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

Can we estimate effective population size from DNA sequence data (CR or cytB sequence)? [closed]

I have DNA sequence data (control region) of two population of a species. Can anybody suggest me any software to calculate effective population size? Is it possible and meaningful?
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How to interpret McDonald-Kreitman test results?

It is easy to get the numbers right and calculate neutrality index. It is easy to memorize "equals", "greater", "lesser", etc. At least on the exams, when certain level of simplicity is assumed. But ...
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Is genetic purging based on random shuffling of the genes of an individual or is it more intentional way of removing deleterious recessive alleles?

Inbreeding depression may be reduced by selection against deleterious alleles, which eliminates, or purges, them from the population. I have two questions: Is genetic purging based on random ...
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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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42 views

Use numbers or algebra when introducing an evolutionary biology concept?

I'm working on an (approximately 20 pg) evolutionary biology paper for submission to a journal. The paper introduces a couple of strategies (I use "strategies" loosely; they can be carried out by ...
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1answer
39 views

Genomic control explanation

I am following the original genomic control article - http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.167.8448&rep=rep1&type=pdf What's the role of $p_i$ in the article? It says that ...
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Replication cohorts in microbial GWAS

Replication in an independent cohort is of course the gold standard in GWAS studies, and many high profile journals will now (quite rightly) not accept finding indicating a phenotype genotype ...
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1answer
49 views

Background (null) distribution for higher observed frequency of an allele [closed]

I am testing the hypothesis that being heterozygote at a certain gene locus, say X, increases the chances of having the good allele of X compared to being homozygote. I have data of more than 6000 ...
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How can someone share 50% of their DNA with their parents yet all humans share 99.9%?

I have heard that humans share 99.9% of their DNA with other humans. I have also heard that a child shares 50% of their DNA with their parents. How do I resolve this apparent contradiction? It has ...
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135 views

Is it mostly true that predators or parasites traverse wider spatial areas than their prey or hosts?

Does it tend to be true that as you go up the food chain, the species tend to cover wider areas? I am basically asking whether a population's prey varies spatially more than a population's predators ...
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1answer
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Question about the consequences of non-random mating and allele frequencies

I just began studying population genetics, and I don't understand something that is written in my lecture: Consequences of non-random mating: More homozygote and less heterozygote individuals in the ...
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1answer
77 views

Why aren't there more Ash-Red pigeons?

My favorite color pigeon is Ash-Red, but I don't see a lot of them. I figured it must be a recessive phenotype, but when I googled it, I found out it's dominant. So why aren't there more Ash-Red ...
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189 views

Text Book Recommendation: Organic Evolution

I was wondering if anyone could point me in the direction of any text books on organic evolution? I have recently become interested in the subject and would like to know more. I think an undergrad ...
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2answers
794 views

How is “selection” best defined?

There is natural selection but there is also sexual selection which some regard as a category of natural selection. There is also artificial selection (by humans). The question is, what is a most ...
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1answer
449 views

How to calculate Fst from AMOVA

I calculated an AMOVA from a genind object, with one hierarchical factor. In the table I obtain there are SSD values (for my grouping factor,"Error" and total) and sigma2 values (for my grouping ...
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0answers
62 views

What is Hamilton's rule for multiple generations?

What is Hamilton's rule as it applies to multiple generations? Is it that the lineage success given up by the actor must be exceeded by the lineage success acquired times the relatedness between ...
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112 views

Isn't heritability more important to genic capture than just genetic variance?

Rowe & Houle (1996) give two criteria for the selection of costly female choice: Condition dependence of sexually selected traits High genetic variance in condition Regarding heritability, ...
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1answer
63 views

How EGDS (endurance genetic distance score) is calculated?

Can anybody please make me understand how EGDS5 has been calculated to 40.8 in this paper at page#31? The formula has been described in this paper but when i tried the same, I am not getting the same ...
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1answer
145 views

Polymorphism in number of chromosomes?

The answer to this question, saying that Down Syndrome - a trisomy of human chromosome 21 - is caused by de novo mutation (rather than resulting from standing variation) made me think about ...
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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 ...
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1answer
70 views

How can one calculate “probability of possessing a ‘perfect’ profile” from “typical optimal genotype frequencies”?

Can anyone please explain how the "Probability of possessing a ‘perfect’ profile" was calculated from "typical frequency of optimal genotype" in Table 1 in this paper? Paper link here
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453 views

Can the value of heritability be greater than 1?

Heritability defined as genetic variance divided by total variance seems to be bounded between 0 and 1. However, I see a way of calculating heritability on this page (http://www.radford.edu/~rsheehy/...
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1answer
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How would you model the evolution of two genotypes across generations?

Say you have a genotype A that produces x offspring and another genotype B that produces y offspring, where x>y. These x offspring are of genotype A but with modest differences in fitness due to ...
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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 $1$, $...
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1answer
95 views

Heritability in population genetics

What is the difference between narrow sense heritability and broad sense heritability? Does heritability in the broad sense refer to the degree of genetic determination? Heritability in the narrow ...
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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 ...
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What are the consequences of inbreeding?

Inbreeding increases the risk of getting two identical recessive genes, alleles, that cause a disease which wouldn't have been activated with mixed genes. That's how I understand it anyway. But I ...
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1answer
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Assumptions of Hardy-Weinberg rule

The post Solving Hardy Weinberg problems offers an easy explanation of Hardy-Weinberg rule. The current top answer explicitly does not talk about the assumptions of Hardy-Weinberg. A model makes sense ...
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How do I solve this problem related to specificity and sensitivity?

Consider an autosomal recessive disease with an incidence of 1/10,000 in the general population of 100,000. Your best friend comes to you very upset because he has just taken a screening test for this ...
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How Can Homosexuality be Genetic? [duplicate]

I hold no strong opinions towards homosexuality one way or the other; I'll personally refrain, but don't apply my personal tastes to the rest of the world. I remember seeing some articles a while ...
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262 views

Example of code with pypgen (python)

I have a VCF file and wish to calculate a few indices of population divergence over a sliding window. I consider using pypgen but the documentation is currently very limited. Can you please give me ...
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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 ...
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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 ...
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1answer
184 views

Hardy Weinberg principle

The principle is that sum total of all allelic frequencies is 1. Individual frequencies for example can be named p,q.In a diploid cell , p and q represent the frequency of allele A and a respectively ...
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2answers
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Is this formula describing the loss of unfixed genes from a population accurate?

In the 1954 science fiction novel Search the Sky by Frederick Pohl and Cyril M. Kornbluth, a formula is featured that "quantitatively describes the loss of unfixed genes from a population". $$L_T=L_0 ...
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63 views

Need clarification on HKA test

I understand that HKA test tests for neutrality. And under neutrality we say that "ratio of segregating sites with species (S1) and fixed differences between locus (F1)" (S1/F2) at one locus is equal ...
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1answer
228 views

How migration creates Linkage Disquilibrium

I want to know how admixture and migration creates linkage disequilibrium? I am reading about it but I really don't quite get it.
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Need clarification on Coalescent with Recombination

I've been reading about recombination with coalescent. The link to that file is as follows: http://www.stats.ox.ac.uk/__data/assets/pdf_file/0008/4688/Reading_for_Recombination.pdf I get the part ...
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1answer
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Is inbreeding really efficient at producing homozygosity?

Inbreeding results in homozygosity. I've come across this concept many times and there's a question that comes to my mind every time I read it. Let us suppose the character we are trying to ...
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241 views

Infinite site model and Watterson's Estimator

Why is it that under migration, the watterson's estimator (theta) is upward biased? What does upward bias means? And why do we have downward bias under exponential growth? Lastly, is it only the ...
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1answer
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Does anyone know of a study supporting predictions #2 or #9 of the Extended Evolutionary Synthesis?

Regarding the 12 predictions made by the Extended Evolutionary Synthesis (http://extendedevolutionarysynthesis.com/about-ees/), does anyone know of a study that supports #2 or #9? It seems like #1, ...
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2answers
754 views

How to distinguish between a genetic bottleneck and directional selection?

Genetic bottlenecks and directional selection should have relatively similar genetic signals: reduced heterozygosity and greater genetic divergence (Fst?) in contemporary populations compared to the ...
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1answer
1k views

How does Genetic drift and selection affect fixation of an allele?

I want to know how does genetic drift, and selection coefficient (s) together affect the fixation of an allele? For example, if there is a neutral allele (s=0), will only genetic drift cause the ...
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1answer
70 views

Linkage disequilibrium

I want to know what ranges of value can D' in linkage disequilibrium take? Because I read in my book (An introduction to population genetics by Nielsen and Slatkin) that D' is guaranteed to be between ...
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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 ...
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223 views

Genotype frequencies and fitness values in haploid population with clonal growth

I found a small problem, and I am not sure at all about my answers. If someone could correct it, that would be awesome. Consider a heterogeneous population with the following genotype frequencies ...
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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 ...
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102 views

Interpretation of table on analysis of genetic diversity between groups

I am very confused about how to interpret Table 8.3 in Smith's Evolutionary Genetics. Is the GST in the table the same as the G,ST (with the comma), which is defined (pg. 156; Box 8.3) as "the ...
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1answer
327 views

Lethal gene and population genetics

In the European population, about 1 in 2500 people suffers from Cystic Fibrosis, a genetically determined (descared), autosomal disease. Healthy parents have a child suffering from Cystic Fibrosis. ...
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409 views

How to determine whether changes of an allele's frequency are due to genetic drift or selection?

Given that both natural/artifical selection and genetic drift are evolutionary mechanisms that influence how allele frequencies shift in a population: Are there ways to determine whether a frequency ...

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