The change of gene frequencies at the AAT-1*and PGM-1*loci was examined in the two guppy strains, S and S3, which had been maintained as a closed colony for a period of 16 years. These strains had been separated from an original strain in 1981. In the S strain, the*a allele frequency at AAT-1*locus changed from 0.282 in 1981 to 0.602 in 1997, and the*a allele at the PGM-1*locus changed from 0.772 to 0.430. On the other hand, in the S3 strain, the*a allele frequency at the AAT-1*locus changed to 0.395 in 1997, and the*a allele at the PGM-1*locus changed to 0.528. The effective population size (Ne) during the maintenance period of the guppy strain was estimated based on the magnitude of the random drift in the gene frequency. The estimated Ne was initially 623 in the S strain and 413 in the S3 strain. The decrease of Ne over a period of 16 years was demonstrated to be 18 in the S strain and 24 in the S3 strain, and these phenomenon may be led by the sampling of mature fish.
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