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In a population that is not at Hardy-Weinberg equilibrium, the frequency of alleles changes over time. Therefore, any deviations from the five conditions of Hardy-Weinberg equilibrium can alter the genetic variation of a given population. Conditions that change the genetic variability of a population include mutations, natural selection, non-random mating, gene flow, and genetic drift (small population size).
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Natural selection influences the frequencies of particular alleles and phenotypes within populations in several different ways. Primarily, natural selection can be directional, stabilizing, or disruptive. Directional selection favors one extreme trait and shifts the population towards that phenotype while selecting against individuals displaying alternate traits. Stabilizing selection favors an intermediate trait with a narrow range of variation. Deviation from the optimal phenotype towards an...
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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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Following the Dynamics of Structural Variants in Experimentally Evolved Populations
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Improving Selection Detection with Population Branch Statistic on Admixed Populations.

Burak Yelmen1,2, Davide Marnetto1, Ludovica Molinaro1,2

  • 1Institute of Genomics, University of Tartu, Estonia.

Genome Biology and Evolution
|February 27, 2021
PubMed
Summary

Detecting ancient natural selection in admixed populations is challenging. This study improves detection using local ancestry inference and haplotype methods, revealing potential selection signals in South Asian populations.

Keywords:
PBSSouth AsiaXP-EHHadmixed populationslocal ancestry inferencenatural selection

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Area of Science:

  • Population Genetics
  • Human Evolution
  • Genomic Analysis

Background:

  • Detecting natural selection in admixed populations is difficult because signals often predate admixture.
  • Ancient DNA (aDNA) aids pre-admixture studies but has geographical and data quality limitations.
  • Local ancestry inference offers a potential method to overcome aDNA limitations.

Purpose of the Study:

  • To explore methods for improving the detection of pre-admixture natural selection signals in admixed populations.
  • To evaluate the effectiveness of local ancestry inference combined with haplotype-based statistics.
  • To identify potential selection signals within the indigenous component of South Asian populations.

Main Methods:

  • Utilized forward simulations to test Population Branch Statistic (PBS) with masked haplotypes and cross-population extended haplotype homozygosity (XP-EHH) with full haplotypes.
  • Employed local ancestry deconvolution to mask haplotypes for PBS analysis.
  • Applied XP-EHH using both admixed and source populations, and analyzed correlations.

Main Results:

  • Masked haplotypes with ancestry deconvolution improved PBS detection quality on simulated data.
  • XP-EHH using the admixed population outperformed the local ancestry method in simulations.
  • Haplotype-based methods require cautious application in recently admixed populations due to score correlations.
  • Identified potential selection signals on the autochthonous South Asian component using PBS with local ancestry deconvolution.

Conclusions:

  • Local ancestry inference can enhance the detection of pre-admixture selection signals.
  • Haplotype-based analyses in admixed populations need careful interpretation.
  • This study provides evidence for selection acting on the ancestral South Asian population component.