Questions tagged [population-genetics]
Questions related to the study of the distributions and changes of allele frequency in a population.
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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 ...
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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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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 ...
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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/...
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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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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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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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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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How does the population fitness change 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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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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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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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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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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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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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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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? ...
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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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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 ...
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Definition of "Effective population size"
Could you explain to me, what is the meaning of "Effective population size ($N_e$)"?
I would appreciate an example as well.
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What does "Mutational Variance" mean?
Background
The concept of mutational variance can be found in many articles including this one for example. The mutational variance of a trait number $i$ can be found in the M-matrix in position $m_{...
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Did Darwin ever reach the conclusion that selection will remove variation?
According to simple models of selection the genetic variance in a population should be reduced by selection. (Fisher's fundamental theorem states that the rate at which a population can evolve is ...
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Heterozygosity and the Wright-Fisher model
I was reading the textbook Probability Models for DNA Sequence Evolution by Durrett. In chapter 1, he discusses the Wright Fisher model and the coalescent theory ...
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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 ...
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Why are recombination rates increasing in mammals?
I have recently become fascinated with an awesome topic in biology and evolution that I feel is rarely covered in biology courses. That is, rates of meiotic recombination, or the the amount that an ...
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Conservation Genetics - Book recommendations
Can you please give me some advice for a book in (evolutionary) conservation genetics that offers an in-depth review of the mathematical formulations used in this field.
I read the book Evolutionary ...
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A question on exclusion of study participants for an Exome genotyping array
I'm reading a paper that used whole exome sequencing on an African
American and European populations to discover novel low frequency and
rare variants associated with lipid levels & the risk of ...
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Investigating rare variants in ethnically different populations (European ancestry & African ancestry)
If you are investigating low-frequency and rare variants for a complex trait using exome sequencing, why would one consider using different populations (African ancestry and European ancestry) ...
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Software to calculate Fst from sequence data
I'm looking for a software to calculate Fst from 3 loci DNA data of individuals from a metapopulation. I don't have any prior on the population structure (have no idea of the number of subpopulations ...
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Assumptions of the models for haploid and diploid selection
For a bi-allelic locus, the model for haploid Natural Selection is:
$$\frac{dp}{dt} = \frac{pW_A}{pW_A + (1-p)W_B}$$
, where $p$ is the frequency of the allele $A$, which relative fitness is $W_A$. ...
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$F_{ST}$ when considering a multi-allelic locus
Sewall Wright defined the $F_{ST}$ in a metapopulation as being:
$$F_{ST} = \frac{\text{Var}(p)}{\bar p (1-\bar p)}$$
, where $p$ is a vector of frequencies of a given allele and $\bar p$ and $\text{...
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Help with the Price equation
The Price equation describes mathematically the evolution of a population of units from one generation to the next.
$\bar{w}\Delta \bar{z}$ = $Cov (w_i,z_i) $+$ E(w_i\Delta z_i)$
I would like to ...
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Various Genetic Loads and their Definitions
In population genetics, we talk about several types of genetic loads (also called just loads). I am asking for a exhaustive list and a short definition.
Here are for example some genetic loads that ...
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Coalescent theory - independence of coalescent times
Let $T_i$ be the time to coalesce from $n(t)=i+1$ to $n(t)=i$, where $n(t)$ is the number of sites that have not coalesced yet. In the below example the maximum $n(0)=6$.
As I understand it, many ...
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Coefficient of relationship and path of coefficient
A path of coefficient of relationship is defined as
$$\rho_{AO} = \left( \frac{1}{2}\right)^n \sqrt { \frac{1+f_A}{1+f_O}}$$
This SE post discusses this definition
From this, the coefficient of ...
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Inbreeding Coefficient and Coefficient of Relationship
Wikipedia gives the following formula to calculate a "path of coefficient of relationship" between an ancestor $A$ and an offspring $O$:
$$\rho_{AO} = 2^{-n} \left( \frac{1+f_A}{1+f_O} \right)^{1/2} =...
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Defining: Evolutionary (quantitative) Genetics and Population Genetics
How do we define the fields that are Evolutionary (quantitative) genetics and population genetics. What set these two fields apart? Can you try to provide definitions?
To my intuitive understanding, ...
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Metapopulation structure - book recommendations
What book would you recommend me to study:
the dynamics of metapopulations,
the structure of metapopulations,
the evolution in structured metapopulations?
I am not looking for an introduction but ...
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Definition of Linkage Desiquilibrium (LD)
According to wiki, linkage disequilibrium $D$ equals
$$D = x_{11} - p_1\cdot q_1$$
where:
$$
\begin{matrix}
\text{Haplotype} & \text{Frequency}\\
A_1B_1 & x_{11}\\
...
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How to interpret the breeders equation?
The univariate breeders equation is defined as,
$\ R = h^2 s$
where $\ R $ is the response, $\ h^2 $ is the heritability (additive genetic variation), $\ s $ is the selection differential. The ...
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Heterozygosity and overdominance
Consider $m$ loci with heterozygote advantage (overdominance) such that the fitness of the two homozygotes is $1-\frac{s}{2}$ and the fitness of the heterozygotes is $1+\frac{s}{2}$, where $s>0$. ...
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Coalescent Theory - Probability for $k$ alleles that of one coalescence event occured $t+1$ generations ago
From this textbook
Under the wright-Fisher model of genetic drift and under the assumption that all alleles are neutral, the probability that $k$ alleles had $k$ distinct parent alleles the previous ...
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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 ...
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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 ...
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Initial population when I count backwards?
My question deals with the number of ancestors it took to produce me:
--> To produce me, it took 2 people (my parents) = ($2^1$) people = 2
--> One generation further included = ($2^1 + 2^2$) ...
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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
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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 ...
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Effective population size when the population sizes varies from season to season
Let's think of a species which has four generations per year and which population size changes from season to season so that the population size is 100 in summer, 200 in spring, 50 in autumn and 20 in ...
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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 $...
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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 ...
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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? ...
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