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Demographic history inference and the polyploid continuum.

Paul D Blischak1,2,3, Mathews Sajan2, Michael S Barker1

  • 1Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.

Genetics
|June 6, 2023
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Summary

New diffusion models help understand polyploid evolution by inferring demographic history and subgenome exchange rates. This advances the study of autopolyploidy and allopolyploidy in diverse species, including crops.

Keywords:
allopolyploidyautopolyploidydemographyhomoeologous exchangesite frequency spectrum

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Area of Science:

  • Evolutionary biology
  • Genetics
  • Computational biology

Background:

  • Polyploidy, or whole-genome duplication, generates evolutionary novelty in many species, including crops.
  • Autopolyploidy (within-lineage doubling) and allopolyploidy (hybridization doubling) have historically been viewed as distinct.
  • Understanding polyploid evolution requires quantitative inference of demographic history and subgenome exchange.

Purpose of the Study:

  • To develop diffusion models for genetic variation in polyploids with inseparable subgenomes.
  • To infer demographic history and subgenome exchange rates in polyploid species.
  • To provide a computational framework for analyzing polyploid evolution.

Main Methods:

  • Developed diffusion models for genetic variation in polyploids.
  • Implemented models in the dadi software.
  • Validated models using forward SLiM simulations and applied them to empirical data.

Main Results:

  • Accurately inferred evolutionary parameters for auto- and allotetraploids, including timing and bottleneck size.
  • Quantified exchange rates in segmental allotetraploids.
  • Found evidence of allelic exchange between subgenomes in Capsella bursa-pastoris.

Conclusions:

  • The new diffusion models provide a foundation for demographic modeling in polyploids.
  • This approach enhances understanding of polyploid formation and evolution.
  • Enables deeper insights into the impact of demography and selection in polyploid lineages.