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Population Structure Shapes Copy Number Variation in Malaria Parasites
Ian H Cheeseman1, Becky Miller2, John C Tan2
1Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX ianc@txbiomed.org.
Molecular Biology and Evolution
|November 29, 2015
Summary
Copy number variants (CNVs) are less common in large Plasmodium falciparum populations. CNVs are more frequent and larger in South American parasite populations, suggesting genetic structure impacts burden.
Area of Science:
- Genetics
- Population Genetics
- Parasitology
Background:
- Copy number variants (CNVs) are expected to be purged more efficiently in large populations.
- Plasmodium falciparum exhibits diverse population structures across different geographic regions.
Purpose of the Study:
- To investigate the impact of effective population size (Ne) on the prevalence and characteristics of CNVs in Plasmodium falciparum.
- To examine how population structure influences the burden of genetic variation in a key human pathogen.
Main Methods:
- Characterized 122 single-clone Plasmodium falciparum parasites from Africa, Southeast Asia, and South America using high-density SNP/CNV microarrays.
- Scored 134 high-confidence CNVs and 10,107 single-nucleotide polymorphisms across the parasite exome.
- Utilized FST outlier analysis to identify high-frequency CNVs under positive selection.
Main Results:
- CNVs were generally rare, small, and skewed towards low frequencies, supporting a deleterious model.
- CNVs were significantly more common, larger, and less frequency-skewed in South American populations compared to African and Southeast Asian populations.
- Identified several high-frequency CNVs, including known adaptive variants (rh2b, pfmdr1) and others requiring further study, under positive selection.
Conclusions:
- Population genetic structure significantly influences the burden and characteristics of CNVs in Plasmodium falciparum.
- The findings support the hypothesis that CNVs are largely deleterious and are subject to different purging efficiencies based on population size and structure.
- Further research is warranted on identified CNVs under positive selection for their role in parasite adaptation.
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