Questions tagged [population-genetics]
Questions related to the study of the distributions and changes of allele frequency in a population.
353
questions
1
vote
1
answer
107
views
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 ...
- 177
0
votes
1
answer
582
views
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?
- 155
4
votes
0
answers
69
views
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 ...
- 163
1
vote
1
answer
86
views
How do we formulate the mutational load for "junk DNA"?
Question(s)
Based on Joe Felsenstein's textbook, I was trying to formulate the mutational load for the majority of eukaryotic genomes that are junk DNA ($L_{most\_of\_genome}$). (See background ...
- 9,152
0
votes
0
answers
111
views
How can we calculate the constants of the SIR model?
I am not a biologist by profession, but I am attempting to implement a simple SIR model from the following paper. The paper assumes the following constants are known:
rc = growth rate of ...
- 109
1
vote
0
answers
53
views
Probabilities in calculating the kinship coefficient
I've been reading up to try to understand how the kinship coefficient (or coefficient of coancestry) is calculated. https://brainder.org/2015/06/13/genetic-resemblance-between-relatives/ this is the ...
- 11
0
votes
2
answers
99
views
Can the apparent drop in insect population be explained by local insects evolving to avoid traps?
In this widely reported Plos One article, it is stated that, after roughly 3 decades of placing Malaise traps in a set of predetermined locations (counting and replacing them regularly), a sharp ...
- 111
0
votes
0
answers
73
views
Will a less favorable allele's frequency go to 0?
For example, a pond is dark in color. There are two alleles. The dark color allele is dominant over the light color one. Let's assume that the relative fitness of both the homozygous dominant and ...
- 101
1
vote
0
answers
403
views
What are the differences between internal organs between sub-saharan Africans and Northern Europeans
Lets take as examples a typical Norwegian and a typical Nigerian.
In terms of human anatonomy the outer differences are more obvious e.g. (on average)
White skin vs dark skin
Pointy nose vs broad ...
- 889
5
votes
2
answers
194
views
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 ...
- 153
0
votes
0
answers
71
views
Why do individuals vary in the number of SNPs for a given gene ( e.g. FOXO3A )?
Individual #1, sequenced by 23andMe and then inputed into Promethease for SNP data has the following SNP output:
1) rs1935949(C;T)
2) rs2802292(G;T)
3) rs13217795(C;T)
4) rs13220810(C;T)
5) rs2764264(...
4
votes
1
answer
74
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 ...
- 141
0
votes
1
answer
316
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.
- 10.3k
2
votes
2
answers
52
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 ...
- 121
1
vote
1
answer
147
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 ...
- 808
0
votes
1
answer
206
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?
- 1
2
votes
0
answers
55
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” ...
- 121
2
votes
2
answers
149
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 ...
- 23
0
votes
2
answers
304
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 ...
- 103
-1
votes
1
answer
81
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?
- 141
1
vote
1
answer
83
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 "...
- 133
1
vote
2
answers
201
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 ...
- 5,094
1
vote
1
answer
30
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?
- 53
1
vote
1
answer
18
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 ...
- 808
1
vote
1
answer
34
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 ...
- 135
0
votes
1
answer
59
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 = ...
- 466
2
votes
0
answers
231
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 ...
- 121
0
votes
1
answer
34
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
0
answers
28
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 ...
- 1
0
votes
1
answer
97
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 ...
user37831
0
votes
1
answer
24
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 ...
user37831
2
votes
0
answers
33
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 ...
- 717
1
vote
0
answers
37
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 ...
- 111
1
vote
1
answer
121
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 ...
- 19
0
votes
1
answer
70
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 ...
- 1
0
votes
1
answer
60
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 ...
- 126
-2
votes
2
answers
9k
views
What is difference between Incest and Inbreeding? [closed]
Are they the same? As both are related to sexual activity between close relatives.
- 7
0
votes
2
answers
132
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
1
answer
71
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.
...
- 1,665
3
votes
0
answers
117
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 ...
- 463
3
votes
0
answers
57
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
1
answer
88
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
0
answers
37
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 ...
- 11
1
vote
0
answers
29
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
0
answers
58
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
...
- 11
2
votes
1
answer
161
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-...
- 21
20
votes
4
answers
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) ...
- 297
0
votes
1
answer
46
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 ...
- 466
12
votes
1
answer
206
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 ...
- 121
1
vote
0
answers
91
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 ...
- 63