Pooled progeny sequencing effectively estimates polyandry in species with large families

Polyandry, multiple mating by females, both benefits females by increases genetic variation within families and provides an opportunity for sexual selection through sperm competition and cryptic female choice. Estimating polyandry in species with large clutches is challenging because genotyping all progeny individually can be impractical. We present a likelihood-based framework for estimating the number of sires and their relative contributions from the maternal genotype and pooled sequencing of entire progeny pools. The method evaluates the probability of observed pooled offspring read counts under alternative paternal genotype mixtures, accounting for Mendelian segregation and sampling variation from finite sequencing depth. We implement this framework for both biallelic SNPs and short-read mini-haplotype markers constructed from closely linked SNPs, which provide multi-allelic information comparable to traditional microsatellite markers. Simulations show that this approach accurately recovers sire number and sire contributions across a range of conditions. We then applied the method to 275 wild-caught Drosophila melanogaster females and their offspring from a Kansas population using 3,053 biallelic SNPs and 239 four-allele mini-haplotype markers. Estimates from the two marker sets were highly concordant, and combined analyses indicate that 57% of families were sired by a single male. These results demonstrate that pooled progeny sequencing provides an efficient genomic approach for estimating polyandry in species with large families.