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Following the Dynamics of Structural Variants in Experimentally Evolved Populations
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Inferring population size changes with sequence and SNP data: lessons from human bottlenecks.

L M Gattepaille1, M Jakobsson, M G B Blum

  • 1Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.

Heredity
|February 21, 2013
PubMed
Summary

This review explores methods for reconstructing human population size changes, focusing on bottlenecks. Newer genomic fragment analyses better detect recent bottlenecks than traditional site-frequency spectrum methods.

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Area of Science:

  • Population genetics
  • Evolutionary biology
  • Genomics

Background:

  • Reconstructing historical population size is crucial for understanding species evolution.
  • Human population size changes, particularly bottlenecks, are extensively studied.

Purpose of the Study:

  • To review methodologies for demographic reconstruction, with a focus on human population bottlenecks.
  • To compare classical and recent approaches for inferring population size history.

Main Methods:

  • Review of methods based on site-frequency spectrum (SFS).
  • Review of methods based on linkage disequilibrium.
  • Review of recent methods using shared genomic fragments (e.g., identity by descent, homozygous segments).

Main Results:

  • Classical SFS-based methods and newer genomic fragment analyses are compared.
  • Genomic fragment methods show promise for detecting recent population bottlenecks.
  • All methods are susceptible to biases from confounding factors like population structure and mutation/recombination rates.

Conclusions:

  • Newer methods using genomic fragments are better for recent bottleneck detection.
  • Confounding factors can bias demographic inference, with effects poorly understood for most methods.
  • Validating demographic models against polymorphism data is essential for accurate population size change reconstruction.