APIS

APIS assigns parentage from genomic marker data and estimates missing parental genotypes by leveraging observed Mendelian transmission probability distributions.

Key Features:

• Auto-Adaptive Algorithm: APIS employs an algorithm that does not require a priori estimates of genotyping error rates or the proportion of missing parents, enabling assignment with incomplete parental data.
• Mendelian Transmission Probability Distributions: The method uses observed average Mendelian transmission probability distributions to estimate likelihoods of offspring inheriting specific genotypes from candidate parents.
• User-Defined Error Rates: Users can set acceptable offspring assignment error thresholds to balance false positives and true positives.
• Comparison with Existing Tools: APIS has been compared with CERVUS and VITASSIGN and exhibits lower type I error rates when parental genotypes are missing, with potentially reduced true positive rates unless theoretical exclusion power is very high.
• Suitability for Large Datasets: The approach is suited for datasets with large numbers of offspring (>200), where observed transmission probabilities enhance assignment accuracy.
• Robustness to Genotyping Errors and Missing Data: APIS maintains performance with genotyping error rates up to 3% and proportions of missing sires up to 50%.

Scientific Applications:

• Genomic Studies in Aquaculture and Conservation Biology: Applicable to species such as European seabass where complete parental genotypes may be unavailable.
• Population Genetics Research: Aids identification of parent-offspring pairs to study genetic relationships within populations.
• Breeding Programs: Supports lineage tracking and selection decisions in selective breeding through reliable parentage assignment.

Methodology:

APIS() integrates offspring and parental genotypes with user-defined error thresholds and computes the distribution of average Mendelian transmission probabilities to estimate missing parental contributions for parentage assignment.