We used microsatellite DNA markers to investigate the maintenance of genetic diversity within and between samples of subpopulations (spanning five captive-bred generations) of the haplochromine cichlid Prognathochromis perrieri. The subpopulations are maintained as part of the Lake Victoria Cichlid species survival plan. Changes in the frequencies of 24 alleles, over four polymorphic loci, were used to estimate effective population size (Ne). Point estimates of Ne ranged from 2.5 to 7.7 individuals and were significantly smaller than the actual census size (Nobs) for all subpopulations (32-243 individuals per generation), with the corresponding conservative Ne/Nobs ratios ranging from 0.01 to 0.12. Approximately 19% of the initial alleles were lost within the first four generations of captive breeding. Between-generation comparisons of expected heterozygosity showed significant losses ranging from 6% to 12% per generation. Seven private alleles were observed in the last sampled generation of four subpopulations, and analysis of population structure by FST indicated that approximately 33% of the total genetic diversity is maintained between the subpopulations from different institutions. To reduce the loss of genetic variation, we recommend that offspring production be equalized by periodically removing dominant males, which will encourage reproduction by additional males. Consideration should also be given to encouraging more institutions to maintain populations, because a significant fraction of the genetic variation exists as among-population differences resulting from random differentiation among subpopulations.
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