Research Document - 2009/095
Conservation of genetic variation in the inner Bay of Fundy Atlantic salmon captive breeding and rearing program
By P.T. O'Reilly and C.J. Harvie
Abstract
In response to the precipitous decline of inner Bay of Fundy Atlantic (iBoF) salmon, the Department of Fisheries and Oceans (DFO) initiated a captive breeding and rearing program, intended to prevent the imminent extirpation of this Species at Risk Act (SARA)-listed species. The goal of the program was to minimize all genetic changes relative to the founding population, including the loss of genetic variation through drift, until conditions at sea improve, and wild self-sustaining populations can be established. Loss of genetic variation was minimized by maintaining large effective population sizes, and by assessing the genetic value, or Mean Kinship (MK), of candidate spawners. Mean kinship determinations were based on pedigree information, which was estimated by reconstructing kinship in the founding generation using molecular genetic marker data and recently developed algorithms for assessing first-order relatedness in the absence of parental information and, in subsequent generations, through molecular genetic marker data and parentage analyses. The objective of this report is to evaluate the ability of the above program to minimize the rate of loss of neutral molecular genetic variation.
Program efficacy was first evaluated by determining the percent of genetic variation present in the large (>1,000) wild juvenile parr collections, captured in the parents (founders, G0) selected for spawning. Loss of gene diversity (He) and number of observed alleles (#A), two commonly used measures of genetic variation, in the selection of founders was minimal, approximately 1%. We also evaluated the rate of loss of genetic variation in the production of the first generation (G1) of salmon from the original G0 founders. In this analysis, we assessed loss of genetic variation by spawning year, and by year class. Evaluations by spawning year involved comparisons of genetic variation in all parents spawned in a given year and all offspring later recovered and spawned, regardless of the year they matured and were genotyped. Gene diversity estimates were generally greater in the offspring relative to the parents and, when less, declined by only 0.24%. Parent-offspring reductions in #A were quite variable between spawning years, and could be quite high, 3.9 to 18.2 percent over one generation. However, because of a number of operational aspects of the current program, including monitoring of egg mortality and previous spawning history of individuals and families, this measure of loss of genetic variation is likely to over-represent the true loss of genetic variation.
In analyses of rates of loss by year class, genetic variation was compared between all parents obtained from the wild in a given year and selected for spawning, and all offspring of these same parents selected for spawning themselves, regardless of the year in which the parents were spawned, and regardless of the year the offspring were recovered and spawned in the production of the next (G2) generation. Gene diversity estimates were again generally greater in the offspring relative to the parents and, when less, declined by only 0.25% or 1.1%. Rates of loss of #A when assessed by year class were variable and sometimes very large (7.8% to 52.0%). However, much of the reported loss for any one year class was due to (1) spawnings having occurred between year classes or generations (though genetic variation will be recovered in these between-group classes, it could not be tabulated and incorporated into within-year class statistics), and (2) incomplete maturity and recovery of offspring, though further genetic variation is expected to be recovered when these offspring mature in subsequent years. When comparing combined year class groups, thereby reducing the effects of factor (1) above, rates of loss of #A between parents and offspring were between 3.5 and 4%. Once offspring of parents collected in 2000 and 2001 mature, rates of loss of #A are expected to be lower, probably on the order of 2-3%. Overall, these results indicate that the rates of loss of genetic variation were indeed low during the period assessed, below 3-4% and probably between 0.25% and 3%, depending on the measure of genetic variation assessed. These analyses indicate that the captive breeding and rearing program being carried out on inner Bay of Fundy Atlantic salmon is indeed effective at maintaining neutral genetic diversity.
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