Demographic history inference and the polyploid continuum.

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.