Questions tagged [population-genetics]
Questions related to the study of the distributions and changes of allele frequency in a population.
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Probability of number of boys and girls being born on a single day [closed]
I am new to genetics, I have the following question at hand :
If four babies are born on a single day, what are the chances that
$A>$ Number of boys and girls will be equal.
$B>$ All $4$ will ...
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Genotypes in diploid/haploid cells under mitotic/meotic cell divisions
I am new to genetics , and am stuck with the following question at hand:
If $2$ cells with genotypes $(A/a)$ and $(A/a,B/b)$ undergo mitotic and meotic cell divisions respectively, what will be the ...
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Fst Differences Between Mature Trees and Seeds
For a single co-dominant locus in two populations of blue oak, I am given genotype frequency data (genotypes are AA, AB, BB) for adult trees (at least 150 years old) in both populations (pop 1 and pop ...
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Allele frequency question
You are heterozygous at locus A. Both of your alleles, A1 and A2, have a 10% allele frequency in the population. If you are one of 22 people in a room, how many people do you expect to share a locus A ...
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Is the variance of a trait related to its rate of evolution?
Posed with a question that has me stuck:
Is increased variance of a phenotypic trait in a population associated with slower evolution of that trait?
I have to either 'disagree or agree' and argue ...
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Method to estimate age of a variant from genotype data
I will obtain array genotype data from approximately 60 related individuals who all share a rare pathogenic variant, which is at such a high frequency in the enlarged family due to a founder effect.
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Summary statistic that can distinguish between migration from pop2 to pop1 vs. pop1 to pop2
Given two sister populations that diverged some time ago, say pop2 migrates to pop1 and breeds there, giving offspring with sequence segments similar to those from pop1 but not in pop2. There are ...
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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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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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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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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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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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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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Outbreeding depression in humans [duplicate]
Is there any evidence of outbreeding depression in human beings?
user21998
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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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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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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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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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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 cell in ...
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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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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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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
...
user21998
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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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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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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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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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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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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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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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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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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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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 ...
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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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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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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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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 ...
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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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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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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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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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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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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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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 ...
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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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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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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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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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How should one interpret heritability? Is it related to $R^2$?
From Wikipedia:
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. ...
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"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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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 ...
