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

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1answer
25 views

How is genetic speciation defined?

What determines speciation at a molecular level? At what point does a scientist determine two lineages are different enough to be considered separate species? Does it have a margin of error?
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39 views

How to seek for available genetic data relevant to ecology and evolution?

I had a quick look online. There seems to exist many different website of database archiving. Some data might be free of charge while some others might not be. I found things such as Dryad, TreeBase, ...
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1answer
54 views

How do bumblebees and hornets avoid the negative effects of inbreeding?

I just learned that all hornets and bumblebees except for the queen die at the end of the year and the queen starts a new nest in spring. But that means the next generation of queens have only ...
7
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1answer
815 views

Term for trait that is advantageous to a population only as long as it is rare

I remember reading about a concept—in evolutionary biology or natural selection, I think—whereby a particular trait is advantageous to the population or species but only so long as that trait is only ...
4
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1answer
71 views

The dominance variance on a single locus

I was reading the book "Genetics and Analysis of Quantitative Traits", by Lynch and Walsh. I how the covariance between two individuals with IBD $\Theta$ gets divided into just the additive variance ...
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15 views

Analytical Methods for Estimating Probability of Fixation

The probability of fixation $P$ of an allele is an very important measure and there exists several solutions to estimate this probability. Each method has its own assumptions and it is often hard to ...
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2answers
41 views

How to compute the regression of individual fitness on individual phenotype

Consider a population structured in groups of two individuals. Individuals' interactions follow an additive prisoner's dilemma: \begin{array}{c |c |c|} & C & D \\ \hline \text{Cooperate (} C ...
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0answers
20 views

pedigree analysis of inbreeding

Under a given situation of cousin inbreeding, I will obtain the same inbreeding coefficient ragardless of using the genealogy or the path approach, i.e. F=1/16 ...
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0answers
11 views

What is the probability of fixation for a mutant under fluctuating selection?

Here is an answer which explain how one can model the frequency of an allele that is under fluctuating selection (selection that varies through time). Not, thinking about fluctuating selection, there ...
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1answer
59 views

Modeling inclusive fitness

Consider a population of two altruist with coefficient of relatedness $r$. The average inclusive fitness of this population will be $w_{0} + br -c$. Like in this example, assignment of inclusive ...
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62 views

Expected time for a neutral allele to reach a frequency of $p_1$ when starting at frequency $p_0$

Kimura and Ohta (1968) showed that the expected time for a neutral allele to reach fixation (given that it will reach fixation) is $$\bar t(p_0)=-4N\left(\frac{1-p_0}{p_0}\right)\ln(1-p_0),$$ where ...
4
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1answer
57 views

Mathematical models of lineage selection

I'm interested in the concept of lineage selection (Aboitiz, 1991) as an explanation for why traits would be selected for that enhance the rate at which evolution can occur, rather than directly ...
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1answer
54 views

Fixation rate at neutral loci

It is a classical result that the expected time for a neutral mutation to occur and to get fixed is $2 N \mu \frac{1}{2N} = \mu$, where $N$ is the population size and $\mu$ is the neutral mutation ...
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3answers
114 views

How is it possible for the absolute fitness to be more than 1?

The wikipedia definition of Absolute fitness is "the ratio between the number of individuals with that genotype after selection to those before selection. It is calculated for a single generation and ...
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1answer
43 views

What is the expected number of children that need to be born for every possible point mutation to occur once? [closed]

I'm reading The Perfect Health Diet, and in it the author says that the probability of a point mutation is (175/3*10^9) per new child. He then goes on to write: In the Paleolithic, with 100000 ...
3
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1answer
152 views

After how many generations descendant is not more related to ancestor, than to a random individual in an ancestral population?

Descendant of n generation has on average 1/2n DNA of ancestor. (For example children have 1/2 DNA of parents and 1/4 DNA of Grandparents, After 10 Generation 1/1024 DNA and after 100 Generations ...
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1answer
77 views

How do you convert mtDNA sequences in FASTA to FSTAT format?

I've got control region sequence data from a population of shark and I'm looking to convert this from FASTA to FSTAT in order to calculated the effective population size of females. The software I ...
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0answers
7 views

Are large depth changes ever a barrier to gene flow in elasmobranchs?

I'm looking to find out if large changes in oceanic depth have ever restricted gene flow between populations of elasmobranch, or any other fish for that matter. I'm particularly interested in deep ...
3
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1answer
63 views

Mutation Rate in Multicellular Eukaryotes

I always hear people saying that the mutation rate is around $10^{-6}$ or $10^{-7}$. I don't even know if this number is the mutation rate of genes or of a single nucleotides and I actually (almost) ...
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2answers
159 views

Hamilton's inclusive fitness approach

The underlying intuition of Hamilton's model of inclusive fitness is that we should study social behaviors from the point of view of actors -- rather than the recipients. To build his model, Hamilton ...
7
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1answer
67 views

Hamilton's derivation of direct fitness from his 1970 paper

In his 1970 paper "Selfish and Spiteful Behaviour in an Evolutionary Model", Hamilton uses Price's equation to derive his well-known rule $rb -c >0$. My question is about one of the steps in his ...
2
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0answers
39 views

How does the population fitness changes after a change in mutation rate

The mean population fitness as given by mutation load theory depends only on the genome-wide mutation rate ($U$). My question is: how many generations is needed to reach a new mutation load ...
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0answers
62 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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2answers
84 views

What is Environmental Robustness? Is it different from plasticity?

Hansen (2006) in his review uses the concept of environmental robustness independently of the other concepts of robustness (at pages 139 and 140) without defining ...
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1answer
82 views

Why estimate linear and full (linear, quadratic, and correlational) selection coefficients separately?

"We then fitted a linear regression including all three life-history traits to estimate the vector of linear selection gradients, β, for each sex (Lande and Arnold 1983). A quadratic regression ...
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0answers
47 views

Mechanisms of genotype*sex interactions [closed]

I'm looking for suggestions of the mechanistic level at which genotype*sex interactions can occur. These give different phenotypes from the same genotype dependent on the sex they are expressed in. ...
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1answer
281 views

Hardy Weinberg problem help!

The three common genotypes at the hemoglobin locus have very different phenotypes: SS individuals suffer from severe anemia, AS individuals have a relatively mild form of anemia but are resistant to ...
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0answers
71 views

How to define “Quasifixation” in continuous approximation of finite population?

Background Many models including the famous very first models derived by Sir Ronald Fisher in his early career, assume infinite population size. In an infinite population, an allele can rise in ...
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1answer
117 views

Interpretation of graph from evolutionary biology

I am studying evolutionary biology, and been presented with this graph: I am having some difficulties understand its meaning. For a start, why is time measured as a fraction of the population size? ...
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2answers
150 views

Simulating substitution rate of neutral mutations

I am trying to computationally simulate a population based on the Wright-Fisher model I would like to get to the classic result of the neutral theory of molecular evolution that the rate of neutral ...
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0answers
156 views

Mutation-Selection-Drift Equilibrium

mutation-selection-drift equilibrium is one of the most important concept of population genetics. I could easily find the calculations for mutation-secltion equilibrium and for mutation-drift ...
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2answers
958 views

Definition of “Effective population size”

Could you explain to me, what is the meaning of "Effective population size ($N_e$)"? I would appreciate an example as well.
6
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1answer
156 views

What does “Mutational Variance” mean?

Background The concept of mutational variance can be found in many articles including this one for example. The mutational variance of a trait number $i$ can be found in the M-matrix in position ...
2
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1answer
105 views

Heterozygosity and the Wright-Fisher model

I was reading the textbook Probability Models for DNA Sequence Evolution by Durrett. In chapter 1, he discusses the Wright Fisher model and the coalescent theory ...
5
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1answer
397 views

Microsatellite shifts (peak calling) GeneMapper! Thesis help!

I'm a masters student attempting to conduct a parentage analysis on a population of fish for my thesis. My advisor and post-docs haven't been very helpful, so I need some help! I have dinucleotide ...
6
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1answer
95 views

Why are recombination rates increasing in mammals?

I have recently become fascinated with an awesome topic in biology and evolution that I feel is rarely covered in biology courses. That is, rates of meiotic recombination, or the the amount that an ...
2
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2answers
67 views

Conservation Genetics - Book recommendations

Can you please give me some advice for a book in (evolutionary) conservation genetics that offers an in-depth review of the mathematical formulations used in this field. I read the book Evolutionary ...
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1answer
29 views

A question on exclusion of study participants for an Exome genotyping array

I'm reading a paper that used whole exome sequencing on an African American and European populations to discover novel low frequency and rare variants associated with lipid levels & the risk of ...
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1answer
36 views

Investigating rare variants in ethnically different populations (European ancestry & African ancestry)

If you are investigating low-frequency and rare variants for a complex trait using exome sequencing, why would one consider using different populations (African ancestry and European ancestry) ...
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0answers
165 views

Software to calculate Fst from sequence data

I'm looking for a software to calculate Fst from 3 loci DNA data of individuals from a metapopulation. I don't have any prior on the population structure (have no idea of the number of subpopulations ...
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1answer
59 views

Assumptions of the models for haploid and diploid selection

For a bi-allelic locus, the model for haploid Natural Selection is: $$\frac{dp}{dt} = \frac{pW_A}{pW_A + (1-p)W_B}$$ , where $p$ is the frequency of the allele $A$, which relative fitness is $W_A$. ...
2
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1answer
49 views

$F_{ST}$ when considering a multi-allelic locus

Sewall Wright defined the $F_{ST}$ in a metapopulation as being: $$F_{ST} = \frac{\text{Var}(p)}{\bar p (1-\bar p)}$$ , where $p$ is a vector of frequencies of a given allele and $\bar p$ and ...
7
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2answers
387 views

Help with the Price equation

The Price equation describes mathematically the evolution of a population of units from one generation to the next. $\bar{w}\Delta \bar{z}$ = $Cov (w_i,z_i) $+$ E(w_i\Delta z_i)$ I would like ...
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1answer
82 views

Various Genetic Loads and their Definitions

In population genetics, we talk about several types of genetic loads (also called just loads). I am asking for a exhaustive list and a short definition. Here are for example some genetic loads that ...
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1answer
84 views

Coalescent theory - independence of coalescent times

Let $T_i$ be the time to coalesce from $n(t)=i+1$ to $n(t)=i$, where $n(t)$ is the number of sites that have not coalesced yet. In the below example the maximum $n(0)=6$. As I understand it, many ...
2
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1answer
59 views

Coefficient of relationship and path of coefficient

A path of coefficient of relationship is defined as $$\rho_{AO} = \left( \frac{1}{2}\right)^n \sqrt { \frac{1+f_A}{1+f_O}}$$ This SE post discusses this definition From this, the coefficient of ...
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0answers
50 views

Inbreeding Coefficient and Coefficient of Relationship

Wikipedia gives the following formula to calculate a "path of coefficient of relationship" between an ancestor $A$ and an offspring $O$: $$\rho_{AO} = 2^{-n} \left( \frac{1+f_A}{1+f_O} \right)^{1/2} ...
0
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1answer
84 views

Defining: Evolutionary (quantitative) Genetics and Population Genetics

How do we define the fields that are Evolutionary (quantitative) genetics and population genetics. What set these two fields apart? Can you try to provide definitions? To my intuitive understanding, ...
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1answer
41 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 ...
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1answer
45 views

Definition of Linkage Desiquilibrium (LD)

According to wiki, linkage disequilibrium $D$ equals $$D = x_{11} - p_1\cdot q_1$$ where: $$ \begin{matrix} \text{Haplotype} & \text{Frequency}\\ A_1B_1 & x_{11}\\ ...