Unravelling population structure heterogeneity within the genome of the malaria vector Anopheles gambiae.

BMC Genomics
Melina CamposRobert M MacCallum

Abstract

Whole genome re-sequencing provides powerful data for population genomic studies, allowing robust inferences of population structure, gene flow and evolutionary history. For the major malaria vector in Africa, Anopheles gambiae, other genetic aspects such as selection and adaptation are also important. In the present study, we explore population genetic variation from genome-wide sequencing of 765 An. gambiae and An. coluzzii specimens collected from across Africa. We used t-SNE, a recently popularized dimensionality reduction method, to create a 2D-map of An. gambiae and An. coluzzii genes that reflect their population structure similarities. The map allows intuitive navigation among genes distributed throughout the so-called "mainland" and numerous surrounding "island-like" gene clusters. These gene clusters of various sizes correspond predominantly to low recombination genomic regions such as inversions and centromeres, and also to recent selective sweeps. Because this mosquito species complex has been studied extensively, we were able to support our interpretations with previously published findings. Several novel observations and hypotheses are also made, including selective sweeps and a multi-locus selection event in Guin...Continue Reading

References

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Software Mentioned

R
SNPRelate
hierfstat
DBScan
UMAP
dist
SNE
bigmemory
topGO R package
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