| Summary: | <p>Abstract</p> <p>Background</p> <p><it>Anopheles darlingi </it>is the most important malaria vector in the Neotropics. An understanding of <it>A. darlingi</it>'s population structure and contemporary gene flow patterns is necessary if vector populations are to be successfully controlled. We assessed population genetic structure and levels of differentiation based on 1,376 samples from 31 localities throughout the Peruvian and Brazilian Amazon and Central America using 5–8 microsatellite loci.</p> <p>Results</p> <p>We found high levels of polymorphism for all of the Amazonian populations (mean <it>R</it><sub>S </sub>= 7.62, mean <it>H</it><sub>O </sub>= 0.742), and low levels for the Belize and Guatemalan populations (mean <it>R</it><sub>S </sub>= 4.3, mean <it>H</it><sub>O </sub>= 0.457). The Bayesian clustering analysis revealed five population clusters: northeastern Amazonian Brazil, southeastern and central Amazonian Brazil, western and central Amazonian Brazil, Peruvian Amazon, and the Central American populations. Within Central America there was low non-significant differentiation, except for between the populations separated by the Maya Mountains. Within Amazonia there was a moderate level of significant differentiation attributed to isolation by distance. Within Peru there was no significant population structure and low differentiation, and some evidence of a population expansion. The pairwise estimates of genetic differentiation between Central America and Amazonian populations were all very high and highly significant (<it>F</it><sub>ST </sub>= 0.1859 – 0.3901, <it>P </it>< 0.05). Both the <it>D</it><sub>A </sub>and <it>F</it><sub>ST </sub>distance-based trees illustrated the main division to be between Central America and Amazonia.</p> <p>Conclusion</p> <p>We detected a large amount of population structure in Amazonia, with three population clusters within Brazil and one including the Peru populations. The considerable differences in <it>N</it><sub>e </sub>among the populations may have contributed to the observed genetic differentiation. All of the data suggest that the primary division within <it>A. darlingi </it>corresponds to two <it>white </it>gene genotypes between Amazonia (genotype 1) and Central America, parts of Colombia and Venezuela (genotype 2), and are in agreement with previously published mitochondrial <it>COI </it>gene sequences interpreted as incipient species. Overall, it appears that two main factors have contributed to the genetic differentiation between the population clusters: physical distance between the populations and the differences in effective population sizes among the subpopulations.</p>
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