Supplementary material from "Efficient amplicon panels for evaluating hybridization and genetic structure in the <i>Schistosoma haematobium</i> species group"

Genetic markers for detecting hybridization and measuring population genetic parameters must be informative and cost-effective. Most population genetic studies within the Schistosoma haematobium species group rely on either a two-marker system consisting of the mitochondrial, cytochrome oxidase 1 (cox1) and the nuclear internal transcribed spacer (ITS) markers or, at the other extreme, millions of single nucleotide variants (SNVs) from whole genome/exome sequencing. cox1 and ITS studies contain minimal population genetic information but whole genome sequencing is cost-prohibitive. We examined ~38 million previously published, whole genome SNVs genotyped in 162 S. haematobium and S. bovis sampled across Africa. We compared population genetic parameters from 4,000 panels of 10-100,000 randomly sampled SNVs to results from the whole genome dataset to test the resolution of reduced representation sequencing in schistosomes. We found that panels of 500 SNVs captured >99% of the population genetic information contained in the whole genome dataset by using Procrustes transformed principal component analyses and ancestry estimates (r² = 0.85). Additionally, the costs of genotyping parasites with an amplicon panel is two to three times less than whole genome sequencing. Our results show that moderately-sized amplicon panels targeting random SNVs provide an efficient approach to large scale, field-based schistosome surveillance.