Estimating admixture pedigrees of recent hybrids without a contiguous reference genome

Area of Science:

• Genomics
• Population Genetics
• Bioinformatics

Background:

• Admixed individuals exhibit unique genetic patterns revealing recent ancestry.
• Interancestry heterozygosity patterns are key indicators of admixture history.
• These patterns are inferable from SNP data, even with limited genomic location information.

Purpose of the Study:

• To implement maximum likelihood estimation for interancestry heterozygosity patterns.
• To develop apoh (Admixture Pedigrees of Hybrids) software for detecting and characterizing recent hybrids.
• To provide tools for exploring, ranking, and visualizing admixture pedigrees.

Main Methods:

• Maximum likelihood estimation using two complementary models.
• Development of the apoh software (command line and GUI) for hybrid detection and pedigree analysis.
• Calculation of hybrid indices to rank potential admixture pedigrees.

Main Results:

• Validated apoh performance using admixed family trios from the 1000 Genomes Project.
• Demonstrated applicability on RAD-seq data of Grant's gazelle.
• Showcased utility with low-depth whole genome data of waterbuck, revealing complex admixture.

Conclusions:

• apoh software effectively detects recent hybrids and reconstructs admixture pedigrees.
• The method is versatile, applicable to various sequencing data types and complex admixture scenarios.
• This tool enhances evolutionary and conservation genomic studies by providing insights into admixture history.