orchard: Paternity program for autotetraploid species.

Area of Science:

• Population Genetics
• Molecular Ecology
• Bioinformatics

Background:

• Advances in molecular markers facilitate population genetics studies in polyploid species.
• Paternity analysis is crucial for understanding gene flow, mating systems, and reproductive success.
• Existing software lacks specific tools for paternity analysis in autotetraploid species.

Purpose of the Study:

• To develop specialized software for paternity analysis in autotetraploid species.
• To introduce orchard, a novel program for paternity assignment in autotetraploids.
• To assess reproductive strategies and gene flow in polyploid populations.

Main Methods:

• Development of the orchard software implementing exclusion and likelihood statistics.
• Utilizing microsatellite markers for paternity assignment.
• Incorporating optional features for allele dosage estimation and pollen flow distance calculation.

Main Results:

• The orchard program successfully performed paternity analysis on microsatellite data.
• Demonstrated the utility of exclusion and likelihood methods for autotetraploid paternity.
• Validated the software using data from Dipteryx odorata, a tetraploid Amazonian tree.

Conclusions:

• orchard provides a valuable tool for population genetic studies of autotetraploid organisms.
• The software enhances the analysis of mating systems and reproductive success in polyploids.
• Facilitates a deeper understanding of gene flow dynamics in complex polyploid systems.