Questions tagged [population-genetics]
Questions related to the study of the distributions and changes of allele frequency in a population.
305
questions
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Practical Question about Evolution, Population Genetics and Speciation
North American cicada male of the genus Magicicada sing depending on the species at different times of the day and attract the females of the corresponding species. The species are very similar, but ...
3
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1answer
737 views
What is the difference between nucleotide polymorphism (θ) and nucleotide diversity (π)?
In my population genetics book (see reference at bottom) they define them as:
Nucleotide polymorphism (θ): proportion of nucleotide sites that are expected to be polymorphic in any sample of size 5 ...
3
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1answer
167 views
Correct migration rate expression in infinite island model
In Sewall Wright's infinite island model, where all demes exchange migrants each generation, I have seen the migration rate stated variously as $m$ or $\frac{m}{d - 1}$ (as in Matthew B. Hamilton's ...
3
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1answer
212 views
How to predict future generations from heritability
The heritability of human intelligence is estimated to be around 0.5. There are of course various estimates, some lower, some higher. But let's work with this value of 0.5 for the moment.
I wanted ...
3
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26 views
ABO allele frequencies: Why use the EM algorithm?
In textbooks and lecture notes and slides posted online, determining allele frequencies using blood type information (ABO), under the assumption of Hardy-Weinberg equilibrium, is accomplished using ...
3
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0answers
107 views
How does the new discovery that mitochondrial dna is inherited from both parents change population genetics and other dates?
This new study seem to have pretty much proven that mtDNA is inherited from both parents. I assume that this would lead to most age estimates of ancient human ...
3
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0answers
51 views
Offspring of parents with different number of chromosomes
Many papers report that dog-whelks (Nucella lapillus) show a distinct chromosomal polymorphism between populations of 2n = 24 up to 2n = 36. Could somebody please tell me how many chromosomes the F1 ...
3
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81 views
How to choose the most appropriate measure of genetic distance
I am conducting a phylogeography study of a fish species and am trying to construct a phylogenetic tree to describe population structure and ancestry. I have constructed trees using various measures ...
3
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0answers
94 views
Why does my simulation not support the idea that inbreeding is bad?
After reading this post, I wrote some code to simulate inbreeding.
We have a population of $N$ creatures. Each creature has two genes, which come in two forms: recessive (a) and dominant (A). The ...
3
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1k views
Are epicanthic folds a dominant trait?
My state (Tripura) originally had a mostly mongoloid-feature-possessing population (ethnic group: Tripuri). Recently a large number of non-mongoloid people (ethnic group: Bengali) have migrated to ...
3
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0answers
114 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 ...
3
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258 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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321 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 ...
3
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0answers
113 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 $F_{ST}$ (...
3
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178 views
How to understand relatedness in an infinite island model?
My understanding is that the relatedness coefficient in kin selection models measures positive assortment. That is, altruism is more likely to evolve if altruists tend to interact with other altruists....
3
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0answers
161 views
Inbreeding Coefficient and Coefficient of Relationship
Wikipedia gives the following formula to calculate a "path of coefficient of relationship" between an ancestor $A$ and an offspring $O$:
$$\rho_{AO} = 2^{-n} \left( \frac{1+f_A}{1+f_O} \right)^{1/2} =...
2
votes
1answer
127 views
Definition of Linkage Desiquilibrium (LD)
According to wiki, linkage disequilibrium $D$ equals
$$D = x_{11} - p_1\cdot q_1$$
where:
$$
\begin{matrix}
\text{Haplotype} & \text{Frequency}\\
A_1B_1 & x_{11}\\
...
2
votes
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 ...
2
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1answer
1k 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 are ...
2
votes
1answer
118 views
Effective population size when the population sizes varies from season to season
Let's think of a species which has four generations per year and which population size changes from season to season so that the population size is 100 in summer, 200 in spring, 50 in autumn and 20 in ...
2
votes
1answer
59 views
What are the long term consequences of settling an isolated territory with an extremely limited gene pool?
I remember reading about a discredited theory - I'm afraid that, despite some frantic Googling, I've been unable to track down a link - which stated that Australia was first settled by a woman, ...
2
votes
2answers
101 views
What proportion of the people who lived 1000 years ago have genetic descendants alive today?
For context, I've been wondering about this for a paper I'm writing (in philosophy). Really, I want to figure out the chances that someone alive today will end up still having descendants 1000 years ...
2
votes
2answers
83 views
What is the conversion between r and FST?
From Schonman (2013):
...allele A can only invade under Hamilton’s condition R=$F_{ST}$ > C/B.
From Harpending (2002):
The best general definition of the coefficient of relation $R_{XY}$ ...
2
votes
1answer
70 views
What is the expected number of children that need to be born for every possible point mutation to occur once? [closed]
I'm reading The Perfect Health Diet, and in it the author says that the probability of a point mutation is (175/3*10^9) per new child. He then goes on to write:
In the Paleolithic, with 100000 ...
2
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1answer
1k views
Hardy Weinberg problem help!
The three common genotypes at the hemoglobin locus have very different phenotypes: SS individuals suffer from severe anemia, AS individuals have a relatively mild form of anemia but are resistant to ...
2
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2answers
114 views
“50% of the variance in antisocial phenotypes is the result of genetic factors” means what?
How can i understand the following sentence:
Overall, the conclusions reached by these studies have been highly consistent in showing that approximately 50% of the variance in antisocial phenotypes ...
2
votes
1answer
88 views
Down syndrome in subsaharan populations
What is the rate of occurrences of Down syndrome in subsaharan African populations? Is it the same as in white European populations?
An interesting hypothesis came to my mind:
Could it be that Down ...
2
votes
1answer
625 views
On the selection coefficient
I'm reading Williams' Adaptation and Natural Selection:
A Critique of Some Current Evolutionary Thought.
In this book the author talks about selection coefficients which, if I understand it ...
2
votes
2answers
84 views
Mixed-mating plants: is the number of mixed mating plants supposed to be trivial?
I am referring to Winn et al. 2011
Last sentence of the first paragraph is
Although sampling bias against both selfing and highly outcrossing species may inflate the frequency of mixed-mating ...
2
votes
1answer
391 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 ...
2
votes
1answer
72 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 cell in ...
2
votes
1answer
298 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, $\...
2
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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 ...
2
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1answer
7k 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 ...
2
votes
1answer
64 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
votes
1answer
141 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 $\text{...
2
votes
1answer
115 views
Coefficient of relationship and path of coefficient
A path of coefficient of relationship is defined as
$$\rho_{AO} = \left( \frac{1}{2}\right)^n \sqrt { \frac{1+f_A}{1+f_O}}$$
This SE post discusses this definition
From this, the coefficient of ...
2
votes
1answer
129 views
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 ...
2
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2answers
42 views
If number of children born were spread more evenly among all parents, would our species' genetics have more variability?
Instead of some parents having lots of kids, if the number of kids were spread more evenly to parents having few kids and people who have no children, would it introduce more genetic variability in ...
2
votes
1answer
61 views
Linkage between chromosomal loci and the Hardy-Weinberg principle
Referring to the Hardy-Weinberg principle, which is always stated with respect to a particular locus on the chromosome, if we observe that two different loci are either always together in Hardy-...
2
votes
1answer
188 views
Fst genetic distance: Autosomal vs. mtDNA
As far as I'm aware, mtDNA is only inherited from the mother. Hence, if I compute Fst from autosomal SNPs, then I'll get the actual genetic distance between two human populations.
If I compute the ...
2
votes
1answer
2k views
Dominance coefficient
I am trying to understand the meaning of the dominance coefficient. I'll be more specific to what I don't understand, in a moment.
Let $A_{11}$, $A_{12}$ and $A_{22}$ be genotypes with fitnesses $1$, $...
2
votes
1answer
2k views
How to determine the probability that a mutation is lost / fixed?
I have a question about how to determine the probability that a mutation is lost or fixed after 1 or 2 generations in population genetics.
Let's say we have a randomly mixing population, with N ...
2
votes
1answer
467 views
What is a typical value of the selection coefficient s?
I am trying to gain an understanding of the real world effects of natural selection from the equations, especially comparing it with drift. However I have been unable to find any examples which give ...
2
votes
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 ...
2
votes
1answer
68 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 ...
2
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1answer
7k 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 ...
2
votes
1answer
218 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....
2
votes
1answer
3k 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 (2002)...
2
votes
2answers
91 views
How to compute the regression of individual fitness on individual phenotype
Consider a population structured in groups of two individuals. Individuals' interactions follow an additive prisoner's dilemma:
\begin{array}{c |c |c|}
& C & D \\
\hline
\text{Cooperate (} C \...
