6

There are quite a lot of articles(1,2, etc.) which have investigated this, I think this article did a great job to give a visual representation of the specificity, reliability and coverage: also this article noticed the following: Compared to electronic annotations, it is not surprising that curated annotations have a considerably lower average ...


6

First of all, here is a program which simulates the evolution of the G-matrix over multiple generations, it's a few years old (they seem to have stopped developing it) and I've only played with it briefly. This could solve how to model the evolution of the G-matrix. Fisher's fundamental theorem is a great place to start off with the theory of this: The ...


5

I think that the simple answer to this question is that the present comparative methodology was largely established by Felsenstein 1985, American Naturalist. For mathematical convenience, he suggested Brownian motion as a null hypothesis, because "...the variance of the distribution of change of a branch is proportional to the length of time of the ...


5

I am presenting a speculative approach since nobody has mentioned about any existent models yet. Assuming that selection is based on performance in certain tasks; performance is a function of traits which in-turn is a function of genotype. Performance is a non-linear function of genotype and selection imposes a cutoff/bandpass filter on the performance ...


4

This is directly following the advice of Lande & Arnold (1983), saying: Linear multiple regression can be used first to estimate the forces of directional selection, $\beta$, and their standard errors. Then a quadratic multiple regression (16) or (Al), can be used to estimate the forces of stabilizing selection, $\gamma$, with their standard errors....


4

[C]an drift overcome sexual selection in the evolution of sexually dimorphic traits? Short answer Yes Long answer There are many ways to consider the effect of genetic drift. Here is one: One can approximate the probability of fixation of new mutations (using diffusion equations) with $$P_{fix}≈\frac{1-e^{-4Ns} }{1-e^{-4s}}$$ , where $s$ is the ...


3

That definition in the wikipedia is misleading at best. Contrary to what it seems to suggest there, absolute fitness is computed across a single generation, not within a single generation. For simplicity, let's look at an example using asexual haploids with discrete non-overlapping generations. If individuals with the A genotype produce an average of 3 ...


3

Whether or not species with less non-coding DNA evolve faster, the assumption that this could be explained by their genomes being more susceptible to mutation would seem to me to be based on a false premise. Let us examine the logic of the assumption by making an analogy to drawing of tickets from an urn in a lottery. If you buy one ticket (coding region), ...


3

This information is given in p.118. In essence $a$ represents the deviation from the population mean due additive genetic effects. Say a trait is controlled solely by locus X with the effect alleles X impacting the phenotype Y in an additive manner (no dominance and epistasis effect), then we can calculate the effect size of carrying the X allele, called $...


2

A classical result from the Wright-Fisher model of genetic drift is that at each generation the heterozygosity ($2x(1-x)$) is expected to decrease by $\frac{1}{2N}$ due to genetic drift. ($x$ is the frequency of one of the two alleles). In your example the expected loss of heterozygosity is $¼$. This same result has been derived from coalescent theory and a ...


2

I found a key paper for myself from an issue of Nature Reviews Genetics last year. It discusses and reviews how recombination affects the rate of genetic variation at the sequence level. A key concept is that of selective interference, which is what I had stumbled across in the question, this is when the efficacy of selection is reduced because "...


2

Sample 1. 4096 / 1024 = 4x more B Sample 2. 16384 / 1024 = 16x more B The average amount more B = (16 + 4) / 2 = 10x more B That is not the right way to go about. You are calculating average expression of B in both samples. It does not mean there is 10x more B. There is just 4x more B in Sample-2 relative to Sample-1. Gene-A does not change its expression ...


2

Question 1: The phenomena you describe in which it matters whether you have one or two copies of an allele (e.g., the AA phenotype being different than the Aa phenotype) are known as dominance effects. Dominance effects can interact with epistatic effects (in which the phenotypic effect of one locus depends on the genotype at the another locus). One good ...


2

From the pheno-geno map and the genotypes frequencies, you have the whole distribution of phenotypes in your population. The mean of the phenoype $n$, $P_n$ is the $$\bar P_n = \sum f_{G_i} P_{G_i}$$ , where $f_{G_i}$ is the proportions of individuals having genotype $G_i$ and $P_{G_i}$ is the phenotype of the individuals with genotype $G_i$. Therefore, ...


2

The field of tensor decompositons has been discovered in many fields simultaneously, each with their own notation. Many modern notation in fields like CS or STAT have originated from the work of Tamara Kolda http://www.kolda.net/publication/koba09/ However, this is restricted to the CP and Tucker decomposition, and we have many others now. See https://arxiv....


1

Just came across a chapter by Felsenstein on phylogenetic inference with quantitative characters. In it, he states this biological justification for using Brownian motion: A quantitative trait that has genetic variation controlled by a single locus will change as the gene frequencies at the locus undergo genetic drift... Brownian motion is a reasonable ...


1

The definition as set by Kenneth Lange's book is indeed quite vague and thus unrigorous. It is a probability not conditioned on observing an allele $a$ at a locus of $i$ but conditioned on the following where we focus on one particular locus. It is rigorously defined as follows. Then we will give the correct formulation of the correct recursive equation akin ...


1

I said that there isn't enough information to tell since the parents genotypes are unknown. It seems like you are misreading the diagrams since you say the parent's genotypes are unknown. All 8 individuals in the two pedigrees have the same information given for each, appearing in the eight columns directly beneath the eight individual's symbols.


1

Two answers follow: Technical experience of many: it should be no problem to have the same protocol with a twice-lower starting concentration, without making any adjustments whatsoever. The suggested 1ug is very much on the safer side of things, 2-fold fewer transcripts makes almost no difference. Maybe at 1 or 2 orders of magnitude (10 to 100s) less will ...


1

For statistical genetics, take a look at: Likelihood, Bayesian, and MCMC Methods in Quantitative Genetics. Daniel Sorenson and Daniel Gianola. (2002. Springer). Warning: heavy on math (calculus). If that doesn't scare you, it's excellent guide to non-frequentist statistical methods applied to problems in genetics.


1

That definition is problematic and incomplete. Absolute fitness can be used in different ways, and can be calculated at different levels of organisation (individuals, genes etc). However, absolute fitness always relate to actual growth rate, actual numbers of offspring or other measures of fitness (so an absolute measure), while relative fitness is ...


1

Does covariance and phenotypic variance have to be for the same trait to calculate narrow-sense heritability? Yes. See below for more information. Can I still calculate the narrow-sense heritability of AA [..] even though they're different traits? No, you can't. A measure of heritability makes sense only for a given trait a given population at a given ...


1

If they are "pure-breeding", that means that they are homozygous. If they were heterozygous, the offspring would not all have the same color as the parents. But tree-breeding" means they all do.


1

First you need two, hopefully homozygous, strains that differ in some measurable quantitative trait. In worms it has been done with lifespan; in mice injected with ethanol it has been done with long-sleep and short-sleep periods. The two strains need to differ in their RFLPs. For flies there are probably lots of behavioural traits one could use. You set up ...


1

The definition of IBD is always the same - an allele or segment of alleles which is shared between two individuals because of descent from a common ancstor. In the context of this paper, the authors are referring to segments of the genome between individuals which are IBD. In this case, they are looking at recently isolated populations who are likely to ...


1

Trait z is represented by k genes: z1....zk (I am using k instead of l because the former is visually differentiable from 1 ). For simplicity let's assume that there is only one mutable site in a gene. So a mutation can impart a change of $\pm \Delta z$. Starting from initial state of z at zero, the system will proceed to equilibrium where the rate of ...


1

Noting that the right hand side can also be written $\mathbf{G}\mathbf{P}^{-1}\mathbf{s}$, we see that the only theoretical limitation of the multivariate breeders equation is the invertibility of the matrix $\mathbf{P}$. This happens when the measures of two traits are the same for all individuals, making two columns of the matrix the same I.e. It becomes ...


1

From what I understood of your code and what you are asking I am guessing that you do the following: Generating a virtual set of 40 individuals (lines) of which you have 200 measurements (repetitions). You say that they are full siblings, so they share both parents. Then you use the lmer function (which I am not familiar with) to give you the total variance,...


1

To construct the G-matrix you need additive genetic variances and covariances for all traits, so you normally need results from breeding experiments (e.g. phenotypic midparent-offspring data), that you can do parent-offspring regressions on. Don't know any good online sources but see Balding et al. 2007 p. 534ff for some info. I've seen methods that claim ...


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