Questions tagged [population-genetics]

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

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2
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0answers
34 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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1answer
172 views

Identity by descent among unrelated individuals

I was reading a couple of papers which talk about IBD (Identity by descent) among unrelated individuals (for eg. http://www.pnas.org/content/109/4/1193.long). However they do not seem to clearly ...
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677 views

Microsatellites and Minisatellites: Which of these form the basis of DNA fingerprinting?

I'm in a fix. Prepare yourself for a long read We've just learned about minisatellites and microsatellites at class (okay, by "learned", I mean we were told their definitions and essentially ...
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2answers
115 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 ...
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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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1answer
141 views

$F_{ST}$ when considering a multi-allelic locus

Sewall Wright defined the $F_{ST}$ in a metapopulation as being: $$F_{ST} = \frac{\text{Var}(p)}{\bar p (1-\bar p)}$$ , where $p$ is a vector of frequencies of a given allele and $\bar p$ and $\text{...
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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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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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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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2answers
529 views

How to interpret McDonald-Kreitman test results?

It is easy to get the numbers right and calculate neutrality index. It is easy to memorize "equals", "greater", "lesser", etc. At least on the exams, when certain level of simplicity is assumed. But ...
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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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2answers
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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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34 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 ...
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92 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 ...
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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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Is this formula describing the loss of unfixed genes from a population accurate?

In the 1954 science fiction novel Search the Sky by Frederick Pohl and Cyril M. Kornbluth, a formula is featured that "quantitatively describes the loss of unfixed genes from a population". $$L_T=L_0 ...
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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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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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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
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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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1answer
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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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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) ...
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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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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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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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1answer
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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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Why is the strength of genetic drift inversely proportional to the population size?

I saw a concept on the Internet that says "the strength of genetic drift is inversely proportional to the population size". I don't know why they are inversely proportional? Can somebody explain? ...
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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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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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What is the probability of fixation for a mutant under fluctuating selection?

Here is an answer which explains how one can model the frequency of an allele that is under fluctuating selection (the selection that varies through time). Not, thinking about fluctuating selection, ...
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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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274 views

Are Richard Lynn's estimates of African IQ inherently innacurate on the basis that most Africans aren't mentally retarded?

I've been looking at Richard Lynn's studies on average African IQ, and he seems to estimate really low IQs in the 60s range (e.g. http://www.sciencedirect.com/science/article/pii/S0160289609001275?via%...
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1answer
144 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 ...
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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 ...
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794 views

How is “selection” best defined?

There is natural selection but there is also sexual selection which some regard as a category of natural selection. There is also artificial selection (by humans). The question is, what is a most ...
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221 views

Mathematical models of lineage selection

I'm interested in the concept of lineage selection (Aboitiz, 1991) as an explanation for why traits would be selected for that enhance the rate at which evolution can occur, rather than directly ...
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1answer
27 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 ...
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1answer
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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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1answer
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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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157 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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27 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 ...
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1answer
28 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 ...
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1answer
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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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