Questions tagged [population-genetics]

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

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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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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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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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217 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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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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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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59 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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39 views

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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441 views

How should one interpret heritability? Is it related to $R^2$?

From Wiki: 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. It ...
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374 views

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 ...
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129 views

Interpretation of F in inbreeding on the population level

The inbreeding coefficient for an individual gives the probability that the individual has two alleles at a locus that are IBD. What interpretation does the inbreeding coefficient have on the ...
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511 views

How do you create a .snp datafile?

I'm looking to use the software DIYABC 2.1.0 to apply approximate bayesian computing (ABC) to some resequenced data that I have. The resequenced data is in FASTA format however, and the software ...
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197 views

How do I import FASTA files into Haploview?

I'm trying to produce a haplotype network and so have decided to use the software haploview. However I'm having some problems importing my sequences into the software. I Have my sequences in a FASTA ...
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Genetic diversity from meeting an isolated tribe?

Assume we make contact to a tribe we did not know existed. We understand the value of genetic diversity for our species. And as we had no contact for a long time, we can assume that the tribe adds to ...
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34 views

What are the consequences of less DARC expression as a result of a Duffy weak allele?

According to codegen.eu I'm a carrier of a Duffy weak allele. For SNP rs34599082 I have alleles C and T. T is a rare allele that found is less thatn ~1% of the population. Codegen.eu directs me to ...
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How can I calculate Fst, Gst, and Nei diversity index?

I got different polymorphisms of Cucumber mosaic virus in different regions of its genome from different libraries of RNAseq. This virus have two coding regions which are 3A and CP regions. I have ...
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19 views

Population structure from mtDNA sequence data: A thought experiment

I have 5'-COI sequences for a species of interest, which were downloaded from the Barcode of Life Data (BOLD) systems. Assuming for the moment that the said species was sampled across its entire ...
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26 views

Selection coefficient of gorillas

I've been reading about selective sweeps. And I found a case study that talks about drosophila and how their selection coefficient is between 0.0001 and 0.005. I want to know what it'll be like for ...
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30 views

What metric(s) is a good proxy for relatedness?

In attempting to seed a simulation, where an individual foregoes resources that go r to same-type individuals and (1-r) to all members (including same-type individuals). What commonly used metrics ...
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92 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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27 views

difference between population genetics and genomics

I don't have a biological question therefore, this might be be quite basic. But I want to know does genomics entail population genetics or these are completely different fields?