An examination of genetic diversity and effective population size in Atlantic salmon populations

Abstract

SummaryEffective population size (Ne) is an important parameter in the conservation of genetic diversity. Comparative studies of empirical data that gauge the relative accuracy ofNemethods are limited, and a better understanding of the limitations and potential ofNeestimators is needed. This paper investigates genetic diversity andNein four populations of wild anadromous Atlantic salmon (Salmo salarL.) in Europe, from the Rivers Oir and Scorff (France) and Spey and Shin (Scotland). We aimed to understand present diversity and historical processes influencing current population structure. Our results showed high genetic diversity for all populations studied, despite their wide range of current effective sizes. To improve understanding of high genetic diversity observed in the populations with low effective size, we developed a model predicting present diversity as a function of past demographic history. This suggested that high genetic diversity could be explained by a bottleneck occurring within recent centuries rather than by gene flow. Previous studies have demonstrated the efficiency of coalescence models to estimateNe. Using nine subsets from 37 microsatellite DNA markers from the four salmon populations, we compared three coalescence estimators based on single and dual samples. ComparingNeestimates confirmed the efficiency of increasing the number and variability of microsatellite markers. This efficiency was more accentuated for the smaller populations. Analysis with low numbers of neutral markers revealed uneven distributions of allelic frequencies and overestimated short-termNe. In addition, we found evidence of artificial stock enhancement using native and non-native origin. We propose estimates ofNefor the four populations, and their applications for salmon conservation and management are discussed.