Questions pertaining to populations of organisms.

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15
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0answers
166 views

Was the recent “conservation hunt” of a black rhino supported by science?

CNN recently covered a sanctioned black rhino hunt in Namibia by Texan Corey Knowlton, who bid US$350,000 for the license. In the story, he claims that the hunt was actually supporting conservation of ...
12
votes
1answer
115 views

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 ...
9
votes
1answer
878 views

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 ...
8
votes
3answers
149 views

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 ...
8
votes
1answer
168 views

What sample sizes are ideal for carrying out Bayesian Skyline Plots?

I am interested in creating Bayesian Skyline Plots to look at demographic changes in certain population groups. However, these populations have very little within population variation. Around 5 ...
7
votes
2answers
118 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 ...
7
votes
1answer
129 views

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] ...
7
votes
1answer
71 views

Basic Modelling in Quantitative Genetics

I am pretty bad in thinking quantitative genetics models. I am trying to get some basic understanding of modelling the evolution of a quantitative trait. I am therefore asking for help to analyze a ...
7
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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 ...
6
votes
1answer
95 views

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 ...
6
votes
1answer
271 views

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 ...
6
votes
1answer
102 views

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 ...
6
votes
1answer
226 views

What percentage of the (additive or not) genetic variance is explained by the 'n'- most important loci?

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 variance (and the ...
5
votes
1answer
2k views

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 ...
5
votes
2answers
169 views

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 ...
5
votes
1answer
89 views

How should species density be calculated for a clumped distribution?

Lets imagine 5 plots of different size are sampled for a target species: ...
5
votes
2answers
114 views

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 ...
5
votes
3answers
410 views

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 ...
4
votes
2answers
123 views

What is called the “area size that an animal usually lives in”?

What is called the "area size that an animal usually lives in" or "needs for a normal life"? Is there any specific term?
4
votes
1answer
948 views

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 ...
4
votes
1answer
359 views

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 ...
4
votes
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 ...
4
votes
1answer
121 views

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 ...
4
votes
1answer
79 views

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 ...
4
votes
1answer
142 views

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 ...
4
votes
0answers
35 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 ...
4
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0answers
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 ...
3
votes
2answers
526 views

Initial population when i count backwards?

My question is dealing with how many ancestors it took to produce me: --> to produce me it took 2 people (my parents) = ($2^1$) people = 2 --> one generation further included = ($2^1 + 2^2$) people ...
3
votes
1answer
94 views

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 ...
3
votes
1answer
68 views

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 ...
3
votes
1answer
72 views

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 ...
3
votes
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) ...
3
votes
2answers
95 views

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 ...
3
votes
1answer
364 views

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 ...
3
votes
2answers
818 views

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, ...
3
votes
1answer
39 views

History: Do evolutionary and ecological processes occur at the same timescales?

Classically, it was thought that evolutionary processes occurred at a much slower pace than demographic/ecological processes. Nobody, ever thought about incorporating both processes into the same ...
3
votes
1answer
100 views

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 ...
3
votes
0answers
30 views

Expected reproduction rate of a dandelion and/or fern

I am working a basic mathematical/computer simulation of an ecosystem, and I need to know the birth rate of each organism in my simulation. However, I could not find any data for how often a small, ...
3
votes
0answers
80 views

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 ...
2
votes
1answer
64 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 ...
2
votes
1answer
43 views

Recessive alleles at Hardy-Weinberg equilibrium

I've run into a question that I disagree with others on but I would like to receive the input of others. The question is: If a population is at Hardy-Weinberg equilibrium, which of the following can ...
2
votes
1answer
51 views

$F_{ST}$ 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 ...
2
votes
0answers
17 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 ...
2
votes
0answers
46 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 ...
2
votes
0answers
219 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 ...
2
votes
0answers
182 views

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 ...
2
votes
0answers
48 views

$F_{ST}$ 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 $F_{ST}$: $$V_{Among Pop} = 2 F_{ST}V_G$$ ...
2
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0answers
33 views

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 ...
1
vote
2answers
101 views

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 ...
1
vote
1answer
40 views

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 ...