Using small numbers of broodstock for breeding often leads to random drift in gene frequencies between generations. Effective population size (Ne) is used as an indicator to assess the rate of inbreeding and loss of genetic variation in small populations. In this study we used six microsatellites, coupled with DNA parentage analyses, to determine the relative contributions from two commercial Yellowtail Kingfish hatchery broodstock groups over four pooled spawning events (two for each group).

Initial broodstock contributions from the dams was found to be highly skewed, with one dominant dam contributing more than 70% of the offspring (1-day post hatch, dph) in three of the pooled spawning events, while two dams contributed fairly equally to the offspring in the fourth pooled spawning event. Two sires were found to be contributing more that 78% of the offspring in one pooled spawning event, while contributions between the sires were fairly equal in the other three spawning events. The student then examined the differential survival of family size through the hatchery production (from 1 to 25 dph) during which time mortality averaged 80%. Parentage analyses indicated that through the process some maternal and paternal contributions that had been initially represented in the 1-dph offspring 3 were lost. There were also significant changes in the frequencies of progeny from individual dams and sires from day 1 to day 25.

These results indicate that hatchery breeding practices and high mortality during early larvae culture would result in poor retention of genetic variability across generations. With the actual Ne being less than half of the census Ne inbreeding rates would be relatively high if the current broodstock population was closed and future broodstock were derived from existing hatchery systems.