Questions tagged [population-genetics]
Questions related to the study of the distributions and changes of allele frequency in a population.
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Why isn't speciation a negative feedback loop?
To rephrase my question more articulately:
Speciation begins when two groups within a species starts to become reproductively isolated, and is complete when the two groups can't interbreed (for the ...
3
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Why is Fst/1-Fst used when calculating isolation by distance?
In population genetics a common analysis when considering the genetic structure of a population is to examine isolation by distance - the relationship between the genetic difference and the geographic ...
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What are the Genes/Enzymes responsible for the supposedly stark between-individual differences in lethargy after eating starches?
Andrew Huberman claims in one if his podcasts episodes that:
[...] because starches cause the release of serotonin in the brain and lend themselves to a state of sleepiness.
Now, I should mention ...
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1answer
92 views
Method of determining base values of traits in isolated populations
Prelude: I came across a discussion about the correct formula for calculating the average IQ of offspring, which goes something like the following
$$ 100 + \frac35 \left( \left(\text{father's IQ} + \...
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53 views
Genetic evolution without crossover
Can someone please point me to the origin of the system of coupled differential equations (1) in Section 2 of Shahshahani's book$^\star$?
$$ \dot{x}_i = x_i \sum_{j=1}^n m_{ij} \frac{x_j}{|x|} $$
...
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Saving a Maize Landrace from Inbreeding Depression
I have 10 seeds of a rare corn landrace. I probably won't be able to acquire more and the cultigen's long term fate is unknown. So, I want to do my best to preserve it for future generations.
Corn is ...
6
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1answer
90 views
Viruses in human history
How much do we know about ancient viruses and the viral evolution throughout the human history?
To my knowledge the HIV history has been rather well documented for about hundred years back (e.g., see ...
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1answer
45 views
Ancestral inference from demographic data
The question is inspired by this one, in the History community:
We consider a population, whereas the data we have the number of migrants arriving every year, as well as the initial and the current ...
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42 views
If crossing over can cause formation of new allele, can it affect Hardy-Weinberg equilibrium?
I was reading about Hardy-Wienberg equilibrium on Wikipedia and there are seven assumptions underlying HW
It is mentioned that sexual reproduction one of the assumption and is a must for HW, but ...
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1answer
62 views
Do mutations that cause the loss of a complex trait occur more often than mutations causing gain of a complex traits?
The Wiki entry on the evolution of biological complexity states that "[m]utations causing loss of a complex trait occur more often than mutations causing gain of a complex trait". There is ...
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What is the methodogy used to determine the exact genetic flow from one area to another and the times in which it flowed?
For example, I take the instance of Central Asian migration into India.
Say geneticists studied a) ancient bones in CA b) ancient bones in India c) living people in Central Asia d) living people in ...
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1answer
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What would cause red-haired people to become fewer?
There is this misconception that red-haired people are going to die out. This person on the Internet ("howstuffworks") also connected it to a marketing campaign of a hair dyer company. But I'...
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Genotype frequency mating question (Hardy Weinberg): X * 2Y = 4XY?
This question relates to the Hardy-Weinberg equation in some ways. I must be missing some biological insight as to how this arises.
Suppose that the genotype frequencies are AA, Aa, and aa with ...
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1answer
55 views
Nonlinear (Quadratic) selection gradients formula
Under scenarios of stabilizing or disruptive selection, we can add a quadratic component to our model of phenotype and fitness like so.
Specifically, I am not clear on where the 1/2 comes from nor do ...
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1answer
101 views
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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1answer
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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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1answer
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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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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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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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1answer
45 views
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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1answer
127 views
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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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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1answer
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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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1answer
45 views
'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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1answer
87 views
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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1answer
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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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1answer
62 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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1answer
68 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
78 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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1answer
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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
78 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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1answer
142 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?
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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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1answer
74 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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63 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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0answers
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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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2answers
132 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 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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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
38 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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2answers
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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
62 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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1answer
110 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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2answers
118 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 ...
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113 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 ...
