Originally published as Genetics Published Articles Ahead of Print on June 15, 2009.

Genetics, Vol. 182, 1233-1249, August 2009, Copyright © 2009
doi:10.1534/genetics.109.101972

Age Structure, Changing Demography and Effective Population Size in Atlantic Salmon (Salmo salar)

Friso P. Palstra*,1, Michael F. O'Connell{dagger} and Daniel E. Ruzzante*

* Biology Department, Dalhousie University, Halifax, Nova Scotia B3H AJ1, Canada and {dagger} Fisheries and Oceans, St. John's, Newfoundland A1C 5X1, Canada

1 Corresponding author: Biology Department, Life Sciences Centre, Dalhousie University, 1355 Oxford St., Halifax, Nova Scotia B3H AJ1, Canada.
E-mail: fpalstra{at}dal.ca

Effective population size (Ne) is a central evolutionary concept, but its genetic estimation can be significantly complicated by age structure. Here we investigate Ne in Atlantic salmon (Salmo salar) populations that have undergone changes in demography and population dynamics, applying four different genetic estimators. For this purpose we use genetic data (14 microsatellite markers) from archived scale samples collected between 1951 and 2004. Through life table simulations we assess the genetic consequences of life history variation on Ne. Although variation in reproductive contribution by mature parr affects age structure, we find that its effect on Ne estimation may be relatively minor. A comparison of estimator models suggests that even low iteroparity may upwardly bias Ne estimates when ignored (semelparity assumed) and should thus empirically be accounted for. Our results indicate that Ne may have changed over time in relatively small populations, but otherwise remained stable. Our ability to detect changes in Ne in larger populations was, however, likely hindered by sampling limitations. An evaluation of Ne estimates in a demographic context suggests that life history diversity, density-dependent factors, and metapopulation dynamics may all affect the genetic stability of these populations.