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Gene flow-was investigated in Anopheles gambiae from eight localities that span the ecological zones of Nigeria (arid savanna zones in the north gradually turn into humid forest zones in the south). Genetic differentiation was measured over 10 microsatellite loci and, to determine any effects of selection, five loci were located within chromosome inversions and the other five were outside inversions. Over all loci, the largest estimates of differentiation were in comparisons between localities in the savanna vs. forest zones (range F-ST 0.024-0.087, Nm 2.6-40.1; R-ST 0.014-0.100, Nm 2.2-16.4). However, three loci located within inversions on chromosome 11, whose frequencies varied clinally from north to south, were responsible for virtually all of the differentiation. When the three loci were removed, genetic distances across the remaining seven loci were markedly reduced even between localities in-the forest and savanna zones (range F-ST 0.001-0.019, Nm 12.7-226.1) or no longer significant (P > 0.05) in the case of R-ST. Although tests of isolation by distance gave seemingly equivocal results, geographical distance does,not appear to limit gene flow. These observations suggest that gene flow is extensive across the country but that selection on genes located within some inversions on chromosome II counters the homogenizing effects of gene flow.