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

• Published in: Genetics Research
• Main Authors: Nikolic, Natacha, Butler, James, Baglinière, Jean-Luc, Laughton, Robert, Mcmyn, Iain, Chevalet, Claude
• Other Authors: Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), James Cook University (JCU), Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Spey Fishery Board and Spey Research Trust, Kyle of Sutherland District Salmon Fisheries Board
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2009
• Subjects: genetic diversity; effective size; livestock population; salmon; atlantic; saumon de l'atlantique; salmo salar; europe; [SDV]Life Sciences [q-bio]; Atlantic salmon; Salmo salar
• Online Access: https://hal.science/hal-01453786; https://doi.org/10.1017/S0016672309990346

Chantier qualité GA Effective population size (Ne) is an important parameter in the conservation of genetic diversity. Comparative studies of empirical data that gauge the relative accuracy of Ne methods are limited, and a better understanding of the limitations and potential of Ne estimators is needed. This paper investigates genetic diversity and Ne in four populations of wild anadromous Atlantic salmon (Salmo salar L.) 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 estimate Ne. Using nine subsets from 37 microsatellite DNA markers from the four salmon populations, we compared three coalescence estimators based on single and dual samples. Comparing Ne estimates 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-term Ne. In addition, we found evidence of artificial stock enhancement using native and non-native origin. We propose estimates of Ne for the four populations, and their applications for salmon conservation and management are discussed.