Biology subjects

Lefebvre, M. J. M.

Publications and source records attributed to Lefebvre, M. J. M..

6 recordsLinked to original sources

bioRxiv2026

Identification of two genomic cryptotypes of Plasmodium malariae in Africa

Plasmodium malariae is a neglected human malaria parasite that causes persistent, often asymptomatic infections and remains difficult to diagnose. Despite being generally associated with lower prevalence and severity than other malaria parasites, P. malariae represents a significant public health concern, particularly in Africa, but also as a zoonosis in South America with monkey-adapted Plasmodium brasilianum. Plasmodium malariae and P. brasilianum population genetic structure, evolutionary history, and adaptive potential remain poorly understood, largely due to the historical scarcity of whole-genome data. By screening 226 monkey samples from two Latin American countries, we identified 20 Plasmodium-positives across multiple primate species, highlighting the persistence of this parasite in sylvatic transmission cycles. We also investigated the evolutionary history and genetic diversity of P. malariae using whole-genome sequencing data. By combining 79 newly sequenced genomes with 248 publicly available genomes, we analyzed a filtered dataset comprising 179 P. malariae, two P. brasilianum, and two P. malariae-like genomes. Population structure analyses revealed the presence of two genetically distinct but recombining clusters across African P. malariae populations. These clusters occur across multiple African countries at varying frequencies, without clear geographic segregation. Genome-wide scans of genetic differentiation and selection further identified numerous cluster-specific signatures of adaptation, including loci putatively involved in interactions with human hosts and mosquito vectors. Our results provide the first evidence for fine-scale population substructure within African P. malariae and reveal ongoing adaptive processes that may contribute to its persistence and transmission. By uncovering previously unrecognized genetic diversity and selection patterns, this study highlights the importance of population genomic approaches for understanding the evolutionary dynamics of this neglected malaria parasite. Author summaryHuman malaria is most often associated with few well-studied parasites (Plasmodium falciparum and Plasmodium vivax), while other species have received far less attention. One such species is Plasmodium malariae, which often causes long-lasting infections with few or no symptoms. Because infections are difficult to detect, the true impact of this parasite is likely underestimated, particularly in Africa, where it is widespread. A closely related form, known as Plasmodium brasilianum, infects monkeys in South America with transmission between humans and wild animals. In our study, we analyzed the parasite genomes from infected people and monkeys to better understand the genetic diversity of these parasites, their population structure, and the molecular evidence of adaptation. We found evidence that P. brasilianum continues to circulate in several wild monkey species in South America. By analyzing nearly 300 genomes, we discovered that African P. malariae consists of two genetically distinct but recombining groups that coexist across the continent. These groups differ in specific regions of their genomes, including genes likely involved in interactions with human hosts and mosquito vectors. Our results reveal cryptic genetic diversity and structure with evidence of ongoing adaptation. These findings highlight the importance of including neglected parasites in malaria surveillance and control efforts.

genomics↗

bioRxiv2026

ViroSeek: a viral detection pipeline for second-generation sequencing

Arbovirus emergences represent a rising public health issue and are exacerbated by climate change and globalization. Virome analysis has become a key approach for monitoring and managing infectious diseases, yet existing tools often remain technically complex and inaccessible to non-specialists. In this context, we present ViroSeek, a reproducible and accessible bioinformatics pipeline specifically designed for the taxonomic analysis of second-generation sequencing data from target-enriched libraries. ViroSeek performs a series of automated steps: quality control, trimming, host and bacterial sequence removal, assembly, taxonomic assignment, read remapping for quantification, and PCR duplicate removal. The whole process is designed to produce a clear, usable viral taxonomy table that is suitable for diversity studies. ViroSeek was empirically validated on enriched control samples containing a known panel of viruses. All the expected viruses were correctly detected. Bacterial and host contaminant sequences were effectively removed. The pipeline is freely available and fully documented, supporting its adoption and adaptation by the research community.

bioinformatics↗

bioRxiv2024

Genomic insights into Plasmodium vivax and Plasmodium simium host shifts in Latin America

Malaria in Latin America is largely caused by Plasmodium vivax, but its lesser-known sister species, Plasmodium simium, has recently emerged from monkeys to infect humans, thus raising new public health concerns. By analyzing 719 monkey samples and whole genome variations for 19 P. simium and 408 P. vivax isolates, we investigated the evolutionary history and population genetics of the two species. P. vivax, typically restricted to humans, was identified in three Colombian and one Brazilian monkeys, suggesting host niche expansion. Genetic analysis reveals recent genetic exchanges between both species and indicates that P. simium originated from a host jump approximately a century ago, possibly linked to P. vivax migration from Mexico to Brazil. Genome-wide scans revealed signals of positive selection in P. simium genes involved in interactions with primate hosts and mosquito vectors. These findings highlight P. simium evolutionary history and zoonotic malaria risks, and underscore the need to include monkeys in malaria prevention measures while ensuring human-wildlife coexistence.

evolutionary biology↗

bioRxiv2024

Genomic exploration of the complex journey of Plasmodium vivax in Latin America

Plasmodium vivax, the predominant malaria parasite in Latin America, has a rich and complex colonization history in the region, with debated hypotheses about its origin. Our study employed cutting-edge population genomic techniques, to collect whole genome sequencing data from 620 P. vivax isolates, including 107 newly sequenced samples, thus representing nearly all potential source populations worldwide. Analyses of the genetic structure, diversity, ancestry, and also, coalescent-based inferences and scenario testing using Approximate Bayesian Computation, have revealed a more complex evolutionary history than previously envisioned. Indeed, according to our analysis, the current American P. vivax populations predominantly stemmed from a now-extinct European lineage, with the potential contribution also from unsampled populations, most likely of West African origin, during post-colonial human migration waves in the late 19th-century. This study provides a fresh perspective on P. vivax intricate evolutionary journey and brings insights into the possible contribution of West African P. vivax populations to the colonization history of Latin America.

genomics↗

bioRxiv2024

Phylogeography of bar-tailed godwits: pre-LGM structure in Beringia and westward colonization of post-glacial Europe

In migratory birds, high mobility may reduce population structure through increased dispersal and enable adaptive responses to environmental change, whereas rigid migratory routines predict low dispersal, increased geographic structure, and limited flexibility to respond to change. We used nextRAD sequencing of 14,318 single-nucleotide polymorphisms to explore the population genetics and phylogeographic history of the bar-tailed godwit, Limosa lapponica, a migratory shorebird with six recognized subspecies and known for making the longest non-stop flights of any landbird. Using scenario-testing in an Approximate Bayesian Computation framework, we infer that bar-tailed godwits existed in three main lineages at the Last Glacial Maximum (LGM), when much of their present-day Arctic and sub-Arctic breeding range persisted in a large, unglaciated Siberian-Beringian refugium. Subsequently, population structure developed at both longitudinal extremes: in the east, a genetic cline exists across latitude in the Alaska breeding range of subspecies L. l. baueri; in the west, one lineage diversified into three extant subspecies L. l. lapponica, taymyrensis, and yamalensis, the former two of which migrate through previously glaciated western Europe. We also detected unrecognized population structure among bar-tailed godwits wintering in Europe, wherein a significant proportion of purported lapponica individuals were in fact taymyrensis, necessitating a re-assessment of the migrations, ecology, and population estimates for these subspecies. In the global range of this long-distance migrant, we found evidence of both (1) fidelity to rigid behavioral routines promoting fine-scale geographic population structure (in the east), and (2) flexibility to colonize recently available migratory flyways and non-breeding areas (in the west).

evolutionary biology↗

bioRxiv2022

Population genomic evidence of adaptive response during the invasion history of Plasmodium falciparum in the Americas

Plasmodium falciparum, the most virulent agent of human malaria, spread from Africa to all continents following the out-of-Africa human migrations. During the transatlantic slave trade between the 16th and 19th centuries, it was introduced twice independently to the Americas where it adapted to new environmental conditions (new human populations and mosquito species). Here, we analyzed the genome-wide polymorphisms of 2,635 isolates across the current P. falciparum distribution range in Africa, Asia, Oceania, and the Americas to investigate its genetic structure, invasion history, and selective pressures associated with its adaptation to the American environment. We confirmed that American populations originated from Africa with at least two independent introductions that led to two genetically distinct clusters, one in the North (Haiti and Columbia) and one in the South (French Guiana and Brazil), and the admixed Peruvian group. Genome scans revealed recent and more ancient signals of positive selection in the American populations. Particularly, we detected positive selection signals in genes involved in interactions with host (human and mosquito) cells and in genes involved in resistance to malaria drugs in both clusters. We found that some genes were under selection in both clusters. Analyses suggested that for five genes, adaptive introgression between clusters or selection on standing variation was at the origin of this repeated evolution. This study provides new genetic evidence on P. falciparum colonization history and on its local adaptation in the Americas.

evolutionary biology↗