Questions tagged [population-genetics]

Questions related to the study of the distributions and changes of allele frequency in a population.

Filter by
Sorted by
Tagged with
1
vote
0answers
450 views

How should one interpret heritability? Is it related to $R^2$?

From Wiki: 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. It ...
0
votes
1answer
62 views

“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(...
1
vote
0answers
404 views

Relation between heterozygosity and allelic diversity in founder effects/bottleneck?

Can someone try to explain me why allelic diversity falls faster than heterozygosity, reminding you that we're talking about bottleneck or a founder effect? Look at this graphic: It's clear to me ...
2
votes
1answer
217 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....
3
votes
1answer
5k views

Why are the genomes of Humans 99.5% the same?

Human's DNA sequence is said to be roughly 99.5% equal. As far as I understand, this means that if I walked up to you and compared our DNA, the sequence of base pairs would be 99.5% the same. My ...
5
votes
2answers
603 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
votes
1answer
2k views

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 ...
5
votes
1answer
222 views

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 $t$ ...
5
votes
1answer
109 views

Why don't the genetic similarities between ‘unrelated’ individuals of the same and different species outweigh the differences?

Ever since starting to learn about the concept of inclusive fitness during my BSc, I've been bugged by this questions: if inclusive fitness can account for many ‘altruistic’ behaviors, why don't the ...
1
vote
1answer
524 views

From STRUCTURE to FSTAT format

From numerical simulations I output a file that is input to STRUCTURE (Hubisz et al. 2009). I now realize that I would need to process my data with FSTAT (Goudet 1995). Both are text files. Is there ...
2
votes
1answer
7k views

Calculating pairwise Fst from allele frequencies

I am trying to refresh my memory on population genetics for a project, and I'm having some trouble. Assume I have genetic data on 3 populations with 5 individuals in each of a given species, with the ...
1
vote
0answers
132 views

Interpretation of F in inbreeding on the population level

The inbreeding coefficient for an individual gives the probability that the individual has two alleles at a locus that are IBD. What interpretation does the inbreeding coefficient have on the ...
1
vote
2answers
3k views

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 ...
1
vote
0answers
574 views

How do you create a .snp datafile?

I'm looking to use the software DIYABC 2.1.0 to apply approximate bayesian computing (ABC) to some resequenced data that I have. The resequenced data is in FASTA format however, and the software ...
4
votes
2answers
465 views

Is it possible for two people to repopulate earth? [closed]

Today I was wondering this question whether it is possible for two people to repopulate Earth. What if everyone else disappeared, except for two people (man & woman)? Can they repopulate? In ...
1
vote
1answer
43 views

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,...
5
votes
1answer
421 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 ...
2
votes
1answer
64 views

Who was the first to coin the terms of soft and hard selection?

Soft and hard selection are sometimes used with different definitions. I have been told that at first place hard and soft selection has been defined in the following way: soft selection: Each deme ...
3
votes
1answer
953 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 ...
4
votes
2answers
169 views

Role of drift in evolution of sexually dimorphic traits

Is there a model for predicting how drift can affect the evolution of a sexually dimorphic (SD) trait? I've been trying wrap my mind around this paradoxical question; sexually dimorphic traits evolve ...
1
vote
1answer
83 views

IBD-value and IBD-fraction

I have some questions about the IBD-value and IBD-fraction for two of the condensed identity states, $S_1$ and $S_7$. My questions: 1) Is the IBD-value for the individuals i and j two (2) in $S_1$ ...
2
votes
1answer
3k views

What is a selective constraint?

I encountered the term selective constraint in Huber et al. 2015, page 4 (last paragraph) in: If invariable sites are included in the analysis, then both the methods of Kim and Stephan (2002)...
3
votes
2answers
433 views

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 ...
2
votes
0answers
315 views

Variance in reproductive success and effective population size

Background The effective population size $N_e$ is the size of the Wright-Fisher population that experience the same amount of drift than the population under consideration. The higher the variance ...
3
votes
1answer
60 views

What is the distribution of the number of heterozygotes in finite populations?

Consider a bi-allelic locus with alleles A and a. We denote the frequency of the A allele by ...
4
votes
1answer
643 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
votes
3answers
4k 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 delicious' which was ...
5
votes
2answers
687 views

Coalescence time: Is it different for haploids and diploids in population genetics?

I'm trying to model Cyanobacteria cells divergence in 2 populations with mutation rate $-\mu$ and I need to verify my model with a valid theory. I don't have much biology background and all the ...
15
votes
1answer
356 views

What is the percentage of people living in England in 1500 AD whose lineage is still alive?

This sounds a bit random, but it stems from a lecture in statistical genetics which I attended a while ago. We were shown a population lineage graph from which it was clear that most lineages ...
6
votes
1answer
290 views

Variance in Fst in the infinite island model

The most famous result in the study of structured populations come from Sewall Wright. He showed that in an island model, where each subpopulation is of size $N$ and the migration rate is $m$, then ...
7
votes
2answers
169 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 (...
2
votes
1answer
1k views

Why does the number of mutations per individuals follow a Poisson distribution?

I was reading this review. On page 11, left column, first paragraph, one can read: [..] there is a Poisson distribution of the equilibrium number of mutations per individual, if fitness effects are ...
7
votes
1answer
707 views

Understanding F-statistics in population genetics

I am reading the classic Weir and Cockerham 1984 paper about $F_{ST}$ estimation. At the beginning (first page, right column), they define 3 statistics. $F$ is the correlation of genes within ...
1
vote
3answers
387 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 ...
2
votes
0answers
119 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 ...
4
votes
1answer
470 views

Forward versus backward numerical simulations in population genetics

My question is closely related to this post. There are a number of existing platforms to perform numerical individual-based simulation in populations genetics. An almost exhaustive list of such ...
6
votes
1answer
116 views

Evolution of diversity and extinction resistance

I saw a comment on an answer to another question that touched on an interesting topic: keeping diversity is useful for parameter exploration or to adapt to future environmental change My initial ...
3
votes
0answers
176 views

How to understand relatedness in an infinite island model?

My understanding is that the relatedness coefficient in kin selection models measures positive assortment. That is, altruism is more likely to evolve if altruists tend to interact with other altruists....
3
votes
1answer
84 views

Altruism in viscous (asexual) populations

The viscosity of a population is the tendency of offspring to remain near their place of birth. Taylor 1992 ("Altruism in viscous populations") provides a model to study how viscosity affects the ...
2
votes
0answers
200 views

Falconer & Mackay population mean calculation & genotypic values

I am reading chapter 7 of Falconer and Mackay where they give a formula to calculate the population mean as a deviation from the heterozygote genotypic value. As an example, imagine a one locus two ...
1
vote
3answers
672 views

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 ...
6
votes
0answers
154 views

Identity by descent among unrelated individuals

I was reading a couple of papers which talk about IBD (Identity by descent) among unrelated individuals (for eg. http://www.pnas.org/content/109/4/1193.long). However they do not seem to clearly ...
8
votes
3answers
277 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?
6
votes
1answer
74 views

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, ...
5
votes
1answer
113 views

How do bumblebees and hornets avoid the negative effects of inbreeding?

I just learned that all hornets and bumblebees except for the queen die at the end of the year and the queen starts a new nest in spring. But that means the next generation of queens have only ...
7
votes
1answer
1k views

Term for trait that is advantageous to a population only as long as it is rare

I remember reading about a concept—in evolutionary biology or natural selection, I think—whereby a particular trait is advantageous to the population or species but only so long as that trait is only ...
4
votes
1answer
141 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 ...
2
votes
0answers
58 views

Analytical Methods for Estimating Probability of Fixation

The probability of fixation $P$ of an allele is an very important measure and there exists several solutions to estimate this probability. Each method has its own assumptions and it is often hard to ...
2
votes
2answers
91 views

How to compute the regression of individual fitness on individual phenotype

Consider a population structured in groups of two individuals. Individuals' interactions follow an additive prisoner's dilemma: \begin{array}{c |c |c|} & C & D \\ \hline \text{Cooperate (} C \...
2
votes
0answers
177 views

What is the probability of fixation for a mutant under fluctuating selection?

Here is an answer which explains how one can model the frequency of an allele that is under fluctuating selection (the selection that varies through time). Not, thinking about fluctuating selection, ...

1
3 4
5
6 7