A call to arms: on refining Plasmodium vivax microsatellite marker panels for comparing global diversity

Abstract

BackgroundMicrosatellite (MS) markers have become an important tool for studying the population diversity, evolutionary history and multiplicity of infection (MOI) of malaria parasite infections. MS are typically selected on the basis of being highly polymorphic. However, it is known that the polymorphic potential (mutability) of each marker can vary as much as two orders of magnitude, which radically changes how diversity is represented in the genome from one marker to the next. Over the past decade, approximately 240 Plasmodium vivax MS have been published, comprising nine major panels of markers. Inconsistent usage of each panel has resulted in a surfeit of descriptive genetic diversity data that are largely incomparable between populations. The objective of this study was to statistically evaluate the quality of individual MS markers in order to validate a refined panel of markers that will provide a balanced picture of P. vivax population diversity.MethodsAll previously published data, including genetic diversity indices, MS parameters, and population parameters, were assembled from 18 different global studies into a flat file to facilitate statistical analysis and modelling using JMP® Genomics 6.0 (SAS Institute Inc, Cary, NC, USA). Statistical modeling was employed to down-select markers with extreme variation among the mean number of alleles, expected heterozygosity, maximum repeat length and/or chromosomal location of the repeat. Individual MS were analysed by step-down whole model linear regression and standard least squares fit models, both stratified by annual parasite incidence to identify MS markers with values significantly different from the mean.ResultsOf the 42 MS under evaluation in this study, 18 (nine high priority) were identified as ideal candidates for measuring population diversity between global regions, while five (two high priority) additional markers were identified as candidates for MOI studies.ConclusionsMS diversity was found to be a function of endemicity and motif structure. Evaluation of individual MS permitted the assembly of a refined panel of markers that can be reliably utilized in the field to compare population structures between global regions.

Higher Complexity of Infection and Genetic Diversity of Plasmodium vivax Than Plasmodium falciparum Across All Malaria Transmission Zones of Papua New Guinea

“…For both species it will therefore be important to investigate diversity using panels of ten or more less diverse genome wide markers such as microsatellite markers 37,82,83 or single nucleotide polymorphisms. 41,84 If chosen carefully, neutral genome wide markers will provide a more accurate estimate of diversity amongst individual parasites and populations, to further investigate the observed variability between regions.…”

Uncovering the transmission dynamics ofPlasmodium vivaxusing population genetics

“…A comprehensive review of these markers and empirical evidence has been gathered to support their use in different applications including the determination of MOI, genetic diversity and population structure. 27 The meta-analysis of 42 microsatellites provides a detailed characterisation of known allele frequency distributions in different endemic areas and recommendations for their use in population genetic applications. 27 Essentially, microsatellite markers are appropriate for different applications depending on the degree of polymorphism and mode of evolution.…”

“…27 The meta-analysis of 42 microsatellites provides a detailed characterisation of known allele frequency distributions in different endemic areas and recommendations for their use in population genetic applications. 27 Essentially, microsatellite markers are appropriate for different applications depending on the degree of polymorphism and mode of evolution. 27 Out of several different multi-locus panels previously developed as putatively neutral markers, [28][29][30] two panels and combinations thereof have been used in many different studies (reviewed below) for the characterisation of parasite population structure.…”

“…27 Essentially, microsatellite markers are appropriate for different applications depending on the degree of polymorphism and mode of evolution. 27 Out of several different multi-locus panels previously developed as putatively neutral markers, [28][29][30] two panels and combinations thereof have been used in many different studies (reviewed below) for the characterisation of parasite population structure. The use of identical marker panels in different transmission settings facilitates direct comparison of results, as differences in diversity reflect differences in the underlying parasite population.…”

Malaria Genomics in the Era of Eradication

“…Numerous groups have put forth proposed collections of nuclear genetic markers for genotyping, while other groups have pursued whole mitochondrial sequencing to make demographic inferences about populations. Comparing findings between studies that employed nuclear and mitochondrial markers (Sutton 2013;Koepfli et al 2015) can be challenging because of the different modes of inheritance, genetic effective population sizes, and mutation rates of those genomes. Use of markers that are neutral or potentially under selection (e.g., immune or drug) adds another level of consideration about which markers are most informative and/or appropriate for a given question.…”