Background: As Anopheles funestus is one of the principal Afro-tropical malaria vectors, a more complete understanding of its population structure is desirable. In West and Central Africa, An. funestus population structure is complicated by the coexistence of two assortatively mating chromosomal forms. Effective population size (Ne) is a key parameter in understanding patterns and levels of intraspecific variation, as it reflects the role of genetic drift. Here, Ne was estimated from both chromosomal forms, Kiribina and Folonzo, in Burkina Faso.
Methods: Short-term Ne was estimated by evaluating variation at 16 microsatellite loci across temporal samples collected annually from 2000-2002. Estimates were based on standardized variance in allele frequencies or a maximum likelihood method. Long-term Ne was estimated from genetic diversity estimates using mtDNA sequences and microsatellites.
Results: For both forms, short-term and long-term Ne estimates were on the order of 10(3) and 10(5), respectively. Long-term Ne estimates were larger when based on loci from chromosome 3R (both inside and outside of inversions) than loci outside of this arm.
Conclusion: Ne values indicate that An. funestus is not subject to seasonal bottlenecks. Though not statistically different because of large and overlapping confidence intervals, short-term Ne estimates were consistently smaller for Kiribina than Folonzo, possibly due to exploitation of different breeding sites: permanent for Folonzo and intermittent for Kiribina. The higher long-term Ne estimates on 3R, the arm carrying the two inversions mainly responsible for defining the chromosomal forms, give natural selection broader scope and merit further study.