All Questions
Tagged with genetics population-genetics
152 questions
2
votes
1
answer
546
views
How to get the average number of pairwise differences among populations?
I have genetic data in .structure and .vcf format (and can easily reach other formats with PGDSpider). The population of interest is structured and I would like to calculate the average number of ...
- 68.3k
2
votes
2
answers
4k
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How to confirm pure-breeding parents
I was reading Genetic Analysis (Sanders, Bowman) and saw the following figure summarizing the 1909 work of Herman Nilsson-Ehle in describing the genetic control of kernel color in wheat:
How did ...
- 121
0
votes
1
answer
55
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Reconstituting genomes of archaic tribes of humans
Will it be logically possible for genome studies to reconstitute the genomes of our local human populations as they were 2000 and 4000 years ago? What is the mathematical precision and science for ...
- 10.5k
2
votes
1
answer
91
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Confusion over equations for population's heterozygosity vs. heterozygous individuals
On page 24 of Gillespie's Population Genetics, 2nd ed, an equation for $H$, the probability that two randomly drawn alleles are different by state, is given.
$H$ is stated to be similar to the ...
- 75
2
votes
1
answer
119
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Is it possible to have a random un-mutation of genes?
According to this article:
Gene mutations can be classified in two major ways:
Hereditary mutations are inherited from a parent and are present throughout a person’s life in virtually every cell in ...
- 133
1
vote
1
answer
602
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ExAC Browser: What does a "dubious variant annotation" mean? [closed]
I am studying a protein in the ExAC browser. However it is flagged with a "LoF flag". What exactly counts as a "dubious" variant in ExAC.
I couldn't find any further information neither at the ...
- 111
-1
votes
1
answer
637
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Why was the study of "Concordance of Monozygotic and Dizygotic twins for traits" designed in this way? [closed]
I am confused by the twin study 'Concordance of Monozygotic and Dizygotic twins for traits.' My questions arose from 3:17-4:17 of the video
And this is the related data I have referred
I have ...
- 99
0
votes
0
answers
121
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Hybridization of an Indo-Aryan ethnic group and a Tibeto-Burmese ethnic group
The state in which I reside houses these two distinct ethnic groups.
Physical Traits of the Indo-Aryan group
Height:Medium
Eyes:does not posses epicanthic fold
Nasal bones:is not flat and broad
...
user21998
3
votes
0
answers
123
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What is the effective population size of a simple two deme metapopulation?
I am confused as to how to compute the effective population size $N_e$ of a theoretical structured population. Let's consider here a simple case study.
Imagine a 2-deme metapopulation. Each deme is ...
- 68.3k
1
vote
2
answers
466
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Are heterozygotes always fitter than homozygotes? Can inbreeding be beneficial?
Inbreeding is mostly not very good because when there is a 'disease' in one allele, the other could/would take over the function. But when you have two of the same genes/alleles, do they, or could ...
- 2,765
0
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1
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123
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How are the dominance and additive effects reflected in the mean and variance of the offsprings of two individuals with known phenotype?
If I estimated the genetic additive σ2A, genetic dominance σ2D and environmental effect σ2E of a trait in a population, what will be the predicted value of the offsprings of two individuals with known ...
- 258
3
votes
1
answer
9k
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What are Codominant vs Dominant Genetic Markers?
When talking about types of genetic markers, the adjective "dominant" and "codominant" are often used. I don't fully understand their definitions and found contradicting definitions.
Foll and ...
- 68.3k
2
votes
1
answer
280
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Statistical genetics: Allele frequencies that follow a Dirichlet distribution
From Foll and Gagiotti (2008) (software BayeScan). They consider a model where several subpopulation are derived from a unique ancestral population.
We consider a set of $I$ loci and let $K_i$ be ...
- 68.3k
1
vote
1
answer
149
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autosomal recessive population numbers
This question is background research for a science fiction / fantasy novel, my knowledge of genetic is very basic.
It seems obvious to me that for genetic disorders that are autosomal recessive, if ...
- 113
2
votes
1
answer
390
views
Relationship between genetic diversity within and between species
Here is a quote from Wagner (2008)
A second line of evidence [against neutralism] comes from the relationship between the mean number of polymorphic differences between alleles within a species, $\...
- 125
3
votes
0
answers
271
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Population size and genetic drift - What are the evidences?
Wright-Fisher model
From the Wright-Fisher model of genetic drift, the random sampling of allele from one generation to the next is taken from a binomial distribution with parameters $2N$ and $p$, ...
- 68.3k
3
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0
answers
117
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Is $F_{ST}$ a probability and a correlation coefficient?
$F_{ST}$ is one of the most famous and most important statistics of all of evolutionary biology. Yet, many people misunderstand it or misuse the classical results from the literature on $F_{ST}$ (...
- 68.3k
3
votes
0
answers
697
views
How should one interpret heritability? Is it related to $R^2$?
From Wikipedia:
Heritability estimates are often misinterpreted if it is not understood that they refer to the proportion of variation between individuals on a trait that is due to genetic factors. ...
- 93
0
votes
1
answer
83
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"Heterozygotic expection" - when heterozygote differs from both homozygotes, but homozygotes are similar
For simple 2-alleles genetic model {a,A} and corresponding quantitative trait Q is typically true that
Q(aa)>=Q(aA)>=Q(AA)
or conversely
Q(AA)>=Q(aA)>=Q(aA).
For example, dominance means that Q(...
- 103
2
votes
1
answer
244
views
What test to apply to detect genomic signatures of selection?
I would like to ask you for your sugestions for selecting a test to detect signatures of selection in the following mouse model:
We have three groups: animals exhibiting trait A, trait B and controls....
- 185
5
votes
2
answers
738
views
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 ...
- 8,798
8
votes
1
answer
3k
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Effect of sex-ratio on the effective population size
As stated on this wikipedia article, the effective population size $N_e$ when the sex ratio differs from $\frac{1}{2}$ is
$$N_e = \frac{4N_mN_f}{N_m+N_f}$$
I understand the biased sex-ratio ...
- 68.3k
6
votes
1
answer
347
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Diffusion approximation to genetic drift
I am reading from the classical textbook Principles of Population Genetics, Hartl and Clark (pdf here).
Introduction
Let $f(p,x,t)$ denote the distribution of allele frequency $x$ at time $t$ ...
- 68.3k
2
votes
2
answers
3k
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What is the difference between fixation and loss of alleles in a population?
When running a simulation in PopG, with parameters:
Population size: 100
AA fitness: 1.0
Aa fitness: 1.0
aa fitness: 1.0
Mutation A to a: 1.0E-6
Mutation a to A: 1.0E-6
Migration rate between ...
- 133
1
vote
1
answer
67
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Genetics of Hybrids
I'm working on this problem, but I'm not sure I've done it correctly. My initial thought was that the answer was $D$, but I don't see anything in the above graph that indicated the Hybrid species is,...
- 171
5
votes
1
answer
533
views
What is meant by "the degree to which a gene is expressed" in an individual?
Here is an excerpt from a text that I was reading,
Here is an example of microarray data. The idea is to take a group of
different individuals and for each of them, you measure how much they
do ...
- 153
3
votes
1
answer
1k
views
Is the fixation rate always equal to the mutation rate for neutral alleles?
Background
A classical result of population genetic is that the rate of fixation of netreual alleles is the mutation rate $\mu$. The reason is that each generation $PN_e\mu$ mutations enter the ...
- 68.3k
3
votes
2
answers
490
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Disease causing variants and Hardy-Weinberg Equilibrium
Is it true that many disease causing variants/mutations do not follow Hardy Weinberg Equilibrium? If so, then please elaborate on why this may be true (or not) and provide examples.
I am interested ...
- 33
4
votes
1
answer
828
views
How could one calculate the gene flow between two populations?
Imagine there are two populations X and Y, and for each population you have the genotypes of each individual in that population (e.g. Aa, AA, aa, etc.), but for multiple loci (e.g. AABb).
How could ...
- 3,597
4
votes
3
answers
5k
views
What exactly is extreme heterozygosity and how does it work?
What does the concept of "extreme heterozygosity" mean?
I first encountered this concept in "The Drunken Botanist". They describe that when planting a seed from, say, a 'red ...
- 383
7
votes
2
answers
224
views
Within and Between Allelic Class Diversity
I am reading Charlesworth et al. 1997. They talk about diversity within and between allelic classes.
Nucleotide diversities ($π$) at each neutral site were estimated from the mean of $2 \sum z_t (1-...
- 68.3k
1
vote
3
answers
461
views
What fraction of sites are expected to be polymorphic?
Question
Consider a very long (eventually infinite) DNA sequence of neutral sites. Consider a panmictic population of constant size $N$ with a per site mutation rate of $\mu$ where all individuals ...
- 68.3k
2
votes
0
answers
128
views
Efficient algorithm to calculate various population divergence statistics
Intro and description of the data
I am simulating the evolution of very long DNA sequences. The model works well, is performant and will output data in the following kind of fasta format
...
- 68.3k
1
vote
3
answers
2k
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Why is it $q^2$ for the individual count in hardy weinberg?
My understanding:
In Hardy-Weinberg problems the frequency of a homozygous recessive genetic occurrence in a population is $q^2$. So if 1 in 100 people in a population have albinism (homozygous ...
- 1,381
10
votes
3
answers
375
views
How is genetic speciation defined?
What determines speciation at a molecular level?
At what point does a scientist determine two lineages are different enough to be considered separate species?
Does it have a margin of error?
sophie silec
6
votes
1
answer
81
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How to seek for available genetic data relevant to ecology and evolution?
I had a quick look online. There seems to exist many different website of database archiving. Some data might be free of charge while some others might not be. I found things such as Dryad, TreeBase, ...
- 68.3k
4
votes
1
answer
163
views
The dominance variance on a single locus
I was reading the book "Genetics and Analysis of Quantitative Traits", by Lynch and Walsh. I how the covariance between two individuals with IBD $\Theta$ gets divided into just the additive variance ...
- 277
4
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1
answer
460
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Fixation rate at neutral loci
It is a classical result that the expected time for a neutral mutation to occur and to get fixed is $2 N \mu \frac{1}{2N} = \mu$, where $N$ is the population size and $\mu$ is the neutral mutation ...
- 68.3k
2
votes
0
answers
79
views
What is the expected number of children that need to be born for every possible point mutation to occur once? [closed]
I'm reading The Perfect Health Diet, and in it the author says that the probability of a point mutation is (175/3*10^9) per new child. He then goes on to write:
In the Paleolithic, with 100000 ...
- 161
5
votes
1
answer
8k
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After how many generations descendant is not more related to ancestor, than to a random individual in an ancestral population?
Descendant of n generation has on average 1/2n DNA of ancestor. (For example children have 1/2 DNA of parents and 1/4 DNA of Grandparents, After 10 Generation 1/1024 DNA and after 100 Generations 1/...
- 51
4
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0
answers
70
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Mechanisms of genotype*sex interactions [closed]
I'm looking for suggestions of the mechanistic level at which genotype*sex interactions can occur. These give different phenotypes from the same genotype dependent on the sex they are expressed in. ...
- 16.1k
5
votes
1
answer
1k
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Microsatellite shifts (peak calling) GeneMapper! Thesis help!
I'm a masters student attempting to conduct a parentage analysis on a population of fish for my thesis. My advisor and post-docs haven't been very helpful, so I need some help! I have dinucleotide ...
- 53
2
votes
1
answer
581
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Defining: Evolutionary (quantitative) Genetics and Population Genetics
How do we define the fields that are Evolutionary (quantitative) genetics and population genetics. What set these two fields apart? Can you try to provide definitions?
To my intuitive understanding, ...
- 68.3k
32
votes
4
answers
7k
views
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 ...
- 3,597
1
vote
1
answer
147
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Population Genetics Question
Can someone please help with this question? Here is my working (just in case it is not clear: 1/300*1/30*1/2) but is this actually correct or do I need to multiply by 0.5 once again? I appreciate any ...
- 103
1
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1
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179
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Quantitative Traits Genetics
Can someone please help with this question? I'm not so sure whether part A should be 11 inches or something else. Also, is part B correct
- 103
5
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1
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4k
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How do I calculate the change in allele frequency in a haploid population under selection?
From this book
For simplicity, let us consider a haploid organism and assume that the frequencies of alleles $A_1$ and $A_2$ are given by $x$ and $y=1-x$, respectively. We also assume that the ...
- 68.3k
7
votes
1
answer
2k
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Why does the slope of parent-offspring regression equals the heritability in the narrow sense?
Background
---- Notations and assumptions ----
let $W_{ij}$ be the fitness associated to the genotype $AiAj$. $x$ is the frequency of the allele $A1$ in the population. The frequency of the allele $...
- 68.3k
7
votes
1
answer
298
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Hill-Roberston effects and effective population size
From this article, first page, middle of the second column:
Even if harmful alleles do not become fixed, they can still reduce the efficacy of selection on neighbouring loci through a process ...
- 68.3k
7
votes
2
answers
3k
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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? ...
user5407