Questions tagged [population-genetics]

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

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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.
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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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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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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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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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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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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 ...
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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 ...
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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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1answer
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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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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 ...
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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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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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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 ...
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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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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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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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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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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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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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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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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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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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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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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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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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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 ...
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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
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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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1answer
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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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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
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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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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 ...
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What are the consequences of inbreeding?

Inbreeding increases the risk of getting two identical recessive genes, alleles, that cause a disease which wouldn't have been activated with mixed genes. That's how I understand it anyway. But I ...
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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 ...
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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 ...
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Do mutant alleles result from mutation of the wild type?

The allele that encodes for the most common form of a phenotype in natural population is called a wild type allele and all the rest of the alleles encoding forms other than the wild type are called ...