Questions tagged [population-genetics]

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

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29 views

Is Panmixia very rare?

I'm reading the wikipidia page on Panmixia. Panmixia (or panmixis) means random mating. A panmictic population is one where all individuals are potential partners. This assumes that there are no ...
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Why dont the key colors match up with the nodes on my MJN network in PopART?

When I run the MJN in popART the key colors don't match up with the nodes on the network. For example, The key color for "Asia" is green but on the network, other populations are showing up ...
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43 views

Estimates of historical human population size

What are the estimates of minimum historical human population size, and how are they obtained from the current human genetic diversity? I seem to recall a Scientific American article from over 30 ...
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What new information does PheWAS add beyond GWAS?

I am trying to understand Phenome-Wide Association Study (PheWAS). If I understand correctly, PheWAS appears to be just the reverse of GWAS (finding gene-trait associations using traits instead of ...
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1answer
42 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 ...
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1answer
69 views

Rigorous definition of the kinship coefficient and proof of a recursion thereof

I am reading Section 5.2, Kinship and Inbreeding Coefficients, of Kenneth Lange, Mathematical and Statistical Methods for Genetic Analysis. There the kinship coefficient $\Phi_{i,j}$ is defined for ...
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What are the long term consequences of settling an isolated territory with an extremely limited gene pool?

I remember reading about a discredited theory - I'm afraid that, despite some frantic Googling, I've been unable to track down a link - which stated that Australia was first settled by a woman, ...
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54 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 ...
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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?
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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 ...
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Lineage inference based on N randomly partitioned copies of a gene

I am interested in reconstructing cell lineages based on the sequences of randomly partitioning plasmids. I can find lots of models to build lineages based on a single sequence (e.g. bacterial gene) ...
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1answer
44 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 ...
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58 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 ...
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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 ...
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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 ...
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48 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 ...
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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 ...
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2answers
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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 ...
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56 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(...
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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 ...
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1answer
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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 ...
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1answer
36 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.
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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 ...
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1answer
36 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 ...
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46 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?
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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” ...
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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 ...
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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 ...
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1answer
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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?
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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 "...
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2answers
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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 ...
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1answer
27 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?
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1answer
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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 ...
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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 ...
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1answer
52 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 = ...
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161 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 ...
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1answer
32 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 ...
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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 ...
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1answer
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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 ...
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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 ...
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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 ...
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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 ...
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1answer
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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 ...
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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 ...
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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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What is difference between Incest and Inbreeding? [closed]

Are they the same? As both are related to sexual activity between close relatives.
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54 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 ...
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1answer
58 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. ...
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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 ...
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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 ...

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