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Detecting adaptive trait loci in nonmodel systems: divergence or admixture mapping?

Jacob E Crawford1, Rasmus Nielsen

  • 1Department of Integrative Biology, University of California, Berkeley, 4134 Valley Life Sciences Building, Berkeley, CA, 94720-3140, USA.

Molecular Ecology
|October 17, 2013
PubMed
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Mapping adaptive trait loci (ATL) is key to understanding ecological divergence. Admixture mapping offers high power for identifying these loci, even with elevated genetic divergence, outperforming traditional divergence mapping in such scenarios.

Keywords:
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Area of Science:

  • Evolutionary genetics
  • Population genetics
  • Genomics

Background:

  • Understanding ecological divergence requires mapping adaptive trait loci (ATL).
  • High-throughput exome sequencing enables functional genetic variant analysis in nonmodel organisms.
  • Traditional divergence mapping may be underpowered with high background genetic divergence.

Purpose of the Study:

  • To assess the power and limitations of divergence mapping for identifying ATL.
  • To evaluate the utility of admixture mapping for locating ATL in admixed populations.
  • To compare the effectiveness of divergence and admixture mapping under varying levels of genetic divergence.

Main Methods:

  • Simulated exomes with a single ATL in two parental populations with varying neutral divergence.
  • Estimated divergence and quantified mapping power for ATL.
  • Simulated admixed populations, phenotypes, and conducted genotype-phenotype association tests for admixture mapping.

Main Results:

  • Divergence mapping showed high power for ATL when background FST < 0.2, but power decreased significantly above this threshold.
  • Admixture mapping provided high power for ATL even with FST = 0.35, where divergence mapping was ineffective.
  • Admixture mapping maintained high power across all divergence levels after 20 generations post-admixture.

Conclusions:

  • Admixture mapping is a powerful tool for mapping ATL, especially in populations with high genetic divergence.
  • Admixture mapping complements high-throughput exome sequencing for ecological genomics studies.
  • Careful experimental design and analytical approaches are crucial for successful ATL mapping using admixture mapping.