Biology subjects

Early, A. M.

Publications and source records attributed to Early, A. M..

12 recordsLinked to original sources

bioRxiv2026

Genotypic evidence of vector-mediated selection on Plasmodium falciparum in infected field-collected Anopheles mosquitoes

Malaria-causing Plasmodium parasites are transmitted between vertebrate hosts via diverse species of Anopheles mosquitoes. The P47 protein in Plasmodium falciparum has been shown to affect transmission in various anopheline species by mediating evasion of mosquito innate immunity in an allele-specific manner. The Pfs47 gene that encodes P47 exhibits high genetic divergence across continents, as well as high genetic diversity within many parasite populations, but the impact of polymorphisms on transmission success in different sympatric vectors has not been previously studied in a field context. Here we report parasite genotyping data from naturally infected, field-collected mosquitoes at sites harboring at least two prevalent sympatric vector species, targeting Pfs47 in addition to the CSP, AMA1, SERA2, and TRAP parasite antigens. Collections took place at Ndangueng, Cameroon and Benguia, Gabon between November 2019 and July 2021, yielding infected Anopheles gambiae at both sites in addition to Anopheles moucheti in Cameroon and Anopheles funestus in Gabon. We found no significant difference in the mean number of parasite strains in infected sympatric mosquito species from each site. However, Pfs47 exhibited a significant difference in the prevalence of an amino acid polymorphism (I248L) between An. moucheti and An. gambiae in Cameroon. Polymorphisms at two additional positions (N272Y/I and P369H) displayed significant linkage disequilibrium with I248L, and there were significant differences in the distribution of Pfs47 haplotypes between sympatric mosquito species at both sites. These findings demonstrate divergent selection on P. falciparum mediated by sympatric vector species, suggesting that parasite genotype significantly impacts local vectorial capacity by modulating species-specific vector competence.

evolutionary biology↗

bioRxiv2026

Lowly polymorphic pathogen proteins may not be under evolutionary constraint

A central challenge in infectious disease biology is anticipating whether pathogen proteins targeted by vaccines, drugs, or diagnostics can evolve in ways that reduce intervention efficacy. Evolutionary constraint is therefore relevant to selecting targets likely to remain effective after deployment. Yet low diversity in contemporary pathogen populations is often interpreted as evidence of evolutionary constraint, an inference that can be misleading. In this Personal View, we use Plasmodium falciparum malaria to illustrate how contemporary population diversity and longer-term cross-species divergence can inform assessments of evolutionary constraint. A severe population bottleneck reduced diversity across the P. falciparum genome, meaning that low diversity in a particular protein-coding gene does not necessarily indicate unusual constraint. We place gene-level diversity in its genome-wide context, compare it with divergence across related ape-infecting malaria parasites, and examine how both relate to experimental essentiality. We then examine diversity and divergence along vaccine, drug, and diagnostic targets, considering them in relation to known resistance-associated mutations and other routes of evolutionary escape. We introduce PEEP (Protein Evolution Explorer for Plasmodium), a public interactive resource for exploring diversity and divergence across P. falciparum protein-coding genes and along individual proteins. Although our analyses focus on P. falciparum malaria, the implications extend across pathogens: low diversity alone is insufficient evidence of evolutionary constraint, and assessments of intervention durability should consider constraint alongside potential routes of evolutionary escape.

evolutionary biology↗

bioRxiv2025

The Portable Microhaplotype Object and Tools

Structured AbstractO_ST_ABSMotivationC_ST_ABSThe rapid increase in the generation of targeted sequencing data offers immense potential for research, medicine, and public health, however the lack of an established standard for these data has led to disparate solutions for data storage. A widely accepted standard is essential for data sharing, reuse, and the coordinated development of interoperable analysis tools. ResultsWe propose the Portable Microhaplotype Object (PMO), a standardized format for efficiently and losslessly storing phased targeted sequencing data (microhaplotypes). The PMO format is JSON-based, allowing efficient, relational storage of genetic data together with relevant metadata to minimize orphaned data. The format includes required fields and a curated set of optional fields leveraging established ontologies. To facilitate ease of use, we developed pmotools-python, an open-source package for creating, manipulating, and exporting PMO data into common formats. Additionally, we provide a simple web-based app to quickly create PMO files from tabular inputs, making the format accessible to a wide variety of users. Example datasets from Plasmodium, Anopheles, Escherichia coli, and Staphylococcus aureus demonstrate the broad applicability of the approach. PMO will streamline data sharing, foster interoperability, and accelerate the development of harmonized analysis tools. Availability and implementationThe Portable Microhaplotype Object (PMO) project, including the ontology specification, software tools, example datasets, and tutorials, is freely available athttps://plasmogenepi.github.io/PMO_Docs/. Key software components and datasets have archived releases with DOIs to ensure permanence, detailed in the Supplementary Text 1-5. Contactkathrynmmurie@gmail.com or nickjhathaway@gmail.com

bioinformatics↗

bioRxiv2025

Population genomics of Anopheles darlingi, the principal South American malaria vector mosquito

Malaria in South America remains a serious public health problem. Anopheles (Nyssorhynchus) darlingi is the most important malaria vector across tropical Latin America. Vector-targeted disease control efforts require a thorough understanding of mosquito demographic and evolutionary patterns. We present and analyze whole genomes of 1094 A. darlingi (median depth 18x) from six South American countries. We observe deep geographic population structure, high genetic diversity including thirteen putative segregating inversions, and no evidence for cryptic sympatric taxa despite high interpopulation divergence. Strong signals of selection are plausibly driven by insecticides, especially on cytochrome P450 genes, one of which we validated experimentally. Our results will facilitate effective mosquito surveillance and control, while highlighting ongoing challenges that a diverse vector poses for malaria elimination in the western hemisphere.

evolutionary biology↗

bioRxiv2025

Heterogeneous constraint and adaptation across the malaria parasite life cycle

Evolutionary forces vary across genomes, creating disparities in how traits evolve. In organisms with complex life cycles, it is unclear how intrinsic differences among discrete life stages impact evolution. We looked for life history-driven changes in patterns of adaptation in Plasmodium falciparum, a malaria-causing parasite with a multi-stage life cycle. Categorizing genes based on their expression in different life stages, we compared patterns of between- and within- species polymorphism across stages by estimating nonsynonymous to synonymous substitution rate ratios (dN/dS) and mean pairwise nucleotide diversity (NS/S). Considering these alongside estimates of Tajimas D, fixation probability, adaptive divergence proportion and rate, and FST, we looked for changes in the drift-selection balance in life stages subject to transmission bottlenecks and changes in ploidy. We observed signals of reduced selection efficacy in genes exclusively expressed in sporozoites, the parasite form transmitted from mosquitoes to humans and often targeted by vaccines and monoclonal antibodies. We discuss implications for how parasites evolve to resist therapeutics and consider functional, molecular, and population genetic factors that could contribute to these patterns.

evolutionary biology↗

bioRxiv2024

Temporal patterns of haplotypic and allelic diversity reflect the changing selection landscape of the malaria parasite Plasmodium falciparum

Populations of the malaria parasite Plasmodium falciparum regularly confront orchestrated changes in frontline drug treatment that drastically alter the parasites selection landscape. When this has occurred, the parasite has successfully adapted to the new drugs through novel resistance mutations. These novel mutations, however, may emerge in a genetic background already shaped by prior drug selection. In some instances, selection imposed by distinct drugs has targeted the same loci in either synergistic or antagonistic ways, resulting in genomic signatures that can be hard to attribute to a specific agent. Here, we use two approaches for detecting sequential bouts of drug adaptation: haplotype-based selection testing and temporal changes in allele frequencies. Using a set of longitudinally acquired samples from French Guiana, we determine that since the introduction of the drug artemether-lumefantrine (AL) in 2007 there have been rapid hard selective sweeps at both known and novel loci. We additionally identify genomic regions where selection acted in opposing directions before and after widespread AL introduction. At four high-profile genes with demonstrated involvement in drug resistance (crt, mdr1, aat1, and gch1), we saw strong selection before and after drug regime change; however, selection favored different haplotypes in the two time periods. Similarly, the allele frequency analysis identified coding variants whose frequency trajectory changed sign under the new drug pressure. These selected alleles were enriched for genes implicated in artemisinin and/or partner drug resistance in other global populations. Overall, these results suggest that drug resistance in P. falciparum is governed by known alleles of large effect along with a polygenic architecture of more subtle variants, any of which can experience fitness reversals under distinct drug regimes.

genomics↗

bioRxiv2024

Temporal and spatial dynamics of Plasmodium falciparum clonal lineages in Guyana

Plasmodium parasites, the causal agents of malaria, are eukaryotic organisms that obligately undergo sexual recombination within mosquitoes. However, in low transmission settings where most mosquitoes become infected with only a single parasite clone, parasites recombine with themselves, and the clonal lineage is propagated rather than broken up by outcrossing. We investigated whether stochastic/neutral factors drive the persistence and abundance of Plasmodium falciparum clonal lineages in Guyana, a country with relatively low malaria transmission, but the only setting in the Americas in which an important artemisinin resistance mutation (pfk13 C580Y) has been observed. To investigate whether this clonality was potentially associated with the persistence and spatial spread of the mutation, we performed whole genome sequencing on 1,727 Plasmodium falciparum samples collected from infected patients across a five-year period (2016- 2021). We characterized the relatedness between each pair of monoclonal infections (n=1,409) through estimation of identity by descent (IBD) and also typed each sample for known or candidate drug resistance mutations. A total of 160 clones (mean IBD [≥] 0.90) were circulating in Guyana during the study period, comprising 13 highly related clusters (mean IBD [≥] 0.40). In the five-year study period, we observed a decrease in frequency of a mutation associated with artemisinin partner drug (piperaquine) resistance (pfcrt C350R) and limited co-occurence of pfcrt C350R with duplications of plasmepsin 2/3, an epistatic interaction associated with piperaquine resistance. We additionally report polymorphisms exhibiting evidence of selection for drug resistance or other phenotypes and reported a novel pfk13 mutation (G718S) as well as 61 nonsynonymous substitutions that increased markedly in frequency. However, P. falciparum clonal dynamics in Guyana appear to be largely driven by stochastic factors, in contrast to other geographic regions. The use of multiple artemisinin combination therapies in Guyana may have contributed to the disappearance of the pfk13 C580Y mutation. Author SummaryMalaria is caused by eukaryotic Plasmodium parasites, which undergo sexual recombination within mosquitoes. In settings with low transmission, such as Guyana, these parasites often recombine with themselves, leading to the propagation of identical clones. We explored the population genomics of Plasmodium falciparum malaria parasites in Guyana over five years to characterize clonal transmission dynamics and understand whether they were influenced by local drug resistance mutations under strong selection, including pfk13 C580Y, which confers resistance to artemisinin, and pfcrt C350R, which confers resistance to piperaquine. Using whole genome sequencing on 1,463 samples, we identified 160 clones, in which all parasites share at least 90% of their genomes through recent common ancestry. We observed a decrease in frequency of the pfcrt C350R mutation, as well as the disappearance of pfk13 C580Y. Our findings contrast with the deterministic rise of drug resistance mutations observed in other geographic regions, sometimes associated with clonality. The simultaneous use of at least two different artemisinin combination therapies may have prevented the spread of an artemisinin-resistant clone in Guyana, suggesting a strategy for resistance management in other geographic regions.

genomics↗

bioRxiv2022

Resolving drug selection and migration in an inbred South American Plasmodium falciparum population with identity-by-descent analysis

The human malaria parasite Plasmodium falciparum is globally widespread, but its prevalence varies significantly between and even within countries. Most population genetic studies in P. falciparum focus on regions of high transmission where parasite populations are large and genetically diverse, such as sub-Saharan Africa. Understanding population dynamics in low transmission settings, however, is of particular importance as these are often where drug resistance first evolves. Here, we use the Pacific Coast of Colombia and Ecuador as a model for understanding the population structure and evolution of Plasmodium parasites in small populations harboring low genetic diversity. The combination of low transmission and a high proportion of monoclonal infections means there are few outcrossing events and clonal lineages persist for long periods of time. Yet despite this, the population is evolutionarily labile and has successfully adapted to multiple drug regimes. Using 166 newly sequenced whole genomes, we measure relatedness between parasites, calculated as identity by descent (IBD), and find 17 distinct but highly related clonal lineages, six of which have persisted in the region for at least a decade. This inbred population structure is captured in more detail with IBD than with other common population structure analyses like PCA, ADMIXTURE, and distance-based trees. We additionally use patterns of intra-chromosomal IBD and an analysis of haplotypic variation to explore the role of recombination in spreading drug resistance mutations throughout the region. Two genes associated with chloroquine resistance, crt and aat1, show evidence of hard selective sweeps, while selection appears soft and/or incomplete at three other key resistance loci (dhps, mdr1, and dhfr). Overall, this work highlights the strength of IBD analyses for studying parasite population structure and resistance evolution in regions of low transmission, and emphasizes that drug resistance can evolve and spread in extremely small populations, as will occur in any region nearing malaria elimination.

evolutionary biology↗

bioRxiv2020

Population Genomics of Plasmodium vivax in Panama to Assess the Risk of Case Importation on Malaria Elimination

Malaria incidence in Panama has plateaued in recent years in spite of elimination efforts, with almost all cases caused by Plasmodium vivax. Notwithstanding, overall malaria prevalence remains low (fewer than 1 case per 1000 persons). We used selective whole genome amplification to sequence 96 P. vivax samples from Panama collected between 2007 and 2019 to study the population structure and transmission dynamics of the parasite. Imported cases resulting from increased levels of human migration could threaten malaria elimination prospects, and four of the samples evaluated came from individuals with travel history. We explored patterns of recent common ancestry among the samples and observed that a single highly genetically related lineage was dominant among the samples (47 out of 59 samples with good sequencing coverage), spanning the entire period of the collection (2007-2019) and all regions of the country. We also found a second, smaller clonal lineage of four parasites collected between 2017 and 2019. To explore the regional context of Panamanian P. vivax we conducted principal components analysis and constructed a neighbor-joining tree using these samples and samples collected worldwide from a previous study. Three of the four samples with travel history clustered with samples collected from their suspected country of origin (consistent with importation), while one appears to have been a result of local transmission. The small number of genetically unique Panamanian P. vivax samples clustered with samples collected from Colombia, suggesting they represent the genetically similar ancestral P. vivax population in Panama or were recently imported from Colombia. The low diversity we observe in Panama indicates that this parasite population has been previously subject to a severe bottleneck and may be eligible for elimination. Additionally, while we confirmed that P. vivax is imported to Panama from diverse geographic locations, the lack of impact from imported cases on the overall parasite population genomic profile suggests that onward transmission from such cases is limited and that imported cases may not presently pose a major barrier to elimination. Author SummaryPanama has greatly reduced P. vivax incidence, however, this progress has plateaued. Understanding parasite transmission patterns and identifying imported cases is critical to help Panama and other countries succeed in their elimination efforts. Genomic epidemiology and population genomics can help provide information needed to inform malaria control policy. In this study, we collected 100 Panamanian P. vivax samples from two collection periods (2007-2009 and 2017-2019), of which 59 yielded usable sequencing data. 4 samples had patient travel history data associated with them. We found that the majority of samples belong to a single highly related lineage, termed CL1. This lineage has persisted since at least 2007. We also highlight how genomic epidemiology can be used to spotlight parasites that may be imported as a result of human migration, as well as corroborate or refute the country of origin as suggested by patient travel history. We observe no evidence of outcrossing between these potentially imported parasites and the local Panamanian parasite population, suggesting that imported parasites are not driving ongoing malaria transmission in Panama. The low diversity we observe in Panama indicates that this parasite population has been previously subject to a severe bottleneck and may be eligible for elimination.

microbiology↗

bioRxiv2020

Dense time-course gene expression profiling of the Drosophila melanogaster innate immune response

BackgroundImmune responses need to be initiated rapidly, and maintained as needed, to prevent establishment and growth of infections. At the same time, resources need to be balanced with other physiological processes. On the level of transcription, studies have shown that this balancing act is reflected in tight control of the initiation kinetics and shutdown dynamics of specific immune genes. ResultsTo investigate genome-wide expression dynamics and trade-offs after infection at a high temporal resolution, we performed an RNA-seq time course on D. melanogaster with 20 time points post Imd stimulation. A combination of methods, including spline fitting, cluster analysis, and Granger causality inference, allowed detailed dissection of expression profiles, lead-lag interactions, and functional annotation of genes through guilt-by-association. We identified Imd-responsive genes and co-expressed, less well characterized genes, with an immediate-early response and sustained up-regulation up to five days after stimulation. In contrast, stress response and Toll-responsive genes, among which were Bomanins, demonstrated early and transient responses. We further observed a strong trade-off with metabolic genes, which strikingly recovered to pre-infection levels before the immune response was fully resolved. ConclusionsThis high-dimensional dataset enabled the comprehensive study of immune response dynamics through the parallel application of multiple temporal data analysis methods. The well annotated data set should also serve as a useful resource for further investigation of the D. melanogaster innate immune response, and for the development of methods for analysis of a post-stress transcriptional response time-series at whole-genome scale.

systems biology↗

bioRxiv2018

Amplicon deep sequencing of low-density Plasmodium falciparum infections: an evaluation of analysis approaches

BackgroundDeep sequencing of targeted genomic regions is becoming a common tool for understanding the dynamics and complexity of Plasmodium infections, but its lower limit of detection is currently unknown. Here, a new amplicon analysis tool, the Parallel Amplicon Sequencing Error Correction (PASEC) pipeline, is used to evaluate the performance of amplicon sequencing on low-density Plasmodium DNA samples. Illumina-based sequencing of two P. falciparum genomic regions (CSP and SERA2) was performed on two types of samples: in vitro DNA mixtures mimicking low-density infections (1-200 genomes/l) and extracted blood spots from a combination of symptomatic and asymptomatic individuals (44-653,080 parasites/l). Three additional analysis tools--DADA2, HaplotypR, and SeekDeep--were applied to both datasets and the precision and sensitivity of each tool were evaluated. ResultsAmplicon sequencing can contend with low-density samples, showing reasonable detection accuracy down to a concentration of 5 Plasmodium genomes/l. Due to increased stochasticity and background noise, however, all four tools showed reduced sensitivity and precision on samples with very low parasitemia (<5 copies/l) or low read count (<100 reads per amplicon). PASEC could distinguish major from minor haplotypes with an accuracy of 90% in samples with at least 30 Plasmodium genomes/l, but only 61% at low Plasmodium concentrations (<5 genomes/l) and 46% at very low read counts (<25 reads per amplicon). The four tools were additionally used on a panel of extracted parasite-positive blood spots from natural malaria infections. While all four identified concordant patterns of complexity of infection (COI) across four sub-Saharan African countries, the COI values obtained for individual samples differed in some cases. ConclusionsAmplicon deep sequencing can be used to determine the complexity and diversity of low-density Plasmodium infections. Despite differences in their approach, four state-of-the-art tools resolved known haplotype mixtures with similar sensitivity and precision. Researchers can therefore choose from multiple robust approaches for analyzing amplicon data, however, error filtration approaches should not be uniformly applied across samples of varying parasitemia. Samples with very low parasitemia and very low read count have higher false positive rates and call for read count thresholds that are higher than current recommendations.

microbiology↗

bioRxiv2017

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

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.

evolutionary biology↗