Towards an evolutionary baseline model of Plasmodium falciparum for population-genomic inference

Abstract

Malaria has caused over 15.7 million deaths in the 21st century and was responsible for [~]600 thousand deaths globally in 2023 alone. Although many effective antimalarial drugs have been developed and widely adopted to reduce the occurrence and severity of the disease, recurrent resistance to the frontline treatment has been of major concern. Multiple drug resistance alleles at intermediate and high allele frequency have been identified in specific Asian and African populations of P. falciparum, the deadliest malaria parasite. With the improvement in throughput of sequencing technologies and global efforts such as the MalariaGEN project to build genomic surveillance, we now have access to tens of thousands of genomes of P. falciparum from across the world. With this data, it is becoming increasingly possible to employ powerful population genetics approaches to understand the selective pressures and demographic history of the parasite. While several empirically motivated outlier-based approaches have been employed to identify targets of drug resistance, there is a lack of a framework that jointly accounts for the multiple concurrent processes occurring in natural populations of P. falciparum. We argue that a baseline evolutionary model that accounts for simultaneously acting evolutionary processes is needed to understand patterns of genomic variation in P. falciparum populations. Here, we identify key components essential for building such a baseline model for the malaria-causing pathogen. The development of an appropriate null model will be important to test evolutionary hypotheses using genomic datasets, will provide a path forward to improve the accuracy of inference of evolutionary parameters, and will help identify new gene candidates involved in drug resistance.