The paper in Nature Communications is here: https://go.nature.com/2I6zyDE
Before I dived into the var gene world of the malaria parasite Plasmodium falciparum in the Pascual lab, I thought the population structure of this multigene family could be understood with traditional population genetics methods. I was quite wrong.
The var gene family encodes the major blood stage antigen PfEMP1. Its vast genetic diversity and the combination of different variants in a genome (termed ‘repertoire’ in our paper) underlie the chronicity of malaria and possibly its robustness to intervention. We would like to know whether and how selection imposed by our immune system shapes the diversity and population structure of these parasite repertoires in a way that matters to epidemiology and control efforts. The unique evolutionary processes of this gene family preclude standard population genetics approaches. In particular, unlike R genes in plants and MHC genes in mammals, var genes continue to undergo promiscuous genetic exchange among homologous genes, despite the ancient root of the gene family. Thus, orthologous and paralogous copies are indistinguishable. The prevalence of such ectopic recombination results in a different history of every single base pair along a gene stretch, which prevents the application of analyses relying on proper sequence alignment.
Another perspective, different from tracking evolutionary history, would be observing it through the lens of community ecology: there are indeed conceptual similarities between our system of parasites competing for hosts and ecosystems of species competing for resources. The var genes in a repertoire can be seen as a set of traits determining the outcome of competition. A specific var variant that has been seen before in a previous infection by a given host will not be expressed, which shortens infection and leads to a faster clearance of the parasite. Thus, although all the var genes are competing for the same resource (non-immune hosts) with similar competence, their fates can be drastically different depending on the other var genes that cohabit within a repertoire. Then another approach to identify selection signatures at the repertoire level would be to properly quantify within and between repertoire diversities with one of many suitable ecological indices (e.g. by considering each var variant as an OTU of a microbial community). Few of these indices display however consistent patterns between selection and neutral scenarios when genetic or epidemiological parameters vary. Thus, it is not clear what patterns would distinguish the importance of these processes at very high diversity (high-dimensional trait space) in our system.
A breakthrough for us came while discussing the problem with my colleague and co-author Shai Pilosof. It occurred to us that the most natural way of analyzing the system would be to represent pairwise differences between repertoires as networks. As repertoires constantly evolve by shuffling gene members through meiotic recombination in the mosquito vector, and genes themselves exchange part of their sequences through ectopic recombination within the same repertoire, we can inspect similarity patterns at both gene and repertoire levels using network analyses. Properties of these networks allow us to identify underlying forces using network classifications. We can specifically distinguish a role of immune selection from pure neutrality (i.e., the result of random extinction, immigration, and transmission in the complete absence of acquired immunity). The network analyses reveal that immune selection clearly shapes these genetic similarity networks, and that the resulting patterns exhibit interesting parallels with features generated by balancing selection in population genetics, and with stabilizing competition in ecological communities. We were also excited when we found that networks constructed from the deep molecular sampling by our collaborators of parasites from a local population in Ghana resembled those generated by our theory at both the gene and repertoire levels under immune selection, which provided clear evidence for the importance of this process.
At the end of the day, it was clear to me that the var gene system can only be understood by interweaving thinking from evolution, ecology, epidemiology and complex systems. Many other fascinating challenges remain to address the diversity of the var gene world in a way that elucidates its consequences for epidemiology and control efforts, while the arms race between humans and malaria continues.