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 cytochsniromeoxidase 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 approximately 38 million previously published, whole genome SNVs genotyped in 162 S. haematobium and Schistosoma bovis sampled across Africa. We compared population genetic parameters from 4000 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 are 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. This article is part of the Royal Society Science+ meeting issue 'Parasite evolution and impact in action: exploring the importance and control of hybrid schistosomes in Africa and beyond'.