The effective population size of Anopheles gambiae in Kenya: implications for population structure

We estimated current and long-term effective population size (Ne) of twoAnopheles gambiae (savanna cytotype) populations in Kenya. Temporalvariation at nine microsatellite loci in each population sampled 7 and 9years apart and genetic diversity in each sample were analyzed to answerthe following questions. (1) Do bottlenecks occur in Kenyan populations ofA. gambiae? (2) How variable are different populations with respect totheir current and long-term Ne values? (3) What are the implications ofthese results on population structure and history? The estimates of Ne ofAsembo and Jego were 6,359 and 4,258, respectively, and the lower 95%limits were 2,455 and 1,669, respectively. Thus, despite the typicalobservation of low density at the village level during the dry season,large populations are maintained annually. Large current Ne is consistentwith previous studies showing low differentiation across the continent,especially under Wright's isolation-by-distance model. Current Ne in Asembowas 1.5-fold higher than in Jego, but this difference was not significant.Long-term Ne in Asembo (22,667) was 2.9-fold higher than that in Jego(7,855) based on the stepwise mutation model. The difference betweenpopulations was significant at both time points regardless of whetherlong-term Ne values were calculated based on the stepwise mutation model orthe infinite-alleles model. Heterozygosity in Jego declined significantlybetween 1987 (59%) and 1996 (54%), whereas heterozygosity in Asembo wasstable (66%-65%). Despite the relatively high and significantdifferentiation between Asembo and Jego (FST = 0.072-0.10, RST = 0.037-0.038), all alleles in Jego were found in Asembo but not vice versa. All ofthese findings suggest that lower Ne in Jego magnifies differentiationbetween the two populations. The long-term Ne was biased downward, becauseits calculation was based on an upper bound estimate of microsatellitemutation rate. Ne values based on mtDNA and allozymes were an order ofmagnitude higher. Long-term Ne therefore, is probably measured in hundredsof thousands and hence does not support a recent expansion of this speciesfrom a small population.