Pooled progeny sequencing effectively estimates polyandry in species with large families

Polyandry, the mating practice where females engage with multiple males, offers advantages such as increased genetic diversity within families and opportunities for sexual selection via sperm competition and cryptic female choice. However, assessing polyandry in species with large broods presents challenges, as individual genotyping of progeny can be unfeasible.

A novel likelihood-based framework has been developed to estimate the number of fathers and their relative contributions by analyzing maternal genotype and pooled sequencing of entire progeny groups. This method considers Mendelian segregation patterns and sampling variation arising from limited sequencing depth.

Applying this framework to both biallelic SNPs and short-read mini-haplotype markers derived from closely linked SNPs, which provide multi-allelic data akin to conventional microsatellite markers, researchers evaluated its performance through simulations. The simulations confirmed that this approach accurately determines the number of fathers and their contributions under various conditions.

The framework was subsequently utilized on 275 wild-caught Drosophila melanogaster females and their offspring from a Kansas population, based on data from 3,053 biallelic SNPs and 239 four-allele mini-haplotype markers. The results from both marker sets showed close agreement, with combined analyses revealing that 57% of families were sired by a single male.

This study showcases the effectiveness of pooled progeny sequencing as a practical genomic tool for estimating polyandry in species characterized by large family sizes.