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

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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 ...
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15 views

Chromosome 17-Ancestry question

I did the 23andme genotyping and was going over my ancestry. I mostly have ancestors that came from the UK which dominates most of my chromosomes. However, just a little bit (~1.4%) of my DNA is ...
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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 ...
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2answers
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What exactly is extreme heterozygosity and how does it work? [closed]

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 ...
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1answer
26 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 ...
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87 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 go ...
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36 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 ...
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2answers
120 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 ...
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1answer
67 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 ...
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30 views

Understanding F-statistics in population genetics

I am reading a classical Weir and Cockerham 1984 paper about Fst estimation. At the beginning (first page, right column), they define 3 statistics. $F$ is the correlation of genes within individuals ...
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3answers
77 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 ...
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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 ...
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1answer
52 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 ...
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1answer
42 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 ...
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51 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 ...
3
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1answer
47 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 ...
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34 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 ...
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3answers
98 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 ...
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51 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 ...
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3answers
113 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?
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1answer
60 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, ...
4
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1answer
64 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
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1answer
858 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 ...
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1answer
82 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 ...
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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 ...
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2answers
49 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 ...
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20 views

pedigree analysis of inbreeding

Under a given situation of cousin inbreeding, I will obtain the same inbreeding coefficient ragardless of using the genealogy or the path approach, i.e. F=1/16 ...
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What is the probability of fixation for a mutant under fluctuating selection?

Here is an answer which explain how one can model the frequency of an allele that is under fluctuating selection (selection that varies through time). Not, thinking about fluctuating selection, there ...
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1answer
67 views

Modeling inclusive fitness

Consider a population of two altruist with coefficient of relatedness $r$. The average inclusive fitness of this population will be $w_{0} + br -c$. Like in this example, assignment of inclusive ...
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Expected time for a neutral allele to reach a frequency of $p_1$ when starting at frequency $p_0$

Kimura and Ohta (1968) showed that the expected time for a neutral allele to reach fixation (given that it will reach fixation) is $$\bar t(p_0)=-4N\left(\frac{1-p_0}{p_0}\right)\ln(1-p_0),$$ where ...
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1answer
72 views

Mathematical models of lineage selection

I'm interested in the concept of lineage selection (Aboitiz, 1991) as an explanation for why traits would be selected for that enhance the rate at which evolution can occur, rather than directly ...
4
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1answer
62 views

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 ...
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3answers
133 views

How is it possible for the absolute fitness to be more than 1?

The wikipedia definition of Absolute fitness is "the ratio between the number of individuals with that genotype after selection to those before selection. It is calculated for a single generation and ...
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1answer
43 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 ...
3
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1answer
276 views

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 ...
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1answer
115 views

How do you convert mtDNA sequences in FASTA to FSTAT format?

I've got control region sequence data from a population of shark and I'm looking to convert this from FASTA to FSTAT in order to calculated the effective population size of females. The software I ...
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0answers
8 views

Are large depth changes ever a barrier to gene flow in elasmobranchs?

I'm looking to find out if large changes in oceanic depth have ever restricted gene flow between populations of elasmobranch, or any other fish for that matter. I'm particularly interested in deep ...
3
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1answer
69 views

Mutation Rate in Multicellular Eukaryotes

I always hear people saying that the mutation rate is around $10^{-6}$ or $10^{-7}$. I don't even know if this number is the mutation rate of genes or of a single nucleotides and I actually (almost) ...
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2answers
167 views

Hamilton's inclusive fitness approach

The underlying intuition of Hamilton's model of inclusive fitness is that we should study social behaviors from the point of view of actors -- rather than the recipients. To build his model, Hamilton ...
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1answer
73 views

Hamilton's derivation of direct fitness from his 1970 paper

In his 1970 paper "Selfish and Spiteful Behaviour in an Evolutionary Model", Hamilton uses Price's equation to derive his well-known rule $rb -c >0$. My question is about one of the steps in his ...
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48 views

How does the population fitness changes after a change in mutation rate

The mean population fitness as given by mutation load theory depends only on the genome-wide mutation rate ($U$). My question is: how many generations is needed to reach a new mutation load ...
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79 views

How do I import FASTA files into Haploview?

I'm trying to produce a haplotype network and so have decided to use the software haploview. However I'm having some problems importing my sequences into the software. I Have my sequences in a FASTA ...
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2answers
99 views

What is Environmental Robustness? Is it different from plasticity?

Hansen (2006) in his review uses the concept of environmental robustness independently of the other concepts of robustness (at pages 139 and 140) without defining ...
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1answer
91 views

Why estimate linear and full (linear, quadratic, and correlational) selection coefficients separately?

"We then fitted a linear regression including all three life-history traits to estimate the vector of linear selection gradients, β, for each sex (Lande and Arnold 1983). A quadratic regression ...
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0answers
48 views

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. ...
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1answer
290 views

Hardy Weinberg problem help!

The three common genotypes at the hemoglobin locus have very different phenotypes: SS individuals suffer from severe anemia, AS individuals have a relatively mild form of anemia but are resistant to ...
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0answers
81 views

How to define “Quasifixation” in continuous approximation of finite population?

Background Many models including the famous very first models derived by Sir Ronald Fisher in his early career, assume infinite population size. In an infinite population, an allele can rise in ...
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1answer
131 views

Interpretation of graph from evolutionary biology

I am studying evolutionary biology, and been presented with this graph: I am having some difficulties understand its meaning. For a start, why is time measured as a fraction of the population size? ...
5
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2answers
173 views

Simulating substitution rate of neutral mutations

I am trying to computationally simulate a population based on the Wright-Fisher model I would like to get to the classic result of the neutral theory of molecular evolution that the rate of neutral ...
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222 views

Mutation-Selection-Drift Equilibrium

mutation-selection-drift equilibrium is one of the most important concept of population genetics. I could easily find the calculations for mutation-secltion equilibrium and for mutation-drift ...