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Questions tagged [population-genetics]

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

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0answers
140 views

How to tell if/how allele frequencies change (USABO question)

This is question number 34 from the 2014 USABO Open Exam: Black and white mice live on an island and have allele frequencies of B=0.20, b=0.80. On the continent, there is a much large population of ...
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1answer
1k views

Hardy weinberg equilibrium and Wright Fisher model

Is the hardy weinberg equilibrium derived by using a model similar to the Wright Fisher model, just without assuming genetic drift and finite pop size? Both seem to use the same assumptions except ...
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1answer
811 views

Ways to distinguish between purifying selection and selective sweep

When looking a population genomic data, regions of low diversity (lower than expected; such as in a region of high recombination) can indicate either purifying selection of deleterious mutations or a ...
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1answer
141 views

Learn Bioconductor the hard way!

I came to analyzing population genetics data from the background of a theoretician and a computer biologist but not with the standard tools that a bioinformatician (or empiricist in population ...
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1answer
378 views

How to get the average number of pairwise differences among populations?

I have genetic data in .structure and .vcf format (and can easily reach other formats with PGDSpider). The population of interest is structured and I would like to calculate the average number of ...
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1answer
4k views

How to confirm pure-breeding parents

I was reading Genetic Analysis (Sanders, Bowman) and saw the following figure summarizing the 1909 work of Herman Nilsson-Ehle in describing the genetic control of kernel color in wheat: How did ...
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1answer
1k views

Outbreeding depression in humans [duplicate]

Is there any evidence of outbreeding depression in human beings?
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2answers
94 views

Interspecies competition and pathogen

Following my answer to this question, a debate ensued on whether the loss in population of one species (namely red squirrels) due to its lesser resistance to a pathogen brought by a competing species (...
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1answer
49 views

Reconstituting genomes of archaic tribes of humans

Will it be logically possible for genome studies to reconstitute the genomes of our local human populations as they were 2000 and 4000 years ago? What is the mathematical precision and science for ...
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1answer
66 views

What factors make a sequence evolve non-randomly?

On the wikipedia page about Fay and Wu's H, it talks about a non-randomly evolving sequence may be due to some selection acting or a selective sweep or population expanding/contracting. My questions ...
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1answer
65 views

Confusion over equations for population's heterozygosity vs. heterozygous individuals

On page 24 of Gillespie's Population Genetics, 2nd ed, an equation for $H$, the probability that two randomly drawn alleles are different by state, is given. $H$ is stated to be similar to the ...
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1answer
65 views

Is it possible to have a random un-mutation of genes?

According to this article: Gene mutations can be classified in two major ways: Hereditary mutations are inherited from a parent and are present throughout a person’s life in virtually every ...
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1answer
485 views

ExAC Browser: What does a “dubious variant annotation” mean? [closed]

I am studying a protein in the ExAC browser. However it is flagged with a "LoF flag". What exactly counts as a "dubious" variant in ExAC. I couldn't find any further information neither at the ...
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1answer
587 views

Why was the study of “Concordance of Monozygotic and Dizygotic twins for traits” designed in this way? [closed]

I am confused by the twin study 'Concordance of Monozygotic and Dizygotic twins for traits.' My questions arose from 3:17-4:17 of the video And this is the related data I have referred I have ...
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0answers
91 views

Hybridization of an Indo-Aryan ethnic group and a Tibeto-Burmese ethnic group

The state in which I reside houses these two distinct ethnic groups. Physical Traits of the Indo-Aryan group Height:Medium Eyes:does not posses epicanthic fold Nasal bones:is not flat and broad ...
3
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1answer
921 views

How do heredity and regression to the mean work with respect to intelligence?

I am trying to understand the heredity of intelligence between generations in general, and how regression to the mean works in detail in particular. The answer I'm looking for should preferably answer ...
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110 views

What is the effective population size of a simple two deme metapopulation?

I am confused as to how to compute the effective population size $N_e$ of a theoretical structured population. Let's consider here a simple case study. Imagine a 2-deme metapopulation. Each deme is ...
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2answers
426 views

Are heterozygotes always fitter than homozygotes? Can inbreeding be beneficial?

Inbreeding is mostly not very good because when there is a 'disease' in one allele, the other could/would take over the function. But when you have two of the same genes/alleles, do they, or could ...
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1answer
86 views

How are the dominance and additive effects reflected in the mean and variance of the offsprings of two individuals with known phenotype?

If I estimated the genetic additive σ2A, genetic dominance σ2D and environmental effect σ2E of a trait in a population, what will be the predicted value of the offsprings of two individuals with known ...
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59 views

Ecological specialization and relative abundance

I am reading Evolution in Changing Environments by R. Levin but have a hard time. Claim At page 25, Levin says as a conclusion The more efficient a caste at meeting the contingency for which it ...
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1answer
6k views

What are Codominant vs Dominant Genetic Markers?

When talking about types of genetic markers, the adjective "dominant" and "codominant" are often used. I don't fully understand their definitions and found contradicting definitions. Foll and ...
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1answer
172 views

Statistical genetics: Allele frequencies that follow a Dirichlet distribution

From Foll and Gagiotti (2008) (software BayeScan). They consider a model where several subpopulation are derived from a unique ancestral population. We consider a set of $I$ loci and let $K_i$ be ...
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1answer
123 views

autosomal recessive population numbers

This question is background research for a science fiction / fantasy novel, my knowledge of genetic is very basic. It seems obvious to me that for genetic disorders that are autosomal recessive, if ...
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0answers
48 views

What model of epistasis best fit the reality?

In theoretical population genetics, it is very common to have to assume a model of epistatic interaction. The two most common models are the additive model and the multiplicative model. Additive ...
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1answer
4k views

How would cloning affect conservation of rare species?

Many species are at risk of extinction, and cloning could be seen as a relatively quick method to produce large numbers of members of the species to aid in conservation efforts, especially if the ...
2
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1answer
291 views

Relationship between genetic diversity within and between species

Here is a quote from Wagner (2008) A second line of evidence [against neutralism] comes from the relationship between the mean number of polymorphic differences between alleles within a species, $\...
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429 views

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

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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0answers
39 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
75 views

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

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 ...
3
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2answers
4k 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
231 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 ...
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247 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
852 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 of ...
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1answer
936 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
3k 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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314 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
111 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
146 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 (...
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0answers
110 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
198 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
437 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
62 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 Q(...
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0answers
368 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
213 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 controls....
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1answer
5k 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
575 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 ...
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1answer
2k 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 ...
5
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1answer
208 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
106 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
497 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 ...