Questions tagged [population-genetics]

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

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264 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
633 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
187 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
114 views

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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64 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
237 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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60 views

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
99 views

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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0answers
249 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
88 views

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
789 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
74 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
238 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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226 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
328 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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1answer
425 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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1answer
354 views

Does covariance and phenotypic variance have to be for the same trait to calculate narrow-sense heritability?

I'm working on a problem where I'm given that the phenotypic variance of the parent, $p$, for trait $A$ is $175.2$ and the phenotypic variance of the offspring, $o$, for trait $A$ is $146.1$. However, ...
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1answer
477 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 ...
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2answers
86 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 ...
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1answer
2k views

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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1answer
683 views

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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1answer
75 views

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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3answers
1k views

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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3answers
424 views

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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38 views

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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1answer
266 views

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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0answers
149 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
892 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
242 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
418 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
2k views

Outbreeding depression in humans [duplicate]

Is there any evidence of outbreeding depression in human beings?
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2answers
98 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
50 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
69 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
71 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
83 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 ...
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1answer
543 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
600 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
95 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 ...
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1answer
999 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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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 ...
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2answers
442 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
89 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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60 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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