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

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51 views

How does the introduction of clones would affect population genetics? [on hold]

Since the ability to clone animals gives another way to preserve species, this could help for the breeding process. It has been noted that with the ability to clone animals, endangered species can ...
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9 views

Effective population size of a continuously spread population

Is there any model to calculate (theoretical predictions) the effective population size of a continuously spread population? Imagine for example a population spread over an infinite 2D landscape. ...
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10 views

Effective population size of a metapopulation structured on a grid

Scenario Consider a rectangular metapopulation consisting of $x \cdot y$ demes, where $x$ is the number of deme horizontally and $y$ is the number of demes vertically. The population size per deme is ...
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1answer
38 views

How big advantage had a trait have to bring to evolve in the human evolution? [on hold]

Yes, I've heard that we have evolved from the common ancestor with primates as intesively, as the chimpanzees. Sometimes I read about some enormously complex traits, evolutionary psychologists think ...
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22 views

Identity By Descent vs Identity By State

Background The concepts of Identity By Descent (IBD) vs Identity By State (IBS) are central in population genetics, yet I fail to fully wrap my head around the definitions. You can find examples ...
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1answer
28 views

Hardy-Weinberg equilibrium generalized to add inbreeding (non-random mating)

Background Quoting from Gillespie's book The level of inbreeding is measured by the inbreeding coefficient, $F_I$, which is the probability that two alleles in an individual are identity by ...
2
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0answers
43 views

Population size and genetic drift - What are the evidences?

Wright-Fisher model From the Wright-Fisher model of genetic drift, the random sampling of allele from one generation to the next is taken from a binomial distribution with parameters $2N$ and $p$, ...
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1answer
33 views

Is there a difference between macroevolution and group selection?

I encountered two different attitudes towards macroevolution: The first one included long-term microevolution such as the evolution of Cetacea. The second one included only macroevolution in terms ...
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1answer
40 views

What's the difference between evolution fitness and reproductive success?

What's the difference biological fitness and reproductive success in the biological terminology?
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1answer
39 views

Why is the probability of fixation of an allele equal to its frequency?

Introduction In a panmictic population, the probability of fixation of an allele at a neutral locus is equal to its frequency at that time. I will refer to this probability of fixation as calculated ...
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0answers
18 views

Runs of homozygosity - degree of inbreeding and disease associations

Been reading recently about methods to determine how inbred a particular person is by measuring their "runs of homozygosity." Loosly, these are defined as regions of the genome (typically >1Mb) where ...
6
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1answer
70 views

Why is there no symmetry in pigmentation when comparing people north and south of the equator?

If you are at the equator and start moving north, the further you travel, the lighter the skin of the indigenous peoples. Considering that we live on a ball, why do we not find the same traveling ...
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1answer
39 views

Can we say it's hybridisation if it's the same species?

If we mixed two population of the same species into the same environment and then they reproduce together, can we say it's hybridisation? The wikipedia definition is the following: Hybridisation ...
3
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0answers
43 views

Is $F_{ST}$ a probability and a correlation coefficient?

$F_{ST}$ is one of the most famous and most important statistics of all of evolutionary biology. Yet, many people misunderstand it or misuse the classical results from the literature on $F_{ST}$ ...
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2answers
103 views

Would a colony with only one male and female collapse?

This is a thought experiment: If we form a population with only a single founder pair, can this population survive? What would happen? Would this inbreeding cause the population to go extinct? Could ...
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0answers
31 views

How should one interpret heritability? Is it related to $R^2$?

From Wiki: Heritability estimates are often misinterpreted if it is not understood that they refer to the proportion of variation between individuals on a trait that is due to genetic factors. It ...
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1answer
25 views

“Heterozygotic expection” - when heterozygote differs from both homozygotes, but homozygotes are similar

For simple 2-alleles genetic model {a,A} and corresponding quantitative trait Q is typically true that Q(aa)>=Q(aA)>=Q(AA) or conversely Q(AA)>=Q(aA)>=Q(aA). For example, dominance means that ...
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0answers
38 views

Relation between heterozygosity and allelic diversity in founder effects/bottleneck?

Can someone try to explain me why allelic diversity falls faster than heterozygosity, reminding you that we're talking about bottleneck or a founder effect? Look at this graphic: It's clear to me ...
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1answer
69 views

What test to apply to detect genomic signatures of selection?

I would like to ask you for your sugestions for selecting a test to detect signatures of selection in the following mouse model: We have three groups: animals exhibiting trait A, trait B and ...
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1answer
215 views

Why are the genomes of Humans 99.5% the same?

Human's DNA sequence is said to be roughly 99.5% equal. As far as I understand, this means that if I walked up to you and compared our DNA, the sequence of base pairs would be 99.5% the same. My ...
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2answers
190 views

Do mutant alleles result from mutation of the wild type?

The allele that encodes for the most common form of a phenotype in natural population is called a wild type allele and all the rest of the alleles encoding forms other than the wild type are called ...
6
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1answer
118 views

Effect of sex-ratio on the effective population size

As stated on this wikipedia article, the effective population size $N_e$ when the sex ratio differs from $\frac{1}{2}$ is $$N_e = \frac{4N_mN_f}{N_m+N_f}$$ I understand the biased sex-ratio ...
3
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0answers
51 views

Diffusion approximation to genetic drift

I am reading from the classical textbook Principles of Population Genetics, Hartl and Clark (pdf here). Introduction Let $f(p,x,t)$ denote the distribution of allele frequency $x$ at time $t$ ...
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1answer
71 views

Why don't the genetic similarities between ‘unrelated’ individuals of the same and different species outweigh the differences?

Ever since starting to learn about the concept of inclusive fitness during my BSc, I've been bugged by this questions: if inclusive fitness can account for many ‘altruistic’ behaviors, why don't the ...
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1answer
55 views

From STRUCTURE to FSTAT format

From numerical simulations I output a file that is input to STRUCTURE (Hubisz et al. 2009). I now realize that I would need to process my data with FSTAT (Goudet 1995). Both are text files. Is there ...
2
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1answer
169 views

Calculating pairwise Fst from allele frequencies

I am trying to refresh my memory on population genetics for a project, and I'm having some trouble. Assume I have genetic data on 3 populations with 5 individuals in each of a given species, with the ...
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0answers
16 views

Interpretation of F in inbreeding on the population level

The inbreeding coefficient for an individual gives the probability that the individual has two alleles at a locus that are IBD. What interpretation does the inbreeding coefficient have on the ...
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2answers
260 views

What is the difference between fixation and loss of alleles in a population?

When running a simulation in PopG, with parameters: Population size: 100 AA fitness: 1.0 Aa fitness: 1.0 aa fitness: 1.0 Mutation A to a: 1.0E-6 Mutation a to A: 1.0E-6 Migration rate between ...
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0answers
52 views

How do you create a .snp datafile?

I'm looking to use the software DIYABC 2.1.0 to apply approximate bayesian computing (ABC) to some resequenced data that I have. The resequenced data is in FASTA format however, and the software ...
4
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2answers
80 views

Is it possible for two people to repopulate earth? [closed]

Today I was wondering this question whether it is possible for two people to repopulate Earth. What if everyone else disappeared, except for two people (man & woman)? Can they repopulate? In ...
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1answer
30 views

Genetics of Hybrids

I'm working on this problem, but I'm not sure I've done it correctly. My initial thought was that the answer was $D$, but I don't see anything in the above graph that indicated the Hybrid species ...
3
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1answer
54 views

What is meant by “the degree to which a gene is expressed” in an individual?

Here is an excerpt from a text that I was reading, Here is an example of microarray data. The idea is to take a group of different individuals and for each of them, you measure how much they ...
2
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1answer
47 views

Who was the first to coin the terms of soft and hard selection?

Soft and hard selection are sometimes used with different definitions. I have been told that at first place hard and soft selection has been defined in the following way: soft selection: Each deme ...
2
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1answer
121 views

Is the fixation rate always equal to the mutation rate for neutral alleles?

Background A classical result of population genetic is that the rate of fixation of netreual alleles is the mutation rate $\mu$. The reason is that each generation $PN_e\mu$ mutations enter the ...
2
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2answers
63 views

Role of drift in evolution of sexually dimorphic traits

Is there a model for predicting how drift can affect the evolution of a sexually dimorphic (SD) trait? I've been trying wrap my mind around this paradoxical question; sexually dimorphic traits evolve ...
0
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1answer
32 views

IBD-value and IBD-fraction

I have some questions about the IBD-value and IBD-fraction for two of the condensed identity states, $S_1$ and $S_7$. My questions: 1) Is the IBD-value for the individuals i and j two (2) in $S_1$ ...
1
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1answer
325 views

What is a selective constraint?

I encountered the term selective constraint in Huber et al. 2015, page 4 (last paragraph) in: If invariable sites are included in the analysis, then both the methods of Kim and Stephan ...
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1answer
68 views

Disease causing variants and Hardy-Weinberg Equilibrium

Is it true that many disease causing variants/mutations do not follow Hardy Weinberg Equilibrium? If so, then please elaborate on why this may be true (or not) and provide examples. I am interested ...
2
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0answers
47 views

Variance in reproductive success and effective population size

Background The effective population size $Ne$ is the size of the Wright-Fisher population that experience the same amount of drift than the population under consideration. The higher the variance in ...
3
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1answer
39 views

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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26 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 ...
3
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1answer
84 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
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2answers
454 views

What exactly is extreme heterozygosity and how does it work?

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 ...
2
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2answers
186 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 ...
13
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0answers
223 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 ...
6
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0answers
62 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 ...
6
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2answers
126 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 ...
2
votes
1answer
174 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 ...
5
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0answers
73 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
106 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 ...