Biased availability of genetic data for parasites: it’s all about the host

Abstract

Advances in DNA sequencing technology have significantly increased the availability of publicly accessible genetic data across various parasite taxa. This genetic data is crucial for elucidating gene flow, connectivity among parasite populations, cryptic diversity, and resolving parasite phylogenies. However, phylogenetic reconstructions are often hindered by incomplete genetic data across taxa, particularly in less-studied taxa like parasitic helminths. We tested whether the availability of genetic data for helminth species is biased and influenced by which hosts they infect using the largest known helminth life cycle database. We compared helminth species with genetic sequences in the NCBI Nucleotide and Gene databases against those without publicly available sequences. We examined the impact of the number of definitive hosts, their higher taxon, conservation status, and habitat on genetic data availability. Our findings reveal significant biases in existing genetic data for helminth parasites, influenced by host-related factors. Helminth species with more definitive hosts species, hosts of conservation concerns, and/or those with terrestrial hosts are more likely to have genetic data available. These biases in genetic data availability raise concerns for phylogenetic studies, as they suggest that the current genetic knowledge of helminth parasites is neither random nor representative of existing biodiversity. Consequently, phylogenetic trees based on biased data may not accurately capture the true evolutionary relationships among parasite taxa, as well as trends in the evolution of key traits, such as host specificity. Comprehensive and unbiased data collection efforts are needed to improve the accuracy of phylogenetic analyses and our understanding of parasite evolution.