SNP Genotyping Defines Complex Gene-Flow Boundaries Among African Malaria Vector Mosquitoes

Abstract

Mosquitoes in the Anopheles gambiae complex show rapid ecological and behavioral diversification, traits that promote malaria transmission and complicate vector control efforts. A high-density, genome-wide mosquito SNP-genotyping array allowed mapping of genomic differentiation between populations and species that exhibit varying levels of reproductive isolation. Regions near centromeres or within polymorphic inversions exhibited the greatest genetic divergence, but divergence was also observed elsewhere in the genomes. Signals of natural selection within populations were overrepresented among genomic regions that are differentiated between populations, implying that differentiation is often driven by population-specific selective events. Complex genomic differentiation among speciating vector mosquito populations implies that tools for genome-wide monitoring of population structure will prove useful for the advancement of malaria eradication.

Population genetics of malaria resistance in humans

“…Support for this hypothesis comes from some molecular analysis of P. falciparum strains that suggests that the African malaria population expanded around 10 000 years ago and spread to other areas (Joy et al, 2003). In addition, chromosomal data from the mosquito vector Anopheles gambiae support contemporaneous speciation (Coluzzi et al, 2002 see also;Lawniczak et al, 2010 andNeafsey et al, 2010). Recent analysis suggests that P. falciparum in humans is the result of cross-species transmission from gorillas (Liu et al, 2010).…”

Malaria Genomics in the Era of Eradication

“…Following the generation of reference genome assemblies, malaria investigators followed the path of other organisms in the postgenomic era and characterized genomic diversity through sequencing surveys (Jeffares et al 2007;Mu et al 2007;Volkman et al 2007;Tan et al 2011;Neafsey et al 2012) and later genome-wide single nucleotide polymorphism (SNP) arrays (Neafsey et al , 2010Mu et al 2010;Tan et al 2011;Van Tyne et al 2011). Such work illuminated the recent demographic history of multiple parasite and vector species, defined sometimes complex gene flow boundaries, and revealed the impact of immune, drug, or insecticide selection on the genomes of malaria parasites and vectors.…”

Spatiotemporal dynamics of gene flow and hybrid fitness between the M and S forms of the malaria mosquito, Anopheles gambiae

“…These single-locus assays misidentify a significant proportion of backcross individuals. In addition, assessment of hybridization frequencies and comprehensive tests for introgression are precluded from these studies because DNA pools were used (21,23,27), sample sizes were too small (24,26), or such assessments may be irrelevant because M and S laboratory colony mosquitoes were used (28). Finally, there are strong limitations in relying on genome scans alone for detecting selection, gene flow, and recombination that occurs during speciation (33,34).…”

“…A number of genomewide scans comparing M and S have been conducted since. These have applied several methods, including the same microarray used by Turner et al (25,26), high-density SNP arrays (12,21,23,27), and whole-genome sequencing (28). These studies likewise revealed little divergence except in a few discrete regions of the genome characterized by high levels of differentiation (islands of divergence).…”