
87 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
114 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
31 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 ...
-2
votes
2answers
2k 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. ...
3
votes
0answers
104 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
47 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
34 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
47 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
48 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
5k 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
38 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 ...
10
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
35 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
158 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
19 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
143 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
232 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 ...