Questions tagged [population-genetics]
Questions related to the study of the distributions and changes of allele frequency in a population.
323
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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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0answers
24 views
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 ...
2
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1answer
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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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0answers
12 views
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 ...
0
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1answer
79 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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42 views
How to figure out frequency of genotypes in generation n+1 AFTER figuring out the recombinants?
I have something that I want to make sure that it makes sense. I am not an expert on population genetics
For example:
I have population at generation 1 individuals : (A,A,B,D)
I know that there was 1 ...
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0answers
26 views
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 ...
2
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2answers
119 views
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 ...
0
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1answer
32 views
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
40 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
64 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 ...
3
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1answer
77 views
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 ...
3
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0answers
40 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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1answer
52 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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0answers
14 views
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 ...
2
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1answer
57 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 ...
3
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1answer
75 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 ...
2
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1answer
64 views
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
60 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
67 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?
4
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0answers
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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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0answers
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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) ...
1
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1answer
62 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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0answers
60 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
35 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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2answers
93 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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0answers
50 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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0answers
334 views
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 ...
3
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2answers
119 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 ...
0
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0answers
58 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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1answer
61 views
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.
2
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2answers
42 views
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 ...
1
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1answer
43 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 ...
0
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1answer
67 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” ...
2
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2answers
111 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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2answers
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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
37 views
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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1answer
47 views
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
114 views
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
29 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?
1
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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 ...
1
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1answer
28 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 ...
0
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1answer
53 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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0answers
165 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 ...
0
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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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0answers
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 ...
