Tracing the origins and signatures of selection of antifolate resistance in island populations of Plasmodium falciparum

Salgueiro, Patrícia; Vicente, José L.; Ferreira, C.; Teófilo, Vânia; Galvão, André Luiz Baptista; Rosário, Virgílio Estólio do; Cravo, Pedro Vitor Lemos; Pinto, João

doi:10.1186/1471-2334-10-163

Cited by 17 publications

(15 citation statements)

References 36 publications

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“…For example, in Malaria parasites, multiple de novo amplification events of the pfmdr1 gene confer resistance to mefloquine [42], while multiple independent mutations in the genes dhfr and dhps confer resistance to sulfadoxine-pyrimethamine [43]. Several studies have observed soft sweeps during the evolution of drug resistance in HIV [44, 45].…”

Section: Signatures and Examples Of Soft Sweepsmentioning

confidence: 99%

Population genomics of rapid adaptation by soft selective sweeps

Messer

Petrov

2013

Trends in Ecology & Evolution

494

567

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Organisms can often adapt surprisingly quickly to evolutionary challenges, such as the application of pesticides or antibiotics, suggesting an abundant supply of adaptive genetic variation. In these situations, adaptation should commonly produce “soft” selective sweeps, where multiple adaptive alleles sweep through the population at the same time, either because the alleles were already present as standing genetic variation or arose independently by recurrent de novo mutations. Most well-known examples of rapid molecular adaptation indeed show signatures of such soft selective sweeps. Here we review our current understanding of the mechanisms that produce soft sweeps and the approaches used for their identification in population genomic data. We argue that soft sweeps might be the dominant mode of adaptation in many species.

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Section: Signatures and Examples Of Soft Sweepsmentioning

confidence: 99%

Population genomics of rapid adaptation by soft selective sweeps

Messer

Petrov

2013

Trends in Ecology & Evolution

494

567

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“…Microsatellites flanking the Pfdhfr (chromosome 4) and Pfdhps (chromosome 8) genes at the following positions were analyzed: for the Pfdhfr gene, loci located 0.3 kb, 4.4 kb, and 5.3 kb upstream of codon 108; and for the Pfdhps gene, loci located 0.8 kb, 4.3 kb, and 7.7 kb downstream of codon 437. The PCR conditions and primers are described in former reports (62,65,67). As a reference, the Southeast Asian P. falciparum K1 laboratory strain was used because its STR profile matches the East African Pfdhps double mutant (GE mutant) haplotype lineage SGE 1 (58).…”

Section: Methodsmentioning

confidence: 99%

“…For haplotype assembly, the resistance-specific polymorphic locus and the corresponding flanking microsatellite loci were considered according to a previous description (67). Isolates for which amplification failed for any of the loci or multiple peaks were generated were excluded from the haplotype grouping.…”

Section: Methodsmentioning

confidence: 99%

Plasmodium falciparum Genetic Diversity in Continental Equatorial Guinea before and after Introduction of Artemisinin-Based Combination Therapy

Guerra

Neres

Salgueiro

et al. 2017

Antimicrob Agents Chemother

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Efforts to control malaria may affect malaria parasite genetic variability and drug resistance, the latter of which is associated with genetic events that promote mechanisms to escape drug action. The worldwide spread of drug resistance has been a major obstacle to controlling Plasmodium falciparum malaria, and thus the study of the origin and spread of associated mutations may provide some insights into the prevention of its emergence. This study reports an analysis of P. falciparum genetic diversity, focusing on antimalarial resistance-associated molecular markers in two socioeconomically different villages in mainland Equatorial Guinea. The present study took place 8 years after a previous one, allowing the analysis of results before and after the introduction of an artemisinin-based combination therapy (ACT), i.e., artesunate plus amodiaquine. Genetic diversity was assessed by analysis of the Pfmsp2 gene and neutral microsatellite loci. Pfdhps and Pfdhfr alleles associated with sulfadoxine-pyrimethamine (SP) resistance and flanking microsatellite loci were investigated, and the prevalences of drug resistance-associated point mutations of the Pfcrt, Pfmdr1, Pfdhfr, and Pfdhps genes were estimated. Further, to monitor the use of ACT, we provide the baseline prevalences of K13 propeller mutations and Pfmdr1 copy numbers. After 8 years, noticeable differences occurred in the distribution of genotypes conferring resistance to chloroquine and SP, and the spread of mutated genotypes differed according to the setting. Regarding artemisinin resistance, although mutations reported as being linked to artemisinin resistance were not present at the time, several single nucleotide polymorphisms (SNPs) were observed in the K13 gene, suggesting that closer monitoring should be maintained to prevent the possible spread of artemisinin resistance in Africa.

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“…Additional examples of adaptation from standing variation have been documented in Drosophila (Magwire et al 2011), Peromyscus (Domingues et al 2012), and humans (Peter et al 2012), among others. Adaptations involving simultaneous selection on multiple alleles of independent origin at the same locus have also been documented across a wide array of species (Menozzi et al 2004;Nair et al 2006;Karasov et al 2010;Salgueiro et al 2010;Schmidt et al 2010;Jones et al 2013). Nonetheless, the general importance of soft sweeps for the adaptive process remains somewhat contentious (see, e.g., Jensen 2014; Schrider et al 2015).…”

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confidence: 99%

A Coalescent Model for a Sweep of a Unique Standing Variant

Berg

Coop

2015

Genetics

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The use of genetic polymorphism data to understand the dynamics of adaptation and identify the loci that are involved has become a major pursuit of modern evolutionary genetics. In addition to the classical "hard sweep" hitchhiking model, recent research has drawn attention to the fact that the dynamics of adaptation can play out in a variety of different ways and that the specific signatures left behind in population genetic data may depend somewhat strongly on these dynamics. One particular model for which a large number of empirical examples are already known is that in which a single derived mutation arises and drifts to some low frequency before an environmental change causes the allele to become beneficial and sweeps to fixation. Here, we pursue an analytical investigation of this model, bolstered and extended via simulation study. We use coalescent theory to develop an analytical approximation for the effect of a sweep from standing variation on the genealogy at the locus of the selected allele and sites tightly linked to it. We show that the distribution of haplotypes that the selected allele is present on at the time of the environmental change can be approximated by considering recombinant haplotypes as alleles in the infinite-alleles model. We show that this approximation can be leveraged to make accurate predictions regarding patterns of genetic polymorphism following such a sweep. We then use simulations to highlight which sources of haplotypic information are likely to be most useful in distinguishing this model from neutrality, as well as from other sweep models, such as the classic hard sweep and multiple-mutation soft sweeps. We find that in general, adaptation from a unique standing variant will likely be difficult to detect on the basis of genetic polymorphism data from a single population time point alone, and when it can be detected, it will be difficult to distinguish from other varieties of selective sweeps. Samples from multiple populations and/or time points have the potential to ease this difficulty.KEYWORDS coalescent theory; genetic hitchhiking; natural selection; soft sweep; standing variation I N recent decades, an understanding of how positive directional selection and the associated hitchhiking effect influence patterns of genetic variation has become a valuable tool for evolutionary geneticists. The reductions in genetic diversity and long extended haplotypes that are characteristic of a recent selective sweep can allow for both the identification of individual genes that have contributed to recent adaptation within a population (i.e., hitchhiking mapping) and understanding the rate and dynamics of adaptation at a genome-wide level (Wiehe and Stephan 1993;Andolfatto 2007;Eyre-Walker and Keightley 2009;Elyashiv et al. 2014).While the contribution of many different modes to the adaptive process has long been recognized, early work on the hitchhiking effect focused largely on the scenario where a single codominant mutation arose and was immediately beneficial, rapidly sweep...

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Tracing the origins and signatures of selection of antifolate resistance in island populations of Plasmodium falciparum

Cited by 17 publications

References 36 publications

Population genomics of rapid adaptation by soft selective sweeps

Population genomics of rapid adaptation by soft selective sweeps

Plasmodium falciparum Genetic Diversity in Continental Equatorial Guinea before and after Introduction of Artemisinin-Based Combination Therapy

A Coalescent Model for a Sweep of a Unique Standing Variant

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