Questions tagged [population-biology]
Questions pertaining to populations of organisms.
150 questions
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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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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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Evolution: One big population vs. many small populations
Let's say I want to evolve a bacterium that is resistant to an antibiotic. I want to do this by growing initially clonal populations of bacteria in presence of this antibiotic for a long time.
I have ...
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Drake's Law. What is the genome-wide mutation rate and what are the estimates?
Drake's rule
Drake's rule states that the genome-wide mutation rate is more or less constant across all species — from E.coli to the house sparrow.
Data
From what I think being Drake's original ...
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How many eukaryotes are there on Earth?
I have been reading:
William B. Whitman, David C. Coleman, and William J. Wiebe, "Prokaryotes: The unseen majority", Proc. Natl. Acad. Sci. USA 95, pp. 6578–6583, June 1998. [Full Text] [PDF]
...
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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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Understanding the meaning of $s$ and $t$ in a population genetics equation
Sewall Wright in this article (1937) at the end of page 313 gives the equation:
$$\Delta q = (s+tq)q(1-q) \space\space\space\space\space\space\space\space\space(1)$$
This equation is an ...
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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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Does a top heavy population grow, decline or stabilize?
Imagine a population that has a larger proportion of older individuals than younger ones, what could possible happen to it in the future?
I am guessing that if the older individuals reproduce, the ...
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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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Can we really 'discover' 85% of mammalian viruses?
This virology [blog] discusses estimates of the number of mammalian viruses and the costs of 'discovering' 85% of them.
My question is whether this is not a forlorn hope. The ".632 rule" in ...
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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 $\text{...
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$F_{ST}$ and the genetic variance in metapopulations
From this video (21'15''), the speaker gives the following formulae in order to calculate the between and among populations genetic variance from the $F_{ST}$:
$$V_{Among Pop} = 2 F_{ST}V_G$$
$$V_{...
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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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Inbreeding depression and dominance
From this article, second paragraph of the second page
A classic theoretical result is that the mean of a character controlled by a single locus i with two alleles Ai1 and Ai2 is only affected by ...
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How important is the womb's environment?
- Background -
Talking about one phenotypic trait, the total phenotypic variance $V_p$ is decomposed into genetic and environmental variance for this trait, represented by the symbols $V_G$ and $V_E$ ...
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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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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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Heterozygosity under genetic drift
The wright-Fisher model of genetic drift is:
$$p_{ij} = \binom{2N}{j}\left(\frac{i}{2N}\right)^j \left(1- \frac{i}{2N}\right)^{2N-j} $$
,where $\binom{2N}{j}$ is a binomial coefficient.
From this ...
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Book recommendation on selective breeding?
I am looking for a good book that gives a nice overview of the science and technics of selective breeding. I am particularly interested in the use of population genetics to support decision in this ...
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Effect on fitness of mutations
What is the distribution/probability density function (PDF) of impacts on fitness of new mutations?
I very welcome any partial answer that does not give the whole PDF but just some information about ...
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Dominance/recessivity of new mutations
What is the distribution/probability density function (PDF) of recessivity/dominance of new mutations?
I very welcome any partial answer that does not give the whole PDF but just some information ...
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Additive genetic variance with $n$ loci
The genetic variance of a quantitative trait (the quantitative trait in question is fitness) can be express as the sum of two components, the dominance and additive variance:
$$\sigma_D^2 + \sigma_A^...
- 68.3k
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Additive genetic variance with $n$ alleles
The genetic variance of a quantitative trait (the quantitative trait in question is fitness) can be express as the sum of two components, the dominance and additive variance:
$$\sigma_D^2 + \sigma_A^...
- 68.3k
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3
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Initial population when I count backwards?
My question deals with the number of ancestors it took to produce me:
--> To produce me, it took 2 people (my parents) = ($2^1$) people = 2
--> One generation further included = ($2^1 + 2^2$) ...
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How do I calculate the change in allele frequency in a haploid population under selection?
From this book
For simplicity, let us consider a haploid organism and assume that the frequencies of alleles $A_1$ and $A_2$ are given by $x$ and $y=1-x$, respectively. We also assume that the ...
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How to calculate the effective population size ($N_e$) with overlapping generations?
From this Source: If generations are overlapping, then the effective population size $N_e$ does not equal the population size $N$.
I know mathematical formulations in order to find the effective ...
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Linkage disequilibrium with multiple alleles and loci
Linkage disequilibrium $\left(D\right)$ for two bi-allelic loci is defined as:
$$D=X_{11}X_{22} - X_{12}X_{21}$$
where $X_{11},\ X_{12},\ X_{21},\ X_{22}$ are the frequencies of the haplotypes $...
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Why will world population keep growing if all women have only 2.1 children
Why is it that, even if we were going to immediately agree that every women will not have more than 2.1 children on average, the world population would continue to grow for another 60 years? I've ...
user5902
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Why do genetic drift generates negative linkage disequilibrium?
The very first sentence of the abstract of this article is:
"In finite populations subject to selection, genetic drift generates negative linkage disequilibrium, on average, even if selection acts ...
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What percentage of the fitness variance is explained by the 'n'- most important loci?
Introduction
Standard models in population genetics look up at the evolution of few loci which impact fitness. The variance in fitness is determined by the genetic variance and the environmental ...
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Definition of "Regime of selection"
How would you define Regime of selection (or Selection regime)?
In addition to a accurate definition, a developped example ...
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How has the use and subsequent ban of DDT affected insect populations?
Living in Australia there were less ticks for example during the use of DDT, now there are more ticks prevalent here. I am wondering if any insect species have declined permanently as the result of ...
user22339
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Is there a website that shows population sizes?
I'm looking for a website that shows the population sizes of a species (doesn't matter which) as a function of time at a geographic coordinate. Is there a government website or other free database ...
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Does a large effective population size result in faster decay of linkage disequilibrium (LD)?
I am thinking about an invasive species that was introduced into North America just a few (<20) generations ago. Using microsatellite genotypes (105 loci), I have identified almost no significant ...
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Population genetics and the fitness probability distribution. Why is the arithmetic mean all we need?
When recording change in allele frequency in diploid, bi-allelic, infinite and panmixic population we usually use this kind of equation:
$\delta_p = \frac{p * q *( p (w11 - w12) + q * (w12 - w22))}{\...
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How many honeybees are there, and how has the number changed across time?
How would you begin to estimate the world population of the European Honeybee (Apis mellifera)? Would recent colony collapse disorder show up as a blip? How about the spread of A. mellifera from ...
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To what extent is immature eggs in insects (beetles) a good approximation for maximum fecundity?
To what extent is the number of immature eggs from dissected, newly emerged individuals a reasonable approximation for maximum/potential fecundity in insects (more specifically beetles)? I know that ...
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Hardy-Weinberg applied to three alleles and stimation of allele frequencies
I have this equation:
Corresponds to HW in equilibria with three alleles:
$(p+q+r)^2=1$
Expanding the square results:
$p^2+2pq+r^2+2pr+q^2+2qr = 1$
I need to separate homozygous and ...
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What is the minimum population size that Hardy-Weinberg calculations can be applied to?
I'm trying to find out if a particular allele is in Hardy-Weinberg disequilibrium, but the data is poor. What's the minimum population number that you can use to get any sort of respectable conclusion?...
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What is the inbreeding coefficient for the female offspring of a sib-mating in a haplodiploid system?
The inbreeding coefficient of a sibling mating for a diploid organism is 0.25 (each allele has a 25% of being identical by descent in the offspring).
In haplodiploid organisms, males result from ...
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Vaccination and population dynamics of an epidemic
I'm trying to figure out how should a vaccination model be built to correlate with population density, and I'm having problems to understand meanings of the results I receive when I apply theory on ...
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Does finite rate of increase depend on mortality of individuals in a population?
As written in my lecture handouts, there two main factors in the Geometric Growth Model of populations:
$R_{0}$ is the expected lifetime reproductive output. This way, for unicellulars, for example, ...
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What's in a Name: Statistical Genetics
The novice often performs population calculations using
what is referred to as Mendelian Genetics. Soon after the
publication of Mendel's results; Hardy and Weinberg presented
their results after the ...
Schenectady
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How do susceptible organisms prevent parasites from overcoming resistance?
Bt corn is genetically modified to kill borers, but "regulations require farmers to plant conventional varieties as well, which is intended to stop the borers becoming resistant."
-Source
How do ...
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How does population stability evolve?
The number of individuals constituting a population is called population size. Over time population size does not remain constant, it fluctuates to different extent over generations because of ...
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Difference between biological control and introducing species for conservation?
I have a biology assignment and we have to explain various methods and strategies for conservation, two of which are:
Biological control
Introduced Species
What is the difference between these? ...
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