Questions tagged [population-genetics]

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

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Best book to read to understand human Genetics for a beginner?

I'm just a person who's interested in human genetics, genetic diseases and the human genome. I have some idea of genetics and humanity as a whole but it is not my profession. Just a hope
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Statistical test of H-W deviation

I have a set of genetic data consisting of alleles at several loci for a number of individuals. The number of alleles per locus varies from 3 to 8. It's an inbred population, so the observed ...
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Can a trait be too successful? Wouldn't overwhelmingly successful traits limit variability, which is one of the requirements of NS? [closed]

Can a trait be too successful? Wouldn't an overwhelmingly successful trait soon limit the gene pool, and if so, how would the process of natural selection react to that? If an individual is born ...
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Will Fst (inbreeding coefficient) always be a value close or at 0 in asexual populations?

FST is the average inbreeding coefficient of a total population. The equation is: $F_{ST} = \frac{Var(S)}{Var(T)} $ $Var(S)$ = variance in the frequency of the allele between different subpopulations, ...
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Population Genetics Using WGS: How do I know when I have enough individuals?

I am having a difficult time finding information about a minimum threshold for number of individuals to use in wgs pop gen analyses. Are there software or formulas/theory available to determine what ...
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Why didn't Escobar's hippos introduced in a single event die out due to inbreeding

Today I read a BBC Report about how Pablo Escobar had once imported 4 hippos (1 male, 3 female) into his estate in Colombia for his private zoo. After his downfall, while other species were shipped ...
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Are the “cocaine hippos” suffering from noticeable inbreeding depression? [duplicate]

Colombia has a population of about 100 "cocaine hippos" founded from a group of one male and three females, which escaped from a drug kingpin's private zoo; it's even estimated that this ...
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Blood and plucked-feather sample storage

This next field season I will be collecting both blood and feather samples and I wondered how best to store the samples. The blood samples will be used for microsatellite and/or SNP analysis. The ...
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Dominance coefficient

I am trying to understand the meaning of the dominance coefficient. I'll be more specific to what I don't understand, in a moment. Let $A_{11}$, $A_{12}$ and $A_{22}$ be genotypes with fitnesses $1$, $...
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Population genetics of pan-genome

I am beginning to work in the field of human gut microbiome, and wondering how (and if) the concepts of population genetics could be applied there. Considering the competition between the species ...
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Deviation from Hardy Weinberg equilibrium (HWE)

I have a set of 10 genes, each gene contains around 15 SNPs. I have tested the deviation from Hardy Weinberg equilibrium (HWE) for all SNPs. All of the SNPs didn't deviate from HWE, except 5 SNPs in ...
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Tradeoff between pathogen adaptability and infectivity

Is there a kind of inverse proportionality relation between a pathogen ability to infect new hosts and its ability to evade the immune defenses/medication? The background: The question is motivated by ...
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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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How does the availability of a reference genome aid in microsatellite analysis?

I'm planning to use microsatellites to examine fine-scale population structure between several breeding colonies of birds. Most of my DNA will be extracted from feathers and the yield isn't sufficient ...
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622 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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Can the mutation rate vary for individuals of the same species, growing in similar environments?

Suppose we consider several populations who originally inherited their genome from the same ancestor, and that we put for a few thousands generations in similar environments. Could the mutation rate ...
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Books on population or evolutionary genetics?

I have recently been involved in collaborations that require me to model the population genetics of eukaryotic populations. I fear I may either be "re-inventing the wheel" or making conceptual ...
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'Big ideas' behind constrained selective breeding (optimization)

I'm looking for help in finding the 'big ideas' behind a project I'm beginning and want to make sure I'm not missing anything since I wasn't trained in Biology. My idea is investigating constrained ...
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Hardy-Weinberg principle

The following paragraph on Wikipedia about the Hardy-Weinberg principle is bothering me. It should be mentioned that the genotype frequencies after the first generation need not equal the genotype ...
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Inbreeding of selfing and outcrossing plant

I am reading John H. Gillespie's Population Genetics A Concise Guide Section 4.3 Inbreeding. I do not understand these two paragraphs quoted below concerning selfing and outcrossing. The first ...
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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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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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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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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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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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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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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 frequent are selective sweeps?

Introduction Selective sweep is the most famous genetic signature of selection. We know of a number of classical examples of selective sweeps, some of them in humans. See the classical example of the ...
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Coalescent theory - independence of coalescent times

Let $T_i$ be the time to coalesce from $n(t)=i+1$ to $n(t)=i$, where $n(t)$ is the number of sites that have not coalesced yet. In the below example the maximum $n(0)=6$. As I understand it, many ...
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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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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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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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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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$F_{ST}$ 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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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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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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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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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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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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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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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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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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