Questions tagged [population-genetics]
Questions related to the study of the distributions and changes of allele frequency in a population.
325
questions
3
votes
1answer
115 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
1answer
30 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 ...
1
vote
1answer
634 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?
0
votes
1answer
194 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"
1
vote
1answer
64 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?
3
votes
1answer
812 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 ...
1
vote
2answers
66 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 ...
0
votes
1answer
78 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
1answer
162 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 ...
0
votes
1answer
182 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 ...
3
votes
1answer
170 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 ...
2
votes
2answers
118 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 ...
0
votes
1answer
757 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 ...
1
vote
1answer
65 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 ...
4
votes
1answer
682 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 ...
5
votes
1answer
150 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 ...
0
votes
1answer
91 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 ...
6
votes
2answers
1k 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 ...
10
votes
3answers
949 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 ...
1
vote
2answers
288 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%...
1
vote
1answer
161 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?
1
vote
2answers
615 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 ...
1
vote
1answer
87 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 ...
3
votes
0answers
84 views
How to choose the most appropriate measure of genetic distance
I am conducting a phylogeography study of a fish species and am trying to construct a phylogenetic tree to describe population structure and ancestry. I have constructed trees using various measures ...
1
vote
0answers
42 views
Use numbers or algebra when introducing an evolutionary biology concept?
I'm working on an (approximately 20 pg) evolutionary biology paper for submission to a journal. The paper introduces a couple of strategies (I use "strategies" loosely; they can be carried out by ...
1
vote
1answer
39 views
Genomic control explanation
I am following the original genomic control article -
http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.167.8448&rep=rep1&type=pdf
What's the role of $p_i$ in the article? It says that ...
1
vote
0answers
49 views
Replication cohorts in microbial GWAS
Replication in an independent cohort is of course the gold standard in GWAS studies, and many high profile journals will now (quite rightly) not accept finding indicating a phenotype genotype ...
0
votes
1answer
49 views
Background (null) distribution for higher observed frequency of an allele [closed]
I am testing the hypothesis that being heterozygote at a certain gene locus, say X, increases the chances of having the good allele of X compared to being homozygote. I have data of more than 6000 ...
7
votes
2answers
1k views
How can someone share 50% of their DNA with their parents yet all humans share 99.9%?
I have heard that humans share 99.9% of their DNA with other humans. I have also heard that a child shares 50% of their DNA with their parents. How do I resolve this apparent contradiction? It has ...
8
votes
2answers
135 views
Is it mostly true that predators or parasites traverse wider spatial areas than their prey or hosts?
Does it tend to be true that as you go up the food chain, the species tend to cover wider areas? I am basically asking whether a population's prey varies spatially more than a population's predators ...
1
vote
1answer
1k views
Question about the consequences of non-random mating and allele frequencies
I just began studying population genetics, and I don't understand something that is written in my lecture:
Consequences of non-random mating:
More homozygote and less heterozygote individuals in the ...
0
votes
1answer
79 views
Why aren't there more Ash-Red pigeons?
My favorite color pigeon is Ash-Red, but I don't see a lot of them. I figured it must be a recessive phenotype, but when I googled it, I found out it's dominant. So why aren't there more Ash-Red ...
3
votes
1answer
194 views
Text Book Recommendation: Organic Evolution
I was wondering if anyone could point me in the direction of any text books on organic evolution? I have recently become interested in the subject and would like to know more. I think an undergrad ...
3
votes
2answers
817 views
How is “selection” best defined?
There is natural selection but there is also sexual selection which some regard as a category of natural selection. There is also artificial selection (by humans). The question is, what is a most ...
1
vote
1answer
469 views
How to calculate Fst from AMOVA
I calculated an AMOVA from a genind object, with one hierarchical factor. In the table I obtain there are SSD values (for my grouping factor,"Error" and total) and sigma2 values (for my grouping ...
1
vote
0answers
62 views
What is Hamilton's rule for multiple generations?
What is Hamilton's rule as it applies to multiple generations? Is it that the lineage success given up by the actor must be exceeded by the lineage success acquired times the relatedness between ...
4
votes
0answers
114 views
Isn't heritability more important to genic capture than just genetic variance?
Rowe & Houle (1996) give two criteria for the selection of costly female choice:
Condition dependence of sexually selected traits
High genetic variance in condition
Regarding heritability, ...
0
votes
1answer
63 views
How EGDS (endurance genetic distance score) is calculated?
Can anybody please make me understand how EGDS5 has been calculated to 40.8 in this paper at page#31?
The formula has been described in this paper but when i tried the same, I am not getting the same ...
4
votes
1answer
151 views
Polymorphism in number of chromosomes?
The answer to this question, saying that Down Syndrome - a trisomy of human chromosome 21 - is caused by de novo mutation (rather than resulting from standing variation) made me think about ...
2
votes
1answer
90 views
Down syndrome in subsaharan populations
What is the rate of occurrences of Down syndrome in subsaharan African populations? Is it the same as in white European populations?
An interesting hypothesis came to my mind:
Could it be that Down ...
1
vote
1answer
71 views
How can one calculate “probability of possessing a ‘perfect’ profile” from “typical optimal genotype frequencies”?
Can anyone please explain how the "Probability of possessing a ‘perfect’ profile" was calculated from "typical frequency of optimal genotype" in Table 1 in this paper?
Paper link here
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0answers
516 views
Can the value of heritability be greater than 1?
Heritability defined as genetic variance divided by total variance seems to be bounded between 0 and 1. However, I see a way of calculating heritability on this page (http://www.radford.edu/~rsheehy/...
1
vote
1answer
34 views
How would you model the evolution of two genotypes across generations?
Say you have a genotype A that produces x offspring and another genotype B that produces y offspring, where x>y. These x offspring are of genotype A but with modest differences in fitness due to ...
3
votes
2answers
2k views
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 $1$, $...
1
vote
1answer
98 views
Heritability in population genetics
What is the difference between narrow sense heritability and broad sense heritability?
Does heritability in the broad sense refer to the degree of genetic determination?
Heritability in the narrow ...
3
votes
0answers
96 views
Why does my simulation not support the idea that inbreeding is bad?
After reading this post, I wrote some code to simulate inbreeding.
We have a population of $N$ creatures. Each creature has two genes, which come in two forms: recessive (a) and dominant (A). The ...
10
votes
4answers
4k views
What are the consequences of inbreeding?
Inbreeding increases the risk of getting two identical recessive genes, alleles, that cause a disease which wouldn't have been activated with mixed genes. That's how I understand it anyway. But I ...
4
votes
1answer
1k views
Assumptions of Hardy-Weinberg rule
The post Solving Hardy Weinberg problems offers an easy explanation of Hardy-Weinberg rule. The current top answer explicitly does not talk about the assumptions of Hardy-Weinberg. A model makes sense ...
2
votes
0answers
57 views
How do I solve this problem related to specificity and sensitivity?
Consider an autosomal recessive disease with an incidence of 1/10,000 in
the general population of 100,000. Your best friend comes to you very
upset because he has just taken a screening test for this ...
4
votes
0answers
59 views
How Can Homosexuality be Genetic? [duplicate]
I hold no strong opinions towards homosexuality one way or the other; I'll personally refrain, but don't apply my personal tastes to the rest of the world.
I remember seeing some articles a while ...
