Questions tagged [population-genetics]
Questions related to the study of the distributions and changes of allele frequency in a population.
353
questions
3
votes
1
answer
391
views
Fst genetic distance: Autosomal vs. mtDNA
As far as I'm aware, mtDNA is only inherited from the mother. Hence, if I compute Fst from autosomal SNPs, then I'll get the actual genetic distance between two human populations.
If I compute the ...
- 63
2
votes
0
answers
26
views
Is there an existing database of mutation rates for mitochondrial loci?
I'm wondering if there exists a database of mutation rates (transitions and transversions) for both mitochondrial loci (such as cytochrome c oxidase subunit I (COI)).
Due to the use of COI as a DNA ...
- 231
-1
votes
1
answer
228
views
Why the SNPs from the earliest human haplogroups are missing in people outside of Africa if they are infact the descendants of it?
The SNPs M91, P97, M31, P82, M23, M114, P262, M32, M59, P289, P291, P102, M13, M171, M118 from haplogroup A and SNPs M60, M181, P90 from haplogroup B are missing in people without recent African ...
- 125
1
vote
0
answers
34
views
The concept of high genetic load of disease and non-random segregation of deleterious variants
I'm new in this field. I was reading Shakeel et al. (2018) and came across the below sentences
The rate of emergence and distribution of deleterious variants in populations is important in ...
- 343
5
votes
1
answer
297
views
Simulating DNA sequences in R with a given value of $\theta = 4N_{e}\mu$
This might not be the most appropriate site to be asking such a question, but perhaps someone has a solution.
My question is: is there an R package or function for simulation of DNA sequences of a ...
- 231
2
votes
0
answers
30
views
Estimating population divergence time with a single mitochondrial marker
Is it possible to estimate population divergence time with a single mitochondrial marker?
Here is additional information for my specific case:
Mitochondrial marker: Cytochrome Oxidase Subunit 1 (...
- 245
2
votes
0
answers
60
views
Appropriateness of PCA to visualize clusters in genetic data
In many genetic studies, PCA is often utilized to examine genetic cluster in human populations. Rarely is the % variance reported for the components. With human data it's been my experience that the ...
- 63
1
vote
0
answers
17
views
Gene flow analysis with a single mitochondrial marker
I am currently studying a mud snail genus called Ecrobia. Several species of this genus occur in both the Mediterranean and Black seas. Therefore, I would like to investigate whether there is:
...
- 245
1
vote
0
answers
19
views
Is there any data to explore the heterozygosity of the South African lion over the last 18 years?
Background:
I need to find data on the heterozygosity of the south African lion over the last 18 years... and I'm struggling: so far I have found a single data point.
Question:
Where can I find ...
- 3,577
-1
votes
1
answer
57
views
Background selection and hitchhiking effect
As I read the maintenance or removal of an allele from a population is dependent upon the alleles in its linkage group; so, when an advantageous mutation occurs in the population, variation in nearby ...
- 343
2
votes
1
answer
2k
views
How to solve these kinds of problems?
16% of people in a population can not roll their tongue .what is the frequency of people which are heterozygous of this character? Please ,any one help and guide me to solve these kind of problems.
...
- 59
0
votes
1
answer
76
views
How much generation of hamster's family it takes to get first bad mutations [closed]
So if I have two humsters and they start to reproduce themselfs then how much generations of hamster's family it takes to get first bad mutations?
The info here does not help to find answer https://...
- 111
0
votes
1
answer
35
views
Looking for book or article that derives formula for estimating the "average heterozygosity"
An online lecture I need to watch on population genetics describes a formula for the "average heterozygosity" as follows:
...we can theoretically predict that the average heterozygosity in the ...
- 179
0
votes
1
answer
61
views
Chart of intra-species genetic diversity across species / phyla?
I am looking for information on how genetic diversity within a species (not between species) differs between taxa. In other words: Is the "spread" in the genetic pool, if measured, for instance, in ...
- 1
7
votes
1
answer
395
views
Easy derivation of Kimura's approximation for the probability of fixation of a mutation
Kimura's approximation for the probability of fixation of a mutation under selection finds recurrent use in population genetics models till date. I am trying to understand the mathematical basis of ...
- 35.2k
1
vote
0
answers
171
views
Coefficient of relatedness for a locus on the Z chromosome
So i know that the ZW determination system is the equivalent for XY in birds. Moreover, I know that the coefficient of relatedness between siblings for the X chromosome is 0.5 so im guessing that the ...
- 21
2
votes
0
answers
29
views
How does one go from a couple of DNA sequences to a distance-matrix?
For a project we need to explain the subject of UPGMA.
We think we understand thee method itself but I fail to see how you go from a number of DNA-sequences to the distance matrix.
I understand ...
- 121
2
votes
2
answers
95
views
What is the conversion between r and FST?
From Schonman (2013):
...allele A can only invade under Hamilton’s condition R=$F_{ST}$ > C/B.
From Harpending (2002):
The best general definition of the coefficient of relation $R_{XY}$ ...
- 466
0
votes
0
answers
36
views
What metric(s) is a good proxy for relatedness?
In attempting to seed a simulation, where an individual foregoes resources that go r to same-type individuals and (1-r) to all members (including same-type individuals). What commonly used metrics ...
- 466
4
votes
1
answer
716
views
Is there a distinction between the fisherian runaway theory and Fisher's sexy son theory?
In many websites/books they are referred to as part of the same process whereby:
"runaway" describing that the process continues even after traits become maladaptive
the "sexy son theory" explains ...
- 53
1
vote
0
answers
73
views
How can census population size be smaller than the effective population size in some species? is that possible?
The only way I can think this could happen is through a recent population bottleneck. Can it be possible though ?
- 21
0
votes
1
answer
169
views
Variation of fixation probability over time in Wright-Fisher model
In Wright-Fisher model of population size N and initial mutation frequency of 1/N, how does the fixation probability vary over generations. So, mathematically, what is the function that maps the ...
1
vote
0
answers
31
views
How does one calculate Rx/a in population genetics?
The ratio of sex-linked to autosome mutation frequencies (R) is Rx/a =(2/3)(2+ α)/(1+ α) for X-linked genes and Ry/a = 2 α /(1+ α) for Y-linked genes. How does one calculate Rx/a, in order to find α?
- 11
1
vote
0
answers
196
views
What is the coefficient of relatedness between a queen bee and her daughter if the male that mated with the queen was the queen’s own son? [duplicate]
What is the coefficient of relatedness between a queen bee and her daughter if the male that mated with the queen was the queen’s own son?
The answer should be 0.75, but I keep getting 1 because 0.5(...
- 196
6
votes
1
answer
543
views
Recommendations for textbooks on statistical and quantitative genetics, and genetic epidemiology
I'm looking for a textbook on statistical genetics, quantitative genetics, association mapping, and genetic epidemiology. My interests include, but are not limited to, complex trait analysis, and the ...
- 161
0
votes
1
answer
577
views
Island model vs. stepping stone model
Wright's Island model and Kimura's stepping stone model are classic explanations for migration/gene flow o individuals between subpopulations within the field of population genetics.
My question ...
- 231
1
vote
1
answer
75
views
The total numbers of mutations on different branches of gene tree are independent or not?
I was reading Tajima's 1989 paper on his test for neutrality.
Tajima, Fumio. "Statistical method for testing the neutral mutation hypothesis by DNA polymorphism." Genetics 123.3 (1989): 585-595.
...
3
votes
1
answer
122
views
Practical Question about Evolution, Population Genetics and Speciation
North American cicada male of the genus Magicicada sing depending on the species at different times of the day and attract the females of the corresponding species. The species are very similar, but ...
0
votes
1
answer
33
views
Low migration rate in Papadopoulou et al. (2008)
In the paper "Speciation and DNA barcodes: testing the effects of dispersal on the formation of discrete sequence clusters" by Papadopoulou et al. (2008), is there an explanation as to why the authors ...
- 231
1
vote
1
answer
1k
views
What would be the Hardy-Weinberg equilibrium condition for a population of haploid organism?
What would be the Hardy-Weinberg equilibrium condition for a population of haploid organism?
Would it always be in Hardy-Weinberg equilibrium?
1
vote
1
answer
267
views
What is a "segregating gene"?
What does the term "segregating" mean in references like the following:
"found 42% of a random sample of loci to be segregating"
"15 blood group systems are known to be segregating"
user39327
1
vote
1
answer
70
views
Simulating Migration in SimBit Software Program
How is migration incorporated into the SimBit program of Remi Matthey-Doret and Michael Whitlock?
Is an island model or stepping stone model assumed?
- 231
3
votes
1
answer
1k
views
What is the difference between nucleotide polymorphism (θ) and nucleotide diversity (π)?
In my population genetics book (see reference at bottom) they define them as:
Nucleotide polymorphism (θ): proportion of nucleotide sites that are expected to be polymorphic in any sample of size 5 ...
- 808
1
vote
2
answers
70
views
Geographic regions as subpopulations/demes
I am developing a computational simulation for DNA barcoding. One of the parameters in my simulation is the number of subpopulation/demes, which I label as $K$. Most studies that use DNA barcodes tend ...
- 231
0
votes
1
answer
82
views
What is the probability that there are no substitution between an ancestor and a modern individual?
What is the probability that there are no differences if you compare the DNA
of the ancient sample to a single DNA sequence from a modern individual? Assuming the individual was diploid and lived T ...
1
vote
1
answer
214
views
Limit on the Number of Facial Phenotype [closed]
Individuals of each species all have unique facial structure variations (shape of nose, position of chin etc) from humans to birds and fish etc. We humans don't seem to be reaching mathematical limit ...
- 11
0
votes
1
answer
202
views
Question on the concept of mitochondrial Eve [closed]
My question is about the very definition of this common ancestor.
Why shouldn't be the mother of mitocondrial Eve the real Eva m (and so on to grand grand ...mother)? All I know on the subject comes ...
- 103
3
votes
1
answer
178
views
Correct migration rate expression in infinite island model
In Sewall Wright's infinite island model, where all demes exchange migrants each generation, I have seen the migration rate stated variously as $m$ or $\frac{m}{d - 1}$ (as in Matthew B. Hamilton's ...
- 231
2
votes
2
answers
143
views
"50% of the variance in antisocial phenotypes is the result of genetic factors" means what?
How can i understand the following sentence:
Overall, the conclusions reached by these studies have been highly consistent in showing that approximately 50% of the variance in antisocial phenotypes ...
- 23
-1
votes
1
answer
1k
views
Does the term "fitness advantage" or "fitness disadvantage" make sense?
Same for the terms "selective advantage" and "selective disadvantage" which I intend to use synonymously. There are usages of each on Google Scholar, but do evolutionary biologists understand what is ...
- 466
1
vote
1
answer
76
views
Do similar adaptations result in similiar genetic code?
Sometimes organisms within the same species evolve similar adaptations to similar living conditions without interbreeding.
Let's say we have two human populations which need to adapt to a colder ...
- 123
4
votes
1
answer
781
views
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 ...
- 1,569
5
votes
1
answer
166
views
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 ...
- 68k
0
votes
1
answer
114
views
About lack of selective pressure
In [1] it is stated that:
the frequency of comutations in FGFR3 and KRAS or PIK3CA and KRAS was lower than predicted by chance, suggesting ... a lack of selective pressure for both mutations to ...
- 820
8
votes
2
answers
2k
views
Are mutations random?
The following claim
Mutations are random
or just the use of the expression
Random mutations
are very common among lay people.
The claim is very common among lay people. The claim is often ...
- 68k
11
votes
3
answers
2k
views
Human genetic diversity in Africa in comparison with the rest of the world
Background
The claim ...
Most of the genetic diversity in humans is in Africa
... is quite common. On Biology.SE, it is easy to find posts that make this claim. Consider for example:
Do humans ...
- 68k
1
vote
2
answers
360
views
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%...
- 161
1
vote
1
answer
192
views
Can we estimate effective population size from DNA sequence data (CR or cytB sequence)? [closed]
I have DNA sequence data (control region) of two population of a species. Can anybody suggest me any software to calculate effective population size? Is it possible and meaningful?
- 11
1
vote
2
answers
834
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 ...
- 171
1
vote
1
answer
102
views
Is genetic purging based on random shuffling of the genes of an individual or is it more intentional way of removing deleterious recessive alleles?
Inbreeding depression may be reduced by selection against deleterious alleles, which eliminates, or purges, them from the population. I have two questions:
Is genetic purging based on random ...
- 13