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Inferring Domestic Goat Demographic History Through Ancient Genome Imputation.

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Area of Science:

  • Ancient Genomics
  • Domestication Studies
  • Population Genetics

Background:

  • Goats are early domesticated animals, valuable for studying domestication's genetic effects.
  • Low genome coverage in ancient samples limits analysis to pseudohaploid genotypes.
  • Genotype imputation can enhance information content and accuracy in low-coverage genomes.

Purpose of the Study:

  • To assess the utility of genotype imputation for improving ancient goat palaeogenome analysis.
  • To investigate the demographic history and genetic consequences of early goat management and dispersal.

Main Methods:

  • Imputing downsampled high-coverage goat palaeogenomes using a large reference panel (VarGoats).
  • Evaluating imputation accuracy by measuring concordance between imputed and high-coverage genotypes.
  • Analyzing runs-of-homozygosity (ROH) and identity-by-descent (IBD) in imputed palaeogenomes.

Main Results:

  • High concordance (>0.97) achieved for 0.5× coverage genomes after filtering for common variants.
  • Trade-offs identified between coverage, genotype probability thresholds, and genotype recovery/accuracy.
  • ROH increased with distance from the Zagros Mountains in Neolithic goats, indicating dispersal effects.
  • Inbreeding levels decreased over time, and IBD patterns reflected early herding site dynamics.

Conclusions:

  • Genotype imputation is a valuable tool for leveraging low-coverage ancient goat genomes.
  • Early goat dispersal significantly impacted population genetics, with decreasing inbreeding over time.
  • The study provides insights into the genetic consequences of early animal management on demography.