A species-specific microsatellite marker to discriminate European Atlantic salmon, brown trout, and their hybrids

Abstract

Atlantic salmon and brown trout frequently cooccur in the same habitats and juveniles of both species are difficult to discriminate. Hybridization between the two taxa has also been widely documented especially in endangered populations hence the need for species-specific molecular markers. Here we show that the microsatellite marker SsAD486 has two species-specific alleles allowing the identification of Atlantic salmon, brown trout, and their hybrids throughout the European range of these species. Since this marker is polymorphic in Atlantic salmon populations from Western Atlantic, it could also help discriminating between North American and European salmon.

Estimating the effective number of breeders from single parr samples for conservation monitoring of wild populations of Atlantic salmon Salmo salar

“…Although some of this variation in N b was explained by redd aggregation, some could also be due to low juvenile survival. Similarly, different demographic configurations may result in similar outcomes in terms of N b as was found for reproductive seasons -2011and 2011-2011, the high number of returning adults encountered favourable environmental conditions for reproduction as shown by the high number of non-aggregated redds observed. Below average estimated number of YOY, however, indicate high mortality in early life stages.…”

“…Genomic DNA was extracted using a salt-chloroform extraction protocol modified from Miller et al (1988) and detailed in Gauthey et al (2015) or Purelink Genomic DNA mini kit (Invitrogen; www.invitrogen.com) following the manufacturer protocol, respectively from fin clips and scales. In order to be able to best discriminate distinct but related individuals on genetic information alone, DNA extracts were used to amplify 16 loci including 15 microsatellite markers previously developed for S. salar (Table S1, Supporting Information; Slettan et al, 1995;O'Reilly et al, 1996;Cairney et al, 2000;Grimholt et al, 2002;Vasemägi et al, 2005), including SsaD486 (King et al, 2005) discriminating brown trout Salmo trutta L. 1758 and hybrid individuals possibly present in the sample (Perrier et al, 2011) and one sex-specific marker linked to the salmonid Y-chromosome (Yano et al, 2013) to ascertain sex determination in combination with phenotypic measurements retrieved from the LITS S. salar River Nivelle database. The 16 loci were amplified in a single highly multiplexed PCR using universal primers for fluorescent labelling (Blacket et al, 2012) to reduce genotyping time and cost .…”

Changes in the genetic structure of Atlantic salmon populations over four decades reveal substantial impacts of stocking and potential resiliency

“…Details on markers and PCR conditions are given in Nikolic et al (2009b). Finally, some samples from French populations (n = 395, 28% of total) were analyzed at the SSAD486 locus in order to document if brown trout or hybrids between S. salar and S. trutta were misidentified as salmon (Perrier et al 2011a). Misidentified fish were discarded from subsequent analyses.…”

“…Although several populations have been found to be moderately to highly admixed following stocking, no admixture was detected in present day samples from several French populations stocked during 1960s–1980s (Perrier et al. ,b). Therefore, samples collected before and during nonnative stocking operations are needed to thoroughly investigate the potential short‐term impacts of stocking on the neutral genetic structure of populations.…”

Molecular identification of the hybrid between the catfish species Pseudoplatystoma corruscans and Pseudoplatystoma reticulatum using a set of eight microsatellite markers

“…Low fitness for mixed stocks or displacement of natural populations is of great concern (Allendorf et al, 2004). Tools for the identification of hybrid has been the objective of several studies (Schwartz & Beheregaray, 2008;Hashimoto et al, 2010;Perrier et al, 2011). These tools are useful for monitoring hybridizations and in restocking programmes (Metcalf et al, 2007).…”