All Questions
Tagged with genetics population-genetics
152 questions
8
votes
2
answers
3k
views
What particular genetic mutations gave Europeans increased resistance to smallpox?
It's widely stated that a large chunk of the Native American population was wiped out by diseases (Notably smallpox) introduced by European colonists to which the natives did not have a resistance. My ...
- 527
1
vote
1
answer
80
views
Does this evolutionary model of mutations have a flaw?
In a youtube video by an evolutionary biologist titled Creation Myths: Genetic Entropy at 14:50 he explains that the ratio between beneficial + neutral mutations and deleterious mutations decreases ...
- 157
1
vote
1
answer
369
views
What does it mean when observed genotype frequency is different from expected genotype frequency in Hardy-Weinberg equilibrium?
As I understand it, if a population is at Hardy-Weinberg equilibrium, then the genotype frequencies should be $$p^2 + 2pq + q^2 = 1,$$ given the allele frequencies of $p$ and $q$, which you can figure ...
0
votes
1
answer
56
views
In the context of GWAS we have an alternate allele and a reference allele. Why do we only have one possible alternate instead of three?
I recently started analyzing a GWAS summary dataset. It has a column for the reference allele in which it mentions the base in the reference genome.
There is another column for the alternate allele (...
- 101
0
votes
3
answers
105
views
If you want to understand evolution from a genetics standpoint what are some must reads be it books or textbooks? [closed]
The question basically sums it up. I'm looking for books/textbooks that explain evolution from a genetic perspective.
- 157
1
vote
2
answers
119
views
Interpretation of narrow-sense heritability over one (using R/S = h^2)
Here is my data:
Mean height score of the total parental population: 5.2
Mean height score of selected parents (those chosen for breeding due to their higher height): 6.4
Mean height score of the ...
- 401
0
votes
0
answers
34
views
Is there a program that demonstrates overall fitness will increase in a population overtime?
Of course this will not always be the case with environmental factors, but generally speaking. I'm searching for a program that shows evolution works from a statistical standpoint.
- 157
0
votes
0
answers
28
views
Why is the expected time to coalesce the same as the ploidy times inbreeding effective population size?
The expected time to coalesce, in generations, is the same as the ploidy (e.g., 2 for humans) times Nef, the inbreeding effective population size, under coalescent
theory. Why?
Both ploidy * Nef and ...
- 401
0
votes
3
answers
114
views
Have there ever been "half-twins" who were halfway between siblings and twins?
Have there ever been two human siblings who were 75% or more genetically related?
- 401
0
votes
0
answers
29
views
Coefficient of fraternity between grandparent and grandchild from full-sib parents
I have the following pedigree and I would like to calculate the coefficient of fraternity between individual 1 and 5. R/AGHmatrix::Amatrix gives a coefficient of 0 for this pair. Shouldn't it be non-...
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0
votes
2
answers
174
views
Hardy-Weinberg Equilibrium Test Result for Merged Genotypes
I was curious if two populations are in Hardy-Weinberg Equilibrium (HWE), and if they are merged, then what happens? To find out, I considered populations from the 1000 genome project data. For ...
- 1
1
vote
1
answer
93
views
Are there two different senses of the word 'heritability' in use?
Target Height as Predicted by Parental Heights in a Population-Based Study states:
The heritability value was taken as the regression coefficient between
final height and midparental height
Is this ...
- 111
0
votes
1
answer
54
views
Is there a term for a sequence of genomes for a family?
Suppose that I am following how a "familial" genome changes throughout generations. That is, I have the genome of a grandmother, father, and daughter, and my objective is to see how the ...
- 103
5
votes
1
answer
151
views
How exactly do mutations cause genetic variation in bilaterians?
I am trying to understand how mutations cause genetic variance, and I'm stuck on one issue that I'm going to try my best to explain.
(I am specifically talking about mutations that cause a ...
- 151
3
votes
1
answer
100
views
How is a haploblock defined with only one SNP location?
I am reading Impact of estrogen receptor gene polymorphisms and mRNA levels on obesity and lipolysis – a cohort study and am looking at Figure 1. I understand that haplotypes are associated with ...
- 303
0
votes
1
answer
137
views
Disease-causing allele frequency and modern medicine
I was thinking about what the impact modern medicine might have on human evolution based on a couple assumptions.
If we assume that:
modern medicine has massively cushioned the selection pressure ...
- 113
2
votes
2
answers
175
views
Really having problem comprehending this Hardy-Weinberg example from biology textbook
Genetic equilibrium is a hypothetical state, but it is often used as a benchmark. Consider how the Hardy–Weinberg equations were used in early studies of an allele that causes hereditary ...
7
votes
1
answer
120
views
How can I find/simulate mixed-ancestry DNA data?
Some collaborators and I are building an ancestral inference tool, and we're having trouble obtaining reliable ground-truth data for samples of mixed ancestry. All the ground-truth DNA datasets we're ...
- 73
2
votes
1
answer
65
views
Making sense of infinite-sites mutation but finite-sites recombination coalescent simulator
Hudson (1983) introduced a coalescent simulator with infinite-sites mutations and finite-sites recombination. This seems paradoxical because the documentation of the simulator (section on crossing ...
- 123
3
votes
2
answers
191
views
Why isn't speciation a negative feedback loop?
To rephrase my question more articulately:
Speciation begins when two groups within a species starts to become reproductively isolated, and is complete when the two groups can't interbreed (for the ...
- 113
2
votes
1
answer
138
views
Method of determining base values of traits in isolated populations
Prelude: I came across a discussion about the correct formula for calculating the average IQ of offspring, which goes something like the following
$$ 100 + \frac35 \left( \left(\frac{\text{father's IQ ...
- 155
5
votes
1
answer
171
views
Saving a Maize Landrace from Inbreeding Depression
I have 10 seeds of a rare corn landrace. I probably won't be able to acquire more and the cultigen's long term fate is unknown. So, I want to do my best to preserve it for future generations.
Corn is ...
- 51
19
votes
1
answer
4k
views
What would cause red-haired people to become fewer?
There is this misconception that red-haired people are going to die out. This person on the Internet ("howstuffworks") also connected it to a marketing campaign of a hair dyer company. But I'...
- 382
0
votes
1
answer
106
views
Can a trait be too successful? Wouldn't overwhelmingly successful traits limit variability, which is one of the requirements of NS? [closed]
Can a trait be too successful? Wouldn't an overwhelmingly successful trait soon limit the gene pool, and if so, how would the process of natural selection react to that? If an individual is born ...
- 1
34
votes
6
answers
7k
views
Why didn't Escobar's hippos introduced in a single event die out due to inbreeding
Today I read a BBC Report about how Pablo Escobar had once imported 4 hippos (1 male, 3 female) into his estate in Colombia for his private zoo. After his downfall, while other species were shipped ...
- 451
0
votes
1
answer
34
views
Can the mutation rate vary for individuals of the same species, growing in similar environments?
Suppose we consider several populations who originally inherited their genome from the same ancestor, and that we put for a few thousands generations in similar environments.
Could the mutation rate ...
- 3
0
votes
1
answer
112
views
Hardy-Weinberg principle
The following paragraph on Wikipedia about the Hardy-Weinberg principle is bothering me.
It should be mentioned that the genotype frequencies after the first generation need not equal the genotype ...
- 155
3
votes
1
answer
93
views
Rigorous definition of the kinship coefficient and proof of a recursion thereof
I am reading Section 5.2, Kinship and Inbreeding Coefficients, of Kenneth Lange, Mathematical and Statistical Methods for Genetic Analysis. There the kinship coefficient $\Phi_{i,j}$ is defined for ...
- 486
1
vote
1
answer
115
views
The significance of haplotype blocks
I looked up haplotype blocks in Google Scholar, and the results returned seemed to show that almost all the relevant articles were published between 2001 and 2009, with almost nothing since 2010.
Why ...
- 307
0
votes
1
answer
791
views
Why is selection less effective in small populations than in larger?
I can understand that the genetic drift has a higher impact on smaller populations, but what does it mean for the selection to be less effective in small populations than higher?
- 155
4
votes
0
answers
84
views
ABO allele frequencies: Why use the EM algorithm?
In textbooks and lecture notes and slides posted online, determining allele frequencies using blood type information (ABO), under the assumption of Hardy-Weinberg equilibrium, is accomplished using ...
- 163
1
vote
0
answers
84
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 ...
- 11
0
votes
2
answers
108
views
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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0
votes
0
answers
85
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 ...
- 101
5
votes
2
answers
200
views
Understanding ancestry testing mathematically
Forgive me if this question has been asked here before, because it is something which should be very easy to find, but I can't seem to find an answer no matter where I search.
The question is simply ...
- 153
0
votes
0
answers
75
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(...
0
votes
1
answer
699
views
What percentage of Americans have Native Indian ancestry? [closed]
What percentage of americans have native indian ancestry?
I tried to find the answer online and it's difficult to search for.
- 10.5k
2
votes
0
answers
59
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” ...
- 121
0
votes
2
answers
426
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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1
vote
1
answer
87
views
What is the cause of "imbalanced" linkage disequilibrium?
With perfect linkage disequilibrium ($D' = 1, R^2 = 1$), you might have the following table of counts for the alleles:
B b
A 100 0
a 0 100
With "...
- 133
1
vote
2
answers
201
views
In marine DNA viral diversity studies, what would "paradigm of rampant mosaicism" refer to?
The recent paper in Cell Marine DNA Viral Macro- and Microdiversity from Pole to Pole describes the (huge) new Global Ocean Viromes 2.0 (GOV 2.0) dataset.
In the Results and Discussion section, the ...
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1
vote
1
answer
36
views
Repopullation after a mass extinction [duplicate]
Is it possible to restart the whole human species with less than 10 individual.
let say that the whole human species was wipe out of the surface of the earth by a catastrophe only 8 different couple ...
- 135
2
votes
0
answers
254
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 ...
- 121
1
vote
0
answers
37
views
Finding intensity of selection against dominant homozygotes
I was looking at some Olympiad questions and came across the following:
If the frequency of a completely recessive allele is $0.2$ and it remains unchanged from generation to generation due to ...
- 111
1
vote
1
answer
128
views
Balancing selection vs introgression? [closed]
Balancing selection can maintain polymorphisms in natural populations for extended periods of evolutionary time. However, in this paper, Dannemann et al. 2016 identify three archaic haplotypes in the ...
- 19
0
votes
1
answer
88
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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0
votes
1
answer
75
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.
...
- 1,675
3
votes
0
answers
122
views
How does the new discovery that mitochondrial dna is inherited from both parents change population genetics and other dates?
This new study seem to have pretty much proven that mtDNA is inherited from both parents. I assume that this would lead to most age estimates of ancient human ...
- 473
3
votes
0
answers
58
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 ...
1
vote
0
answers
39
views
Can Tajima's D and other population genetic tools be used to copare Arabidopsis ecotypes?
I am currently investigating 2 genes in Arabidopsis taliana that are a product of a recent duplication even (observable from synteny and phylogenetic analysis). In addition to the molecular and ...
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