Admixture analysis of stocked brown trout populations using mapped microsatellite DNA markers: indigenous trout persist in introgressed populations

Abstract

Admixture between wild and captive populations is an increasing concern in conservation biology. Understanding the extent of admixture and the processes involved requires identification of admixed and non-admixed individuals. This can be achieved by statistical methods employing Bayesian clustering, but resolution is low if genetic differentiation is weak. Here, we analyse stocked brown trout populations represented by historical (1943 -1956) and contemporary (2000s) samples, where genetic differentiation between wild populations and stocked trout is weak (pairwise F ST of 0.047 and 0.053). By analysing a high number of microsatellite DNA markers (50) and making use of linkage map information, we achieve clear identification of admixed and non-admixed trout. Moreover, despite strong population-level admixture by hatchery strain trout in one of the populations (70.8%), nonadmixed individuals nevertheless persist (7 out of 53 individuals). These remnants of the indigenous population are characterized by later spawning time than the majority of the admixed individuals. We hypothesize that isolation by time mediated by spawning time differences between wild and hatchery strain trout is a major factor rescuing a part of the indigenous population from introgression.

Genetic and phenotypic changes in an Atlantic salmon population supplemented with non-local individuals: a longitudinal study over 21 years

“…Various mechanisms may explain the preferential reproduction of Gave individuals together including behavioural or genetic cues (e.g. genes of the major histocompatibility complex, [50]) as well as spatial or temporal isolation of spawners [20]. Post-zygotic isolation may have also occurred but it was probably weak as several admixed genotypes were detected (electronic supplementary material, figure S2 and table S6).…”

“…While the analysis of historical samples allowed assessment of the 'natural' genetic structure of wild populations prior to stocking operations, the analysis of postintroduction samples revealed variable loss of genetic integrity of target populations in terms of increased admixture [18][19][20], reduced differentiation with donor stocks [21] or disruption of relationships between genetic structure and geographical distance [17]. However, even if such comparisons between preand post-stocking situations inform on the degree of admixture in stocked populations, they do not provide any information on the temporal dynamics of admixture or on the phenotypic consequences of stocking in recipient populations.…”

Genetic adaptation to captivity can occur in a single generation

“…Environmental effects of captive rearing, for example, could produce differences in fitness between captive-born and wildborn individuals but would not create differences in fitness among individuals that experienced identical captive environments (12,13). Relaxed natural selection in captivity is a compelling hypothesis because it can manifest in a myriad of forms.…”

“…Identifying the mechanisms that cause reduced fitness in the wild is vital for deciding if, when, and how captive breeding programs should be applied for conservation and management purposes (5,7). Explanations for the rapid fitness declines (8)(9)(10)(11)(12) include environmental effects of captive rearing (including heritable epigenetic effects), inbreeding among close relatives, relaxed natural selection, and unintentional domestication selection (adaptation to the novel environment). Each of these mechanisms creates subtle but testable differences in patterns of reproductive success.…”

A conservation plan for Atlantic salmon (Salmo salar) and anadromous brown trout (Salmo trutta) in a region with intensive industrial use of aquatic habitats, the Hardangerfjord, western Norway

“…However, developments in statistical analysis, molecular techniques and genomic tools mean that DNA-SNP and/or microsatellite markers distributed across the genome can now be analysed. Various assignment tests (Anderson & Thompson 2002;Falush et al 2003) can subsequently be used to classify individuals as wild, farmed or F1 hybrids (Vähä & Primmer 2006;Hansen & Mensberg 2009;Glover et al 2010Glover et al , 2012Karlsson et al 2011). Thus, farmed and F1 hybrids can subsequently be eliminated from spawning populations or from brood stock for the gene banks.…”