Questions tagged [population-genetics]

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

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206 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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66 views

Geographic regions as subpopulations/demes

I am developing a computational simulation for DNA barcoding. One of the parameters in my simulation is the number of subpopulation/demes, which I label as $K$. Most studies that use DNA barcodes tend ...
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1answer
124 views

Limit on the Number of Facial Phenotype [closed]

Individuals of each species all have unique facial structure variations (shape of nose, position of chin etc) from humans to birds and fish etc. We humans don't seem to be reaching mathematical limit ...
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Can the apparent drop in insect population be explained by local insects evolving to avoid traps?

In this widely reported Plos One article, it is stated that, after roughly 3 decades of placing Malaise traps in a set of predetermined locations (counting and replacing them regularly), a sharp ...
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53 views

Metapopulation structure - book recommendations

What book would you recommend me to study: the dynamics of metapopulations, the structure of metapopulations, the evolution in structured metapopulations? I am not looking for an introduction but ...
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1answer
78 views

About lack of selective pressure

In [1] it is stated that: the frequency of comutations in FGFR3 and KRAS or PIK3CA and KRAS was lower than predicted by chance, suggesting ... a lack of selective pressure for both mutations to ...
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41 views

What does the MAF/MinorAlleleCount mean?

I'm not sure why reporting the second most frequent allele is helpful? what is the Major allele?
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2answers
53 views

Equation relating probability of fixation and number of generations

I am trying to find an equation that relates the variables of probability of fixation and generations. Or, how does number of generations affect the probability a gene will fix, if population size ...
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1answer
57 views

What is the population limit that makes consanguinity an issue?

A recent incident brought in the news one of the last uncontacted people - the Sentinelese: the Sentinelese appear to have consistently refused any interaction with the outside world. ...
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165 views

Question on the concept of mitochondrial Eve [closed]

My question is about the very definition of this common ancestor. Why shouldn't be the mother of mitocondrial Eve the real Eva m (and so on to grand grand ...mother)? All I know on the subject comes ...
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2answers
268 views

Are Richard Lynn's estimates of African IQ inherently innacurate on the basis that most Africans aren't mentally retarded?

I've been looking at Richard Lynn's studies on average African IQ, and he seems to estimate really low IQs in the 60s range (e.g. http://www.sciencedirect.com/science/article/pii/S0160289609001275?via%...
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For allele frequency determination, is it good to take samples from a college/school or a hospital or any other technique?

I am trying to determine allele frequency of a hla allele. Preliminary analysis shows the prevalence of the allele (homo or heterozygous both) is 3%. The allele is related to a disease (After exposure ...
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21 views

Pentaploid genotype frequencies

I know that if I am dealing with a diploid case, and I have 3 alleles, then I can have 6 possible genotypes. I am doing this by adding up all the numbers from 1 to 3. $$1+2+3 = 6$$ But if I want to ...
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47 views

Why does the HLA show a high degree of polymorphism?

I know how the HLA undergoes high degree of polymorphism (random genetic rearrangements), but I have not understood why it undergoes rearrangements. What is the advantage offered when HLA shows a high ...
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1answer
57 views

How much generation of hamster's family it takes to get first bad mutations [closed]

So if I have two humsters and they start to reproduce themselfs then how much generations of hamster's family it takes to get first bad mutations? The info here does not help to find answer https://...
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29 views

Looking for book or article that derives formula for estimating the “average heterozygosity”

An online lecture I need to watch on population genetics describes a formula for the "average heterozygosity" as follows: ...we can theoretically predict that the average heterozygosity in the ...
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1answer
374 views

Island model vs. stepping stone model

Wright's Island model and Kimura's stepping stone model are classic explanations for migration/gene flow o individuals between subpopulations within the field of population genetics. My question ...
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30 views

Low migration rate in Papadopoulou et al. (2008)

In the paper "Speciation and DNA barcodes: testing the effects of dispersal on the formation of discrete sequence clusters" by Papadopoulou et al. (2008), is there an explanation as to why the authors ...
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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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62 views

“Heterozygotic expection” - when heterozygote differs from both homozygotes, but homozygotes are similar

For simple 2-alleles genetic model {a,A} and corresponding quantitative trait Q is typically true that Q(aa)>=Q(aA)>=Q(AA) or conversely Q(AA)>=Q(aA)>=Q(aA). For example, dominance means that Q(...
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1answer
52 views

Is it trivial to assume a version of Hamilton's rule that applies for numerous generations?

Is it trivial to assume that a version of Hamilton's rule that applies to numerous generations is: C > rB C = lineage fitness lost by an actor, B = lineage fitness gained from the act, and r = ...
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1answer
27 views

Finding specific genotype occurrences given allele frequency

So let's say I have a tetraploid species and I have 4 possible alleles for a particular locus. I have found that I can have 35 total possible genotypes and I know the allele frequencies for each of ...
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1answer
45 views

Gene frequency — database/site

Is there any free database when one can check the gene frequency in a healthy population? For example I would like to check it for genes like BIN1, CLU or CR1. On the English Wikipedia I found a gene ...
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1answer
32 views

Simple interpretation of effective population size?

I'm looking for alternate ways to explain effective populations size, in more conceptual terms. These need not be perfectly accurate "definitions" but should at least be generally accurate in non-edge ...
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1answer
40 views

Chart of intra-species genetic diversity across species / phyla?

I am looking for information on how genetic diversity within a species (not between species) differs between taxa. In other words: Is the "spread" in the genetic pool, if measured, for instance, in ...
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1answer
131 views

Variation of fixation probability over time in Wright-Fisher model

In Wright-Fisher model of population size N and initial mutation frequency of 1/N, how does the fixation probability vary over generations. So, mathematically, what is the function that maps the ...
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1answer
76 views

What is the probability that there are no substitution between an ancestor and a modern individual?

What is the probability that there are no differences if you compare the DNA of the ancient sample to a single DNA sequence from a modern individual? Assuming the individual was diploid and lived T ...
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1answer
597 views

Does the term “fitness advantage” or “fitness disadvantage” make sense?

Same for the terms "selective advantage" and "selective disadvantage" which I intend to use synonymously. There are usages of each on Google Scholar, but do evolutionary biologists understand what is ...
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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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1answer
351 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
1k 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. $B>$ ...
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1answer
49 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
87 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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1answer
862 views

Is there a difference between macroevolution and group selection?

I encountered two different attitudes towards macroevolution: The first one included long-term microevolution such as the evolution of Cetacea. The second one included only macroevolution in terms of ...
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12 views

Lineage inference based on N randomly partitioned copies of a gene

I am interested in reconstructing cell lineages based on the sequences of randomly partitioning plasmids. I can find lots of models to build lineages based on a single sequence (e.g. bacterial gene) ...
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30 views

How do we formulate the mutational load for “junk DNA”?

Question(s) Based on Joe Felsenstein's textbook, I was trying to formulate the mutational load for the majority of eukaryotic genomes that are junk DNA ($L_{most\_of\_genome}$). (See background ...
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27 views

Probabilities in calculating the kinship coefficient

I've been reading up to try to understand how the kinship coefficient (or coefficient of coancestry) is calculated. https://brainder.org/2015/06/13/genetic-resemblance-between-relatives/ this is the ...
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41 views

Will a less favorable allele's frequency go to 0?

For example, a pond is dark in color. There are two alleles. The dark color allele is dominant over the light color one. Let's assume that the relative fitness of both the homozygous dominant and ...
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54 views

Why do individuals vary in the number of SNPs for a given gene ( e.g. FOXO3A )?

Individual #1, sequenced by 23andMe and then inputed into Promethease for SNP data has the following SNP output: 1) rs1935949(C;T) 2) rs2802292(G;T) 3) rs13217795(C;T) 4) rs13220810(C;T) 5) rs2764264(...
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21 views

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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46 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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13 views

Finding genotype/allele frequencies of second generation in Hardy-Weinberg equilibrium given that the recessive allele is deleterious [duplicate]

A population in Hardy-Weinberg equilibrium has p=0.6 and q=0.4, and allele q (recessive) is deleterious. If 25% of heterozygous individuals and 50% of homozygous recessive individuals die before ...
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2answers
57 views

What's the difference between reaction norms and phenotypic plasticity?

I'm trying to understand better these two concepts, but I cannot see a clear difference yet. Reaction norm: "set of phenotypes that can be produced by an individual genotype when exposed to different ...
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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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33 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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1answer
166 views

What is a “segregating gene”?

What does the term "segregating" mean in references like the following: "found 42% of a random sample of loci to be segregating" "15 blood group systems are known to be segregating"
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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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93 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
44 views

Background selection and hitchhiking effect

As I read the maintenance or removal of an allele from a population is dependent upon the alleles in its linkage group; so, when an advantageous mutation occurs in the population, variation in nearby ...
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1answer
77 views

How big advantage had a trait have to bring to evolve in the human evolution? [closed]

Yes, I've heard that we have evolved from the common ancestor with primates as intesively, as the chimpanzees. Sometimes I read about some enormously complex traits, evolutionary psychologists think ...

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