Quantifying connectivity between local Plasmodium falciparum malaria parasite populations using identity by descent

Aimee R. Taylor, Stephen F. Schaffner, Gustavo C. Cerqueira, Standwell C. Nkhoma, Timothy J.C. Anderson, Kanlaya Sriprawat, Aung Pyae Phyo, François Nosten, Daniel E. Neafsey, Caroline O. Buckee

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

With the rapidly increasing abundance and accessibility of genomic data, there is a growing interest in using population genetic approaches to characterize fine-scale dispersal of organisms, providing insight into biological processes across a broad range of fields including ecology, evolution and epidemiology. For sexually recombining haploid organisms such as the human malaria parasite P. falciparum, however, there have been no systematic assessments of the type of data and methods required to resolve fine scale connectivity. This analytical gap hinders the use of genomics for understanding local transmission patterns, a crucial goal for policy makers charged with eliminating this important human pathogen. Here we use data collected from four clinics with a catchment area spanning approximately 120 km of the Thai-Myanmar border to compare the ability of divergence (FST) and relatedness based on identity by descent (IBD) to resolve spatial connectivity between malaria parasites collected from proximal clinics. We found no relationship between inter-clinic distance and FST, likely due to sampling of highly related parasites within clinics, but a significant decline in IBD-based relatedness with increasing inter-clinic distance. This association was contingent upon the data set type and size. We estimated that approximately 147 single-infection whole genome sequenced parasite samples or 222 single-infection parasite samples genotyped at 93 single nucleotide polymorphisms (SNPs) were sufficient to recover a robust spatial trend estimate at this scale. In summary, surveillance efforts cannot rely on classical measures of genetic divergence to measure P. falciparum transmission on a local scale. Given adequate sampling, IBD-based relatedness provides a useful alternative, and robust trends can be obtained from parasite samples genotyped at approximately 100 SNPs.

Original languageEnglish (US)
Article numbere1007065
JournalPLoS Genetics
Volume13
Issue number10
DOIs
StatePublished - Oct 1 2017
Externally publishedYes

Fingerprint

Falciparum Malaria
malaria
Plasmodium falciparum
connectivity
parasite
Parasites
parasites
relatedness
Population
Single Nucleotide Polymorphism
single nucleotide polymorphism
genomics
Myanmar
polymorphism
sampling
Biological Phenomena
divergence
Parasitic Diseases
Haploidy
Population Genetics

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics
  • Genetics(clinical)
  • Cancer Research

Cite this

Taylor, A. R., Schaffner, S. F., Cerqueira, G. C., Nkhoma, S. C., Anderson, T. J. C., Sriprawat, K., ... Buckee, C. O. (2017). Quantifying connectivity between local Plasmodium falciparum malaria parasite populations using identity by descent. PLoS Genetics, 13(10), [e1007065]. https://doi.org/10.1371/journal.pgen.1007065

Quantifying connectivity between local Plasmodium falciparum malaria parasite populations using identity by descent. / Taylor, Aimee R.; Schaffner, Stephen F.; Cerqueira, Gustavo C.; Nkhoma, Standwell C.; Anderson, Timothy J.C.; Sriprawat, Kanlaya; Pyae Phyo, Aung; Nosten, François; Neafsey, Daniel E.; Buckee, Caroline O.

In: PLoS Genetics, Vol. 13, No. 10, e1007065, 01.10.2017.

Research output: Contribution to journalArticle

Taylor, AR, Schaffner, SF, Cerqueira, GC, Nkhoma, SC, Anderson, TJC, Sriprawat, K, Pyae Phyo, A, Nosten, F, Neafsey, DE & Buckee, CO 2017, 'Quantifying connectivity between local Plasmodium falciparum malaria parasite populations using identity by descent', PLoS Genetics, vol. 13, no. 10, e1007065. https://doi.org/10.1371/journal.pgen.1007065
Taylor AR, Schaffner SF, Cerqueira GC, Nkhoma SC, Anderson TJC, Sriprawat K et al. Quantifying connectivity between local Plasmodium falciparum malaria parasite populations using identity by descent. PLoS Genetics. 2017 Oct 1;13(10). e1007065. https://doi.org/10.1371/journal.pgen.1007065
Taylor, Aimee R. ; Schaffner, Stephen F. ; Cerqueira, Gustavo C. ; Nkhoma, Standwell C. ; Anderson, Timothy J.C. ; Sriprawat, Kanlaya ; Pyae Phyo, Aung ; Nosten, François ; Neafsey, Daniel E. ; Buckee, Caroline O. / Quantifying connectivity between local Plasmodium falciparum malaria parasite populations using identity by descent. In: PLoS Genetics. 2017 ; Vol. 13, No. 10.
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