Captive‐bred ancestry affects spatial patterns of genetic diversity and differentiation in brown trout (Salmo trutta) populations

Abstract

1. Intraspecific genetic diversity is heterogeneously distributed in natural landscapes and often forms repeatable spatial patterns. For instance, in rivers, genetic diversity increases towards downstream areas, whereas genetic differentiation increases in isolated upstream areas. Nonetheless, these patterns can be modified by human-induced perturbations, and documenting the extent to which human activities alter these natural patterns is important for conservation. Among the human pressures that affect freshwater biodiversity, stocking natural populations with captive-bred strains is a common practice worldwide that can strongly alter the genetic integrity of wild populations.2. The main objectives of this study were to document the spatial distribution of captive-bred ancestry in brown trout (Salmo trutta) populations from four French basins having been stocked according to different practices, and to quantify for each basin the effect of captive-bred ancestry on the spatial distribution of genetic diversity and differentiation. The four basins were sampled along their upstream-downstream gradient, and a total of 1,686 individuals were genotyped at 192 single nucleotide polymorphism loci.3. For all basins, individuals with a strong assignment to the captive strain were mostly found in upper reaches, although the average proportion of captive-bred ancestry varied strikingly among rivers (from 1.9 to 58.7%). Although spatial patterns of genetic differentiation were not affected by introgression and showed an expected increase with increasing distances from the river mouth in all basins, there was evidence that the classical pattern of downstream increase in genetic diversity was reversed when considering highly introgressed populations.4. These findings demonstrate that the stocking of captive-bred strains can strongly modify natural spatial patterns of diversity, even when stocking occurred many generations ago and has now ended. The study illustrates the major impacts of humans on intraspecific biodiversity patterns, and emphasizes the importance of conservation plans that take into account this artificial distribution of genetic diversity.Jérôme G. Prunier and Keoni Saint-Pé are co-first authors.

Comparing the Utility of Microsatellites and Single Nucleotide Polymorphisms in Conservation Genetics: Insights from a Study on Two Freshwater Fish Species in France

“…However, as in the case of the ARZMas population, we cannot exclude the probability that individuals from the Dordogne River basin were stocked in the RANMar population (for instance, from the geographically very close CERSan population) before 2011, possibly just before the first sampling session. The fact that this "Dordogne" signature of the RANMar population was not detected with SNPs in 2014 could have resulted from the natural extirpation of allopatric strains within three years [48][49][50]. These two discrepancies could therefore be explained by unrecorded stocking events and are not sufficient to discredit STRs compared to SNPs without further investigation.…”

Population genetics, demography and conservation of Mediterranean brown trout from Sardinia

“…Brown trout ( S. trutta complex L., 1758) is a fish of great economic (mainly in aquaculture) and recreational value both in its original range and worldwide. Habitat degradation coupled with massive and uncontrolled stocking activities with non‐native lineages (mainly from northern Europe) has compromised the conservation status of native populations in several European countries (Araguas et al, 2017; Caputo et al, 2004; Prunier et al, 2022; Splendiani, Giovannotti, et al, 2019; Vera et al, 2018; Weiss et al, 2001). Brown trout is an appealing and iconic species for scientists because of taxonomic controversies that are still unresolved, the complex evolutionary history and the intricate patterns of life history traits (Lobón‐Cerviá & Sanz, 2018), as well as for its biological conservation needs (Piccolo et al, 2018).…”