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Related Concept Videos

Frequency-dependent Selection01:21

Frequency-dependent Selection

23.0K
When the fitness of a trait is influenced by how common it is (i.e., its frequency) relative to different traits within a population, this is referred to as frequency-dependent selection. Frequency-dependent selection may occur between species or within a single species. This type of selection can either be positive—with more common phenotypes having higher fitness—or negative, with rarer phenotypes conferring increased fitness.
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Two-Dimensional (2D) NMR: Overview01:12

Two-Dimensional (2D) NMR: Overview

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The 1D NMR spectrum of large and complex molecules like natural products has complicated splitting patterns and overlapping signals, which can be easily interpreted using 2-dimensional (2D) NMR. Unlike 1D NMR, 2D NMR has two frequency axes that provide the coupling information between the nucleus A and nucleus B in a molecule. The process from which 2D spectra are obtained has four steps.
The first step is the preparation period, during which nucleus A is excited with a radiofrequency pulse....
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Expected Frequencies in Goodness-of-Fit Tests01:19

Expected Frequencies in Goodness-of-Fit Tests

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A goodness-of-fit test is conducted to determine whether the observed frequency values are statistically similar to the frequencies expected for the dataset. Suppose the expected frequencies for a dataset are equal such as when predicting the frequency of any number appearing when casting a die. In that case, the expected frequency is the ratio of the total number of observations (n)  to the number of categories (k).
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Aliasing01:18

Aliasing

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Accurate signal sampling and reconstruction are crucial in various signal-processing applications. A time-domain signal's spectrum can be revealed using its Fourier transform. When this signal is sampled at a specific frequency, it results in multiple scaled replicas of the original spectrum in the frequency domain. The spacing of these replicas is determined by the sampling frequency.
If the sampling frequency is below the Nyquist rate, these replicas overlap, preventing the original...
499
¹H NMR: Interpreting Distorted and Overlapping Signals01:02

¹H NMR: Interpreting Distorted and Overlapping Signals

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Spin systems where the difference in chemical shifts of the coupled nuclei is greater than ten times J are called first-order spin systems. These nuclei are weakly coupled, and their chemical shifts and coupling constant can generally be estimated from the well-separated signals in the spectrum.
As Δν decreases and the signals move closer, the doublets appear increasingly distorted. The intensities of the inner lines increase at the cost of those of the outer lines as the signals are...
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¹³C NMR: ¹H–¹³C Decoupling01:04

¹³C NMR: ¹H–¹³C Decoupling

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The probability of having two carbon-13 atoms next to each other is negligible because of the low natural abundance of carbon-13. Consequently, peak splitting due to carbon-carbon spin-spin coupling is not observed in spectra. However, protons up to three sigma bonds away split the carbon signal according to the n+1 rule, resulting in complicated spectra.
A broadband decoupling technique is used to simplify these complex, sometimes overlapping, signals. Broadband decoupling relies on a...
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Two-dimensional site frequency spectrum for detecting, classifying and dating incomplete selective sweeps.

Yoko Satta1, Wanjing Zheng1, Kumiko V Nishiyama1

  • 1School of Advanced Sciences, SOKENDAI (The Graduate University for Advanced Studies).

Genes & Genetic Systems
|December 13, 2019
PubMed
Summary

The two-dimensional site frequency spectrum (2D SFS) effectively analyzes intra-allelic variability and recombination signatures. This method helps distinguish between hard and soft selective sweeps and identify non-adaptive variants in human populations.

Keywords:
SNPintra-allelic variabilitylinkage disequilibriumrecombinationsoft and hard sweeps

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Following the Dynamics of Structural Variants in Experimentally Evolved Populations
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Area of Science:

  • Population Genetics
  • Evolutionary Biology
  • Genomics

Background:

  • Intra-allelic variability (IAV) within derived allele groups is crucial for understanding evolutionary dynamics.
  • Selective sweeps, both incomplete and complete, significantly impact genetic diversity and ancestral relationships.

Purpose of the Study:

  • To investigate the utility of the two-dimensional site frequency spectrum (2D SFS) for characterizing IAV and recombination.
  • To develop robust 2D SFS-based statistics for evaluating IAV, recombination effects, and distinguishing between hard and soft selective sweeps.
  • To apply the 2D SFS method to human populations to assess neutrality and identify recent selective sweeps.

Main Methods:

  • Utilized coalescent simulations to generate powerful 2D SFS-based statistics.
  • Applied the 2D SFS method to intronic linkage disequilibrium regions in East Asian populations.
  • Analyzed six genomic regions in Eurasian populations previously identified as potentially undergoing selective sweeps.

Main Results:

  • The 2D SFS effectively reveals recombination signatures and genealogical structure, including mutation size and time to the most recent common ancestor (TMRCA).
  • Analysis of East Asian populations suggests approximately 96% of intronic variants are non-adaptive under a neutral, nonequilibrium demographic model.
  • Four out of six Eurasian genomic regions showed significant signals of hard and soft selective sweeps, dated after the out-of-Africa dispersal.

Conclusions:

  • The 2D SFS is a powerful tool for dissecting complex evolutionary processes like incomplete selective sweeps and recombination.
  • The findings provide insights into the proportion of non-adaptive variation in human populations and validate the method for detecting recent selection.
  • The study successfully identified and dated recent hard and soft selective sweeps in Eurasian populations.