Questions tagged [population-genetics]

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

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156 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 ...
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1answer
177 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 ...
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47 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 ...
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79 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 ...
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91 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 ...
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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 ...
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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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251 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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315 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 ...
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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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174 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....
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157 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} =...
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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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1answer
121 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}\\ ...
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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
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
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1answer
114 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 ...
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2answers
78 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
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1answer
69 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 ...
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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
112 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
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1answer
87 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
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1answer
612 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
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2answers
83 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
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1answer
380 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
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1answer
296 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 ...
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1answer
6k 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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1answer
63 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
907 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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1answer
109 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
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1answer
120 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 ...
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2answers
39 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
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1answer
47 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
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1answer
156 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
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1answer
1k 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
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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
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1answer
456 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
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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 ...
2
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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
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 ...
2
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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....
2
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1answer
2k 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
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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 \...
2
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1answer
116 views

Modeling inclusive fitness

Consider a population of two altruist with coefficient of relatedness $r$. The average inclusive fitness of this population will be $w_{0} + br -c$. Like in this example, assignment of inclusive ...
2
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1answer
625 views

How do you convert mtDNA sequences in FASTA to FSTAT format?

I've got control region sequence data from a population of shark and I'm looking to convert this from FASTA to FSTAT in order to calculated the effective population size of females. The software I ...
2
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1answer
496 views

Heterozygosity and the Wright-Fisher model

I was reading the textbook Probability Models for DNA Sequence Evolution by Durrett. In chapter 1, he discusses the Wright Fisher model and the coalescent theory ...
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0answers
39 views

What the “due to” means in the definition of heritability?

According to Wray and Visscher, heritability is formally defined as the proportion of phenotypic variation (VP) that is due to variation in genetic values (VG). My question is, what does “due to” ...
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108 views

what is the difference between homozygous and heterozygous duplication?

In a genetic test result it's written homozygous duplication or heterozygous duplication Does it mean four copies of the ...
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19 views

Is there an existing database of mutation rates for mitochondrial loci?

I'm wondering if there exists a database of mutation rates (transitions and transversions) for both mitochondrial loci (such as cytochrome c oxidase subunit I (COI)). Due to the use of COI as a DNA ...