Research Document 2018/044

Genetic Change in Inner Bay of Fundy Atlantic Salmon (Salmo salar) Across Three Generations of Captive Breeding and Rearing

By O'Reilly, P.T., Harvie, C., McWilliam, S., Lenentine, B., and Jones, R.

Abstract

The Live Gene Bank program for inner Bay of Fundy Atlantic Salmon (Salmo salar) has now been in operation for a little over 15 years, and across 3 generations.  In this review, we assess expected rates of loss of genetic variation through to 2015 in the Stewiacke River reference population, using 3 different approaches.  First, the program PMx and multi-generation pedigree information is used to monitor gene diversity, founder allele retention, and levels of inbreeding in spawner-year groups (sets of salmon spawned in a given year) across years; since kinship estimates of G0 (founder) salmon were included in the pedigree, metrics reported actually pertain to the unseen, unsampled parents (G-1 salmon) of the G0 founders.  Second, we report levels of molecular genetic variation, including number of observed alleles, allele richness, effective heterozygosity, and observed heterozygosity, for spawner-year groups across years.  Third, we use demographic information (including adult census population size, sex ratio information and variance in family size at maturity) to estimate the effective number of breeders and, in some instances, effective population size; where appropriate, this information is used to estimate expected rates of loss of gene diversity and accumulation of inbreeding through time.  Overall, we expect some, but generally minimal, loss of genetic variation and accumulation of inbreeding between G0 and G2 or G3 generation salmon.  Much of the genetic variation that is expected to be lost, and inbreeding accrued, can be directly related to very uneven G0 half-sib family size and, ultimately, the timing of the original founder collections.

We also investigate genetic change in inner Bay of Fundy Atlantic Salmon associated with possible introgression of genes from nearby wild and farm Atlantic Salmon sources.  Evidence from several different analyses is consistent with historic gene flow from wild outer Bay sources into nearby inner Bay of Fundy river populations along the New Brunswick side of the inner Bay.  Changing population dynamics post 1995 have likely resulted in ongoing and possibly increased rates of gene flow from outer Bay to Chignecto Bay populations in recent years; populations on the Minas Basin side of the inner Bay may have been more isolated.  We also find evidence for the presence and successful spawning of European farm salmon in several rivers (across multiple years) of the inner Bay of Fundy, particularly those on the Chignecto Bay side.

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