Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/212209

Within-infection diversity of Plasmodium falciparum antigens reflects host-mediated selection

Early, A. M.·Lievens, M.·MacInnis, B.·Ockenhouse, C. F.·Volkman, S. K.·RTS,S Clinical Trial Partnership Committee of Inve,·Wirth, D. F.·Neafsey, D. E.
View original source ↗Export metadata ↓

Abstract

Host immunity exerts strong selection on pathogens, but it does not act in a uniform manner across individual hosts. By providing a direct approach for understanding host-specific selection pressures, patterns of intra-host pathogen diversity complement population genetic analyses performed on broad geographic scales. Here, we perform a combined analysis of inter- and intra-host diversity for the malaria parasite Plasmodium falciparum with haplotype sequences of three antigens sampled from over 4,500 natural infections in sub-Saharan Africa using targeted deep sequencing. We find that multi-strain infections in young children contain non-random combinations of parasite genotypes, and identify individual amino acid positions that may contribute to strain-specific blocking of infections. These results demonstrate for the first time that natural host defenses to Plasmodium detectably impact which infections proceed to the blood stage within a given host. This selection partially explains the extreme amino acid diversity observed at many parasite antigens and suggests that vaccines targeting such proteins should account for the impact of allele-specific immunity.

Source connections

Explore related subjects

evolutionary biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Early, A. M., Lievens, M., MacInnis, B., Ockenhouse, C. F., Volkman, S. K., RTS,S Clinical Trial Partnership Committee of Inve,, Wirth, D. F., Neafsey, D. E.. 2017-11-01. Within-infection diversity of Plasmodium falciparum antigens reflects host-mediated selection. https://doi.org/10.1101/212209

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Dairy cattle movement networks govern the spread and persistence of H5N1 B3.13 in the United States

Avian influenza virus H5N1 is predominantly found in wild and domestic birds. H5N1 genotype B3.13 was first detected in United States dairy cattle in March 2024 and spread through much of the country during 2024 and 2025, resulting in the largest known H5N1 outbreak in domestic mammals. By analysing viral genomic data jointly with historical cattle movement patterns, we find that live cattle movement is the predominant contributor to H5N1 spatial spread, rather than wild or domestic birds. Using phylogeographic methods we estimate that >40% of interstate viral transmissions occurred before B3.13's first detection and >70% occurred before interstate dairy cattle movement restrictions were implemented in April 2024. After this implementation, interstate transmission slowed but within-state spread persisted, driven by local cattle network density and movement volume. Our epidemic simulations demonstrate that the connectivity of counties within and around the Texas Panhandle - where the earliest cases were documented - predisposed the region to become an outbreak epicentre. Counterfactual simulations indicate that interstate restrictions needed to have begun 2-3 months earlier in order to limit the epizootic substantively, given the extent of cryptic spread before detection. Network-informed interventions outperformed geographically-defined containment, but response speed (rather than intervention strength) was the limiting factor in our epidemic models, underscoring the need for surveillance systems capable of detecting pathogen emergence before widespread dissemination.

evolutionary biology↗
bioRxiv2026

Termite-Like Phylogenetic Conservation of Gut Microbiota in Passalid Beetles Suggests Evolutionary Convergence in Decaying Wood Degradation

Beetles of the family Passalidae are an important group of subsocial wood-decomposing (saproxylophagous) insects, spending their entire life cycle living inside and feeding on rotten logs. Decaying wood is an abundant resource, but nutritionally poor and challenging to digest. As in other saproxylophagous insects, digestion for passalids is only possible through symbiotic relationships with their gut microbiota, highlighting the critical roles of these symbionts in the evolution of wood-decomposing insects. Despite its importance, this critical symbiotic relationship remains poorly understood, hindering our ability to identify the factors shaping this association and assessing its role in the evolution of Passalidae. Using high-throughput sequencing of the microbial 16S rRNA we comparatively analyzed the composition and abundance of symbiont lineages in the anterior hindguts of passalid beetles from two independent mountain systems in the Colombian Caribbean region. We tested the influence of geographical co-occurrence and phylogenetic relatedness on gut microbial composition and structure. We posit that if shared locality was the primary driver of gut microbiome assembly, then sympatric species should harbor more similar microbiomes regardless of their phylogenetic relationships. Alternatively, if host evolutionary history is the dominant factor, congeneric species should exhibit more similar microbiomes regardless of geographic co-occurrence. Our results support that phylogenetic relatedness explained substantially more variation in both bacterial and archaeal communities than geographic locality, indicating that gut microbiome composition is primarily structured by host evolutionary history. Furthermore, bacterial and archaeal communities exhibited evidence of phylosymbiosis, although at different phylogenetic scales: bacterial communities more closely reflected relationships among genus level clades, whereas archaeal communities retained congruence mainly at deeper host lineages. We also uncovered extensive bacterial taxonomic novelty, with nearly half of bacterial reads remaining unclassified at the genus level, highlighting the large undescribed microbial diversity associated with Passalidae. These findings lead to establishing Passalidae as a promising comparative model for investigating the evolutionary processes governing gut microbiome assembly and the evolution of lignocellulose-feeding symbioses.

evolutionary biology↗
bioRxiv2026

How to stand out to a mate - Flash colour of Photinus fireflies maximizes signal contrast against ambient light

During twilight, flying male Photinus fireflies flash in search for conspecific females, which sit on the vegetation below and flash back in response. However, before darkness sets in, the green vegetation in the habitat makes the detection of flashes more difficult. Twilight active fireflies tend to emit more yellow flashes than nocturnal fireflies and it has been proposed that firefly flash colour evolved to enhance the contrast of firefly flashes against their signalling background. There is indirect evidence for this contrast hypothesis, but it remains to be rigorously tested. This is the first study to directly test the contrast hypothesis by recording ambient light spectra in three different habitats throughout the daily flash activity of Photinus pyralis and P. australis and comparing these ambient light spectra to the male flash spectra of the two species. The contrast hypothesis predicts that during peak activity, firefly light colour will maximally contrast with the signalling background. Our data show that male flash spectra fit into a gap in the ambient light spectrum that opens during peak flashing activity of each species, effectively enhancing the visual contrast between male flashes and their background and making males more visible to their potential mates.

evolutionary biology↗