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

PLoS Genetics
Aimee R TaylorCaroline O Buckee

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....Continue Reading

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Citations

Jan 23, 2019·The Journal of Infectious Diseases·Carol Hopkins Sibley
Sep 4, 2019·Malaria Journal·Sofonias K TessemaBryan Greenhouse
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Dec 21, 2021·PLoS Genetics·Tyler S BrownHsiao-Han Chang

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Methods Mentioned

BETA
genotyping

Software Mentioned

STRUCTURE
R
ChromoPainter
fineSTRUCTURE
hmmIBD
ChomoPainter

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