Aquaculture 544 (2021) 737043

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Aquaculture
journal homepage: www.elsevier.com/locate/aquaculture

Genetic diversity of domestic brown trout stocks in Europe

Patrick Berrebi a, *, Ákos Horvath b, Andrea Splendiani c, Stefan Palm d, Rafał Bernaś e
a
Genome - Recherche & Diagnostic, 697 avenue de Lunel, 34400 Saint-Just, France
b
Hungarian University of Agriculture and Life Sciences, Institute of Aquaculture and Environmental Safety, H-2100 Gödöllő, Páter K. u. 1., Hungary
c
Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
d
Swedish University of Agricultural Sciences, Department of Aquatic Resources, Institute of Freshwater Research, Stångholmsvägen 2, SE-178 93 Drottningholm, Sweden
e
Inland Fisheries Institute in Olsztyn, Department of Migratory Fishes, Rutki, 83-330 Żukowo, Poland

A R T I C L E I N F O A B S T R A C T

Statement of relevance: Genetic composition of Brown trout (Salmo trutta) is composed of numerous geographical forms in the wild and a multitude of stocks
hatchery strains all over Europe. reared in hatcheries. Practices impacting this species are domestication and fish farming. Thousands of hatch­
eries are producing domestic trout which are frequently released in the wild without real knowledge of the origin
Keywords: and genetic composition of the strains and of the receiving populations. The present study contains an analysis of
Brown trout (Salmo trutta)
the genetic structure (using twelve microsatellites) of 26 hatchery strains from Europe (Sweden, Poland, Czech
Hatchery stocks
Republic, Slovakia, Hungary, France, Italy and Spain) and one from North America (Minnesota). Several new
Microsatellites
Domestic strains observations improved our knowledge on this domestic part of S. trutta. First, a cross-border commercial strain of
Conservation the North Atlantic lineage occupies most of European hatcheries and the American one, as a probable conse­
quence of intensive exchanges of broodstock materials over time. In addition to the common Europe-wide
commercial Atlantic strain, local strains stemming from domesticated regional wild fish also occur. Second,
the level of genetic polymorphism of most hatchery strains is high to very high, likely reflecting genetic
admixture counteracting expected losses of diversity through random genetic drift and domestication. This study
emphasizes the value of identifying the genetic composition of hatchery stocks used for releases. It further
stresses the need for caution when stocking a common stock across the whole geographical range of a species,
with risks for reducing the intraspecific genetic diversity and local adaptation.

1. Introduction
Brown trout (Salmo trutta L.) is one of the most commonly manipu­
lated fish in the world, together with other salmonids as well as cichlid,
silurid and cyprinid species. In Europe, manipulation consists mainly of
domestication and production of eggs, fry, sub-adults and adults.
Stocking practices to enhance natural populations by release of
hatchery-produced trout have been common in Europe for over a cen­
tury (Hansen and Loeschcke 1994). The main purpose of stocking with
hatchery-reared brown trout is to support angling and, in case of
anadromous forms, coastal fisheries. Started in the 18th century, arti­
ficial production has exploded since the 1950s (Naish et al. 2008; ICES
2019).
The natural range of brown trout covers Europe, Western Asia and
North Africa. However, the real present range of this species is world­
wide because of active introduction to all continents, mainly in the
beginning (Elliott, 1989) but also in the middle (Berrebi et al. 2020) of
the last century. According to the D-loop marker of the mitochondrial
DNA, five main geographic lineages exist: Atlantic (AT), Mediterranean
(ME), Adriatic (AD), marble trout (MA, north of Adriatic Sea) and
Danube (DA) (Bernatchez et al. 1992). Several secondary lineages,
phylogenetically at the base of the main ones, have also been described,
e.g. Duero (DU), Tigris (TI) and North Africa (NA) (Suarez et al. 2001;
Bardakci et al. 2006; Tougard et al. 2018, respectively).
The taxonomic organization of brown trout has not reached a general
consensus. Among taxonomy-oriented ichthyologists, focusing mainly
on morphology, many species have been described; Kottelat and Freyhof
(2007) reviewed the published nomenclature and reached a total
number of 28 nominal species. This number has been augmented by
more than fifteen additional species during the last 15 years (Delling and
Doadrio 2005; Turan et al. 2009, 2010, 2011, 2012, 2014a, 2014b;
Delling 2010; Doadrio et al. 2015). Among more molecular oriented
scientists, this part of the Salmo genus diversity is most often simply
referred to as brown trout, Salmo trutta or the “brown trout complex”

* Corresponding author.
E-mail address: patrick.berrebi@laposte.net (P. Berrebi).

https://doi.org/10.1016/j.aquaculture.2021.737043
Received 10 November 2020; Received in revised form 4 June 2021; Accepted 10 June 2021
Available online 17 June 2021
0044-8486/© 2021 Elsevier B.V. All rights reserved.
P. Berrebi et al.
(Sanz 2018).
At the same time as numerous studies on the genetic diversity in wild
European brown trout and other salmonids have been carried out, in
step with the rapid development in molecular methodology (e.g.
Antunes et al. 1999; Sanz 2018), natural populations are constantly
being admixed with domestic strains, resulting in progressive genetic
homogenization (i.e. reduced differentiation between populations, often
paralleled by increased diversity at the local level). As an example, based
on genotyping of 19 microsatellite loci in adult lake trout (Salvelinus
namaycush), a halving of genetic differentiation and an increase in ge­
netic diversity was observed among stocked populations compared to in
unstocked ones (Valiquette et al. 2014). Examples of mixed genetic
lineages after stocking can also be found for brown trout in almost all
European countries (e.g. Largiadèr and Scholl 1995; Apostolidis et al.
1996; Lerceteau-Köhler et al. 2013; Almodóvar et al., 2006; Fruciano
et al. 2014; Berrebi et al. 2019; Bernaś and Wąs-Barcz 2020). Clear
conflicts of interests often exist between groups of anglers and ichthy­
ologists advocating large-scaled releases of farm-raised trout to support
fisheries on one side, and nature conservationists (including other an­
glers and most evolutionary biologists) trying to preserve local native
trout diversity on the other side.
While intra-specific diversity and genetic structure in wild brown
trout often follows a logic related to hydrology, geography and post­
glacial recolonization, the genetic structure of domestic strains is un­
predictable, as it is entirely driven by human actions such as strain
creations, long-distance translocations and strain admixtures. Therefore,
knowledge about the diversity of domestic strains across Europe is
crucial to understand effects of stocking: the more similar captive stocks
are to each other and distinct from local wild populations, the greater
risks are associated with stocking and supplementation as these may
result in an overall reduction in genetic diversity (Valiquette et al. 2014;
Bohling et al. 2016).
On the basis of molecular information, Bohling et al. (2016) pro­
posed a classification for French hatcheries which can be easily extended
to stocks in other parts of Europe: ComATL refers to genetically similar,
internationally-distributed, Atlantic trout strains (the only one category
of strain dispatched everywhere in France), whereas LocATL refers to
strains derived from local rivers within the Atlantic watershed. Simi­
larly, LocMED denotes stocks derived from local rivers within the
Mediterranean watershed. Finally, the MIX category refers to assem­
blages stemming from mixing between ComATL and local-based
(Atlantic or Mediterranean) strains.
The production of hatchery fish is typically associated with various
constraints, resulting in losses of genetic diversity and low effective
population sizes (e.g. Wąs and Bernaś 2016), founder effects (e.g. Skaala
et al. 2004) and random genetic drift (e.g. Klütsch et al. 2019).
Furthermore, unnatural selection pressures in hatcheries, differing
markedly from those in nature, result in domestication affecting multi­
ple traits like warm water adaptation, growth rate and stress adaptation
(e.g. Gjedrem 2000). In France, for example, experimental within-group
selection to improve growth provided significant improvement in body
weight in captive-reared brown trout (Chevassus et al. 1992, 2004) and
an unknown number of farms today rear stocks derived from this
experimentally selected population. Additionally, many hatcheries are
working with closed reproductive cycles using only their own “gene
pool” without a proper supplement of fish from the wild. Consequently,
genetic origin, levels of introgression and inbreeding of stocks varies,
and the success and risk associated with release of hatchery fish in
natural environments is highly unpredictable (e.g. Aparicio et al. 2005;
Berrebi et al. 2000; Delling et al. 2000).
The main objective of the present work is to assess the genetic
structure and levels of diversity within and among brown trout from
hatcheries distributed around Europe, from central Sweden to western
Spain, with a particular focus on Eastern European countries. So far, few
genetic studies have been devoted to hatchery brown trout strains (but
see, e.g., Bohling et al. 2016), and a broader survey is necessary. A better
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Aquaculture 544 (2021) 737043
understanding of genetic structure across European brown trout hatch­
ery strains can provide a better understanding of effects from decades of
traditional domestic management. Such knowledge also allows infer­
ence on the history of used hatchery strains, biodiversity protection,
population management on particular river basins and monitoring of
stocking activities. A description of European domestic stocks may
further be of value for research on the evolution of introduced trout
outside Europe, especially in order to detect the geographic origin of
historic introductions (Dieterman et al. 2012; Hoxmeier and Dieterman
2013; French et al. 2016; Berrebi et al. 2020).
2. Material and methods
2.1. Sampling
The present analysis includes 779 trout sampled from 26 European
hatcheries (see supplementary document), with a concentration on its
eastern part. Northern and western samples have been added in order to
develop a comparative perspective, together with a North American one
(stemming from 19th century introductions, when acclimatization so­
cieties encouraged the introduction of non-native species at the world
scale with the hope of their adaptation).
Tissue samples (fin-clips in ethanol) were collected between years
2000 and 2017, and sent to Montpellier (France) where the molecular
analyses were done (sub-contracted by Labofarm, private company at
Loudéac, France). Eleven collectors assured sampling in 9 countries.
Samples and collectors are described in Table 1, whereas geographic
positions are shown in Fig. 1.
2.2. Molecular techniques
Fin clips were cleared of alcohol and a small piece of fin was used for
DNA extraction, following the improved Chelex extraction protocol of
Estoup et al. (1996). A set of twelve nuclear microsatellite loci were
selected for analysis (Mst543, Mst85, Omm1105, Omy21Dias, Oneμ9,
Sfo1, Ssa197, SsoSL311, SsoSL438, SsoSL417, Str591 and StrBS131) ac­
cording to high levels polymorphism observed in previous studies of
brown trout. The characteristics of the markers are given in Table 2. The
twelve loci were amplified within three multiplex PCR reactions
(Table 2). PCR amplifications were carried out using the Qiagen multi­
plex PCR kit in a 10 μL volume containing 3 μL of genomic DNA diluted
at 10 ng/μL, 5 μL of Qiagen PCR Master Mix, 1 μL of Qiagen Q-solution,
1 μL of primer mix of variable concentration (Table 2) with forward
primers labelled at 5′ end using different fluorescent dyes (FAM, HEX, or
NED). Amplifications were conducted using a GeneAmp PCR System
2700 thermal cycler (Applied Biosystems), according to the supplier's
instructions (Qiagen multiplex PCR kit): initial denaturation step at
95 ◦ C for 15 min; followed by 35 cycles of denaturation at 94 ◦ C (30 s),
annealing (59 ◦ C, 90 s) and extension (72 ◦ C, 59 s); with a final extension
step at 59 ◦ C during 30 min. Amplified PCR fragments were then diluted
and separated on a capillary ABIPRISM 3130xl sequencer (Applied
Biosystems) with the use of GeneScan500Rox dye as standards size.
Fragment lengths were assessed using the GENEMAPPER v4.1 software
system (Life Technologies TM).
2.3. Population parameters and equilibriums
Levels of genetic diversity were estimated using the GENETIX software
4.05.2 program (Belkhir et al. 2004) for the following four basic pa­
rameters: Ho (observed heterozygosity based on the relative proportions
of homozygote and heterozygote genotypes); He (expected heterozy­
gosity in a theoretical population in Hardy-Weinberg-Equilibrium
(HWE)); Hnb (unbiased heterozygosity compensating for sample size
disparity according to Nei 1978); A (mean number of alleles per locus).
Additionally, estimates of allelic richness (which allows comparison
of allele numbers without the bias associated with different sample
P. Berrebi et al. Aquaculture 544 (2021) 737043

Table 1
Listing and characteristics of the 26 samples analyzed, totalizing 779 trouts. See Fig. 1 for map. Expected lineages are the types of strain deduced from local infor­
mation, generally without genetic analysis (see supplementary document).
N◦ Map Hatchery name Expected lineage Year COUNTRY N Collector

St. 01 Dalälven (VBF river strain) Local Atlantic 2002 Sweden 18 Stefan Palm
St. 02 Dalälven (HBF river strain) Local Atlantic 2003 Sweden 16 Stefan Palm
St. 03 Gullspang (Lake Vänern strain) Local Atlantic 2010 Sweden 33 Stefan Palm
St. 04 Bartush Local Atlantic 2017 Poland 23 Rafał Bernaś
St. 05 Rutki Local Atlantic 2016 Poland 40 Rafał Bernaś
St. 06 Dabie Domestic Atlantic 2017 Poland 29 Rafał Bernaś
St. 07 Aquamar Local Atlantic 2016 Poland 30 Rafał Bernaś
St. 08 Czarci Jar Local Atlantic 2017 Poland 24 Rafał Bernaś
St. 09 Folutsz Local Atlantic 2017 Poland 23 Rafał Bernaś
St. 10 Turnov (Austrian strain) Unknown 2009 Czech Rep. 26 Jan Kohout (1)
St. 11 Turnov (Italian strain) Unknown 2009 Czech Rep. 28 Jan Kohout (1)
St. 12 Borová Lada Unknown 2007 Czech Rep. 28 Jan Kohout (1)
St. 13 Východná Unknown 2007 Slovakia 29 Jan Kohout (1)
St. 14 Slovryb Unknown 2017 Slovakia 24 Rafał Bernaś
St. 15 Lillafüred domestic Atlantic 2015 Hungary 30 Akos Horvath
St. 16 Cantiano Domestic Atlantic 2006 Italy 43 Vincenzo Caputo (2)
St. 17 Visso Domestic Atlantic 2000 Italy 40 Vincenzo Caputo (2)
St. 18 Roquebillière Local Mediterranean 2008 France 29 Genesalm (3)
St. 19 Murgat Domestic Atlantic 2008 France 30 Genesalm (3)
St. 20 Brantôme (Dronne strain) Local Atlantic 2007 France 56 Genesalm (3)
St. 21 Babeau (Gravezon strain) Local Mediterranean 2014 France 40 Eric Ravel (4)
St. 22 Soueich Domestic Atlantic 2011 France 29 François Dauba (5)
St. 23 Cauterets Domestic Atlantic 2014 France 32 Eric Ravel (4)
St. 24 Baga Unknown 2014 Spain 25 Jose-Luis García-Marín (6)
St. 25 O Veral-Lugo Unknown 2004 Spain 27 Carmen Bouza (7)
St. 26 Lanesboro Domestic Atlantic 2016 USA 27 Doug Dieterman (8)

Collectors: (1) Institute of Zoology, Bratislava, Slovakia; (2) Università Politecnica delle Marche, Ancona, Italy; (3) French national project (2009–2013) for brown
trout genetic structure, Université Montpellier II, Montpellier, France; (4) Fédération de pêche de l'Hérault, Octon, France; (5) INTP-ENSAT, Castanet-Tolosan, France;
(6) Universidad de Girona, Girona, Spain; (7) Universidad de Santiago de Compostela, Lugo, Spain; (8) Minnesota Department of Natural Resources, Lake City,
Minnesota, USA.

sizes) and private allelic richness (alleles limited in a single population)
were calculated using the rarefaction method in the HP-RARE 1.1. soft­
ware (Kalinowski 2005). The frequency of private alleles provide an
indication of the extent of gene flow between populations (Slatkin 1985;
Barton and Slatkin 1986) and is a useful criterion in genetic diversity
preservation, by allowing evaluation of the uniqueness of each popula­
tion in terms of allele composition (Foulley and Ollivier, 2006).
Deviations from panmixia were estimated through the FIS parameter,
using the estimator f of Weir and Cockerham (1984). Panmixia (FIS = 0)
characterizes a population in which reproduction between all adult
members is at random. Deviations in terms of a deficiency (FIS > 0) or
excess (FIS < 0) of heterozygotes may be observed in numerous bio­
logical cases, the most frequent being related to sampling of population
mixtures, migration, or a low population size (few parents, few families).
Deviations of FIS from zero were tested statistically using 5000 permu­
tations of alleles within each locus, using the GENETIX software. Likewise,
genetic differentiation between samples was quantified using the FST
parameter through the estimator Ɵ (Weir and Cockerham 1984), using
5000 permutations of individuals among samples to assess the signifi­
cance of departures of Ɵ from zero.
Markov Chain Monte Carlo simulations to partition individuals into K
clusters (here set between 1 and 10). Assignment criteria are the mini­
mization of deviations from HWE and linkage disequilibria (LD) within
clusters. Different run lengths were used at each step (from 50,000 to
100,000 burn-in and 100,000 to 200,000 total lengths, repeated 5 to 10
times for each K) depending on convergence (proportion of identical
structure among the 5 repeated runs at each step). The admixture
ancestry model and correlated allele frequency options were chosen.
Sampling location was not used as prior information. The ΔK method
(Evanno et al. 2005) was applied as a decision help, as implemented in
STRUCTURE HARVESTER (Earl and von Holdt 2012). In order to detect
differentiated subgroups of hatchery populations, a ‘hierarchical STRUC­
TURE analysis’ (cf. Vähä et al. 2007; Marić et al. 2017; Berrebi et al. 2019)
was performed. After the first analysis and determination of the most
probable K according to the ΔK method of Evanno et al. (2005), which
define the first hierarchical level, each sub-group of the first level was
analyzed separately, allowing a grouping of individuals without elimi­
nating mixed individuals. We repeated the same procedure until no
more substructure was observed (indicated by red crosses in Fig. 5). This
hierarchical approach was preferred because a global run tended to
detect only major groups.

2.4. Research of hatchery genetic clustering

In order to depict the overall genetic structure of the involved
hatchery samples in a single diagram, a Factorial Correspondence
Analysis (FCA, Benzécri 1973) was first performed, as implemented
within the GENETIX program. This method is well adapted to genotypic
data (simplified mathematical details are given in She et al. 1987). Each
trout is positioned in a hyperspace according to its 24 alleles. Clusters
(clouds) detected on the diagram correspond to homogeneous groups
gathering individuals with similar multilocus genotypes, regardless of
their geographical origin.
An alternate clustering method is the assignment analysis imple­
mented in the program STRUCTURE 2.3.2 (Pritchard et al. 2000). It runs
2.5. Parentage investigation
In order to describe each strain in terms of family structure and
abundance of genitors, parentage structure was explored using the
COLONY software (Jones and Wang 2010). The main objective was full-sib
and half-sib dyads detection, together with the number of families
within each analyzed sample. A genotyping error rate of 0.001 was used,
following Palm et al. (2008). Sibs identified were not removed because,
with the exception of a few samples, there was no excess of sibs.
Effective population size was estimated, using the sibship assignment
method implemented in COLONY (Wang 2009). This method makes
several assumptions that could be violated in reality. The most critical

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P. Berrebi et al. Aquaculture 544 (2021) 737043

Fig. 1. Geographic position of the 25 European samples of domestic stocks of brown trout (Salmo trutta) (the 26th one, from Minnesota, USA, is not shown). The
numbers refer to the first column, of Table 1.

Nb/Ne ratios if necessary (Waples et al. 2013). However, from the point
Table 2
of view of breeding stocks, Nb values seem more informative because the
Twelve microsatellite loci used to characterize domestic stocks of brown trout
number of fish in stocks may change over time depending on production
(Salmo trutta) in Europe and North America.
needs.
Locus Multiplex Primers concentration Reference

Mst543 C 0.15 μM Presa et al. 1994

Mst85 B 0.15 μM Presa and Guyomard 1996 2.6. Phylogenetic analysis
Omm1105 A 0.8 μM Rexroad et al. 2002
Omy21Dias B 0.1 μM Holm and Bendixen 2000
As a complement to the clustering analyses described above, a
Oneμ9 C 0.2 μM Scribner et al. 1996
Sfo1 A 0.1 μM Angers et al. 1995 neighbor-joining (NJ) tree was constructed based on pairwise Nei's
Ssa197 A 0.2 μM O'Reilly et al. 1996 standard genetic distance without sample size correction (DST, Nei
SsoSL311 C 0.6 μM Slettan et al. 1995 1972) with 10,000 bootstrap replications, using the POPTREE2 software
SsoSL417 A 0.1 μM Slettan et al. 1995
(Takezaki et al. 2010).
SsoSL438 C 0.1 μM Slettan et al. 1996
Str591 B 0.2 μM Presa and Guyomard 1996
Because most samples are of Atlantic lineage, the two Mediterranean
StrBS131 C 0.4 μM Charles et al. 2005 ones (St. 18 and 21) were treated as outgroups. The objective of this kind
of phylogeny is to link apparently independent hatchery stocks implic­
itly suggesting a history of exchanges, which has not been recorded. This
assumption is that the sample has been taken at random (with respect to information allows understanding how hatchery exchanges can shape
kinship) from a single cohort of the population. If there are several co­ the constitution of trout strains.
horts in the sample, it is possible that some individuals are actually
parents to other sampled individuals. As a consequence, some parental-
3. Results
offsprings relationships may be mistakenly inferred to be full-sibs (FS),
increasing the estimate of FS frequency and decreasing the estimate of
3.1. Population parameters
effective size. In the present study, this potential bias was neglected
since most samples contained single cohorts. Thus, the effective size
The results obtained on diversity, panmixia (Table 3) and differen­
estimates produced mostly relate to the effective number of annual
tiation (Table 4) are based on predefined samples from different
breeders (Nb), rather than to the effective population size per generation
hatchery strains. About 70% of the hatchery stocks were in HWE. Few
(Ne) (cf. Waples et al. 2013). Knowing that the values of Nb and Ne are
hatchery strains showed low polymorphism (St. 5, 6 and 21), most
correlated (Ferchaud et al. 2016), values of Ne can be estimated from
exhibited high polymorphism (yellow and orange cells in Table 3) and

4
P. Berrebi et al.
Table 3
Different parameters of population genetic diversity, highlighted by heat colors: grey, white, yellow, orange and red cells indicate increasing levels of polymorphism.
Details on the meaning of each parameter are given in the text (Material and methods). (For interpretation of the references to colour in this figure legend, the reader
is referred to the web version of this article.)
one, the Východná sample, was exceptionally polymorphic compared to
French hatchery strains considered as highly polymorphic (Bohling et al.
2016). Allelic richness (30 individuals) followed more or less the level of
heterozygosity, being greatest in the St. 13 and St. 22 stocks (8.22 and
8.03). High allelic richness values were also obtained for stocks St. 14
and St. 17. By contrast, the lowest values were observed in the popu­
lation St. 21 and St. 11 (Table 4). Private alleles are described in Table 3;
their richness was significantly higher in stocks St. 18, St. 20 and St. 25
than in the remaining sampling. No private alleles were observed in
stocks St. 4 and St. 6.
3.2. Clustering analyses
The FCA diagrams depicted in Figs. 2 to 4 clearly indicated a com­
mon origin of most European hatchery stocks (i.e. the “black ellipse” of
Figs. 2 to 4), constituting a homogenous group including all countries,
also USA (Fig. 5). Outside this common group, several local strains
emerged of presumed Mediterranean and Atlantic origin (Figs. 2 and 3).
The hierarchical STRUCTURE analysis presented in Fig. 5 required seven
main steps, based on different subsets of the material. Without neces­
sarily describing all these steps in detail (see Fig. 5), some important
results can be highlighted. The first step separated Mediterranean strains
from Atlantic ones, with the exception of the Brantôme hatchery (St. 20)
and the O-Veral hatchery (St. 25), breeding distinct local southern
Atlantic populations that clustered with Mediterranean strains. The
second step clustered Swedish hatcheries (St. 1 to 3) with Italian and
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Aquaculture 544 (2021) 737043
French ones, the former leaving the latter ones at the next step. This
second step also clustered east European hatchery strains (Poland, Czech
Republic, Slovakia and Hungary) with the North America (Minnesota)
captive population (St. 26).
3.3. Phylogenetic relationships among strains
A bootstrapped NJ phylogenetic tree including the examined 26
brown trout stocks revealed that they were divided in two main sub­
groups of uneven size (Fig. 6). The first subgroup comprised most
samples, probably of Atlantic origin, subdivided into at least three
smaller clusters: Swedish, Eastern European and French/Italian stocks.
The second subgroup represented two Mediterranean stocks (St. 18, St.
21) clearly separated with high bootstrap support from the presumed
Atlantic populations, and with two Southern European stocks (St. 20,
France and St. 25, Spain) located in-between.
3.4. Familial structure and effective population size
In Table 5 are indicated, for each strain sample, the number of
detected fullsib families and the proportion (%) of unrelated vs fullsib
and halfsib dyads. Estimates of current effective population sizes are also
shown. Proportions of unrelated individuals within samples were high,
from 68 to 97.4% (mean 93.5%), whereas full-sib proportions varied
from 0 to 15.4% (1%) and half-sib proportions from 2.6 to 16.6 (5.5%).
Finally, the effective size estimates were very heterogeneous, ranging
P. Berrebi et al. Aquaculture 544 (2021) 737043

Table 4
Heat-map of pairwise FST comparing each fish farm. All estimates were significantly different from zero at the p < 0.05 level (after Bonferroni correction), with the
only exception of the two Swedish strains from the same river (samples 1 and 2, green cell). Mediterranean strains (St.18 and 21) are especially differentiated from
the rest. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)
N° Map Hatchery name 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
St. 01 Dalälven (VBF river strain) 0 -0,01 0,12 0,15 0,16 0,15 0,08 0,19 0,10 0,14 0,20 0,15 0,13 0,09 0,09 0,07 0,06 0,23 0,13 0,14 0,40 0,07 0,09 0,19 0,18 0,14
St. 02 Dalälven (HBF river strain) 0 0,10 0,13 0,14 0,14 0,07 0,17 0,08 0,12 0,19 0,12 0,12 0,08 0,08 0,06 0,04 0,20 0,11 0,13 0,38 0,06 0,07 0,17 0,15 0,11
St. 03 Gullspang (Lake Vänern strain) 0 0,19 0,18 0,18 0,14 0,23 0,15 0,18 0,25 0,17 0,18 0,16 0,13 0,13 0,11 0,23 0,15 0,17 0,43 0,11 0,15 0,24 0,21 0,16
St. 04 Bartush 0 0,15 0,13 0,10 0,05 0,11 0,14 0,18 0,10 0,09 0,09 0,10 0,13 0,12 0,21 0,17 0,18 0,38 0,11 0,12 0,13 0,21 0,14
St. 05 Rutki 0 0,03 0,09 0,17 0,09 0,16 0,24 0,14 0,18 0,09 0,13 0,14 0,12 0,28 0,16 0,20 0,45 0,15 0,14 0,23 0,24 0,13
St. 06 Dabie 0 0,10 0,16 0,08 0,14 0,23 0,14 0,17 0,08 0,10 0,13 0,11 0,27 0,14 0,20 0,44 0,14 0,14 0,21 0,23 0,12
St. 07 Aquamar 0 0,12 0,04 0,09 0,17 0,11 0,10 0,05 0,06 0,06 0,06 0,21 0,12 0,12 0,37 0,07 0,06 0,14 0,14 0,09
St. 08 Czarci Jar 0 0,13 0,18 0,21 0,13 0,12 0,13 0,14 0,15 0,16 0,21 0,19 0,20 0,39 0,13 0,14 0,18 0,24 0,18
St. 09 Folutsz 0 0,08 0,18 0,11 0,10 0,03 0,05 0,08 0,05 0,20 0,11 0,13 0,38 0,07 0,07 0,13 0,15 0,05
St. 10 Turnov (Austrian strain) 0 0,19 0,15 0,13 0,09 0,07 0,08 0,07 0,23 0,13 0,13 0,40 0,07 0,10 0,14 0,14 0,08
St. 11 Turnov (Italian strain) 0 0,14 0,14 0,17 0,16 0,16 0,15 0,26 0,19 0,21 0,40 0,17 0,18 0,19 0,25 0,20
St. 12 Borová Lada 0 0,05 0,11 0,11 0,13 0,11 0,18 0,16 0,17 0,37 0,12 0,12 0,13 0,19 0,13
St. 13 Východná 0 0,08 0,09 0,11 0,09 0,15 0,15 0,14 0,32 0,09 0,09 0,11 0,17 0,13
St. 14 Slovryb 0 0,04 0,07 0,06 0,20 0,10 0,14 0,37 0,09 0,08 0,14 0,16 0,08
St. 15 Lillafüred 0 0,07 0,06 0,20 0,10 0,12 0,38 0,06 0,08 0,13 0,14 0,07
St. 16 Cantiano 0 0,02 0,19 0,08 0,10 0,36 0,02 0,06 0,14 0,15 0,11
St. 17 Visso 0 0,19 0,07 0,09 0,34 0,01 0,04 0,12 0,13 0,08
St. 18 Roquebillière 0 0,22 0,21 0,35 0,18 0,17 0,22 0,23 0,21
St. 19 Murgat 0 0,15 0,39 0,08 0,10 0,18 0,18 0,13
St. 20 Brantôme (Dronne strain) 0 0,35 0,08 0,12 0,18 0,15 0,15
St. 21 Babeau (Gravezon strain) 0 0,34 0,34 0,38 0,38 0,40
St. 22 Soueich 0 0,04 0,12 0,13 0,10
St. 23 Cauterets 0 0,14 0,14 0,11
St. 24 Baga 0 0,20 0,15
St. 25 O Veral-Lugo 0 0,16
St. 26 Lanesboro 0

Fig. 2. Factorial Correspondence Analysis (FCA) di­

agram presenting the total material (779 brown trout
individuals sampled in 26 locations in Europe and
North America) with most samples concentrated in
the black ellipse (top right), probably representing
strains belonging to the Atlantic lineage, and three
samples outside (likely representing strains from the
Mediterranean lineage). The numbers between pa­
rentheses are those of the first column of Table 1. (For
interpretation of the references to colour in this
figure legend, the reader is referred to the web
version of this article.)

from only 4 to 74 (mean 37.7). This variation may reflect different
breeding practices (e.g. number of spawners used, proportion of males/
females, etc.). A few hatchery samples deviated from the average values:
the Turnov hatchery (Italian strain; St. 11; Czech Republic) had the
lowest effective size and proportion of unrelated genotypes (4 and 68%
respectively) and the highest full-sib and half-sib proportions (15.4 and
16.6% respectively). At the opposite, the Soueich hatchery sample (St.
22; France) had the highest effective size and unrelated proportion (74
and 97.4%) and the lowest fullsib and halfsib proportions (0 and 2.6%).
Most other samples showed intermediate values, except Babeau hatch­
ery (St. 21, France) close to the Turnov excess, and Isère (St. 19, France)
hatchery close to the Soueich one.
4. Discussion
Population genetic surveys of brown trout frequently describe
admixture between native wild populations and introduced domestic
stocks. Such induced hybridization is generally considered as a negative
consequence of stocking, reducing the original natural diversity and its
adaptive value (e.g. Hansen et al. 2000; Poteaux et al. 2000; Kohout
et al. 2012; Valiquette et al. 2014; Berrebi et al. 2017; Leitwein et al.
2018). While analyzing trout from very different natural contexts and
disparate geographic regions, most of these surveys refer to a domestic
lineage characterized by four main mtDNA haplotypes named 1, 2, 3 and
4 or Atcs1 to 4 (Cortey et al. 2004). However, a more complete genetic
description of European domestic stocks based on nuclear markers has
remained missing. By analyzing twelve microsatellites in 26 European

6
P. Berrebi et al. Aquaculture 544 (2021) 737043

Fig. 3. Factorial Correspondence Analysis (FCA) diagram of 683 brown trout individuals sampled in 23 locations in Europe and North America following removal of
three strains of presumed Mediterranean lineage origin (cf. Fig. 2); the “black ellipse” is still dominant, but four samples (11, 12 and 13, and especially 20) are clearly
different, while included in the black ellipse of the Fig. 2. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version
of this article.)

Fig. 4. Factorial Correspondence Analysis (FCA) diagram of 542 brown trout individuals sampled in 19 locations in Europe and North America following removal of
three strains of presumed Mediterranean lineage origin as well as 3 + 4 deviating samples identified in Figs. 2 and 3; the “black ellipse” has been further subdivided,
with most samples in the middle and few of them at the border. (For interpretation of the references to colour in this figure legend, the reader is referred to the web
version of this article.)

(with one American) domestic stocks, the present survey confirmed the
domination of an “international strain” of north Atlantic origin, and has
revealed high diversity within hatcheries.
To understand the history of hatchery establishments and the ex­
change of genes between hatcheries, we used three main statistical
methods for clustering our samples (i.e. multidimensional FCA, Bayesian
assignment and a phylogenetic NJ-tree). Common main structures
among these analyses were (1) a clear subdivision between Atlantic and
Mediterranean lineage strains, and (2) further subdivision of the Atlantic
lineage into three groups including the well-separated Swedish samples,
hatcheries in eastern Europe (Poland, Slovakia, Czech Republic), less
strongly separated from those in the west (France and Italy).
However, although results generally agreed between methods, some
discrepancies also appeared. Most of these differences concerned special
cases (e.g. the Atlantic St. 20 pooled with Mediterranean strains ac­
cording to the Bayesian assignment analysis). More fundamental dif­
ferences emerged between multidimensional analysis and the other two
methods. In Figs. 2 to 4, the mass of Atlantic samples are not structured
and, in particular, an east-west structure does not appear. Such differ­
ences can be explained by a less discriminating power of the FCA (east-
west structure) or by strongly different methods of discrimination
(search for subgroups approaching populations in equilibrium HW and
LD for the Bayesian assignment vs. genetic distances calculated pairwise
between samples and used for the NJ tree).
One main result is that all-around Europe, in countries with different
traditions and histories (north-south for climate, east-west for the recent
political regimes), genetically similar commercial strains are bred (i.e.
the black ellipse in Figs. 2 to 4, the main central composite cluster in

7
P. Berrebi et al.
Fig. 5. Representation of the sequential assignment analysis of domestic stocks
of brown trout (Salmo trutta) using STRUCTURE software. The sequential
analysis on separate parts of the total material was continued until no more
subdivision could be found (indicated by a red cross). The first column repre­
sents the first partition (ΔK method) for K = 2: mainly Atlantic and Mediter­
ranean lineages. The second column shows results for the partition of the
Atlantic lineage (for K = 2) into two major groups (mainly west and north vs.
east Europe) and the independent partition of the Mediterranean lineage into
four separate population clusters (for K = 4). The colors within each column
have no sense and were chosen at random. The sample numbers are those of the
first column of Table 1. (For interpretation of the references to colour in this
figure legend, the reader is referred to the web version of this article.)
Fig. 6), suggesting a common origin. Most likely this dominating cluster
corresponds to what Bohling et al. (2016) have referred to as ComATL
(Common Atlantic strains). One possible reason for this widespread
genetic similarity is inter-hatchery trade, mainly of domestic commer­
cial Atlantic strains whose success is primarily due to high hatching rates
(close to 90–100%), even using standard facilities (Chevassus et al.
1992, 2004; Czerniawski et al. 2010).
The scale of these exchanges seems to be Europe-wide. For example,
the phylogenetic position of the Spanish Baga strain (St. 24) which
clustered with samples from the Czech Republic (Fig. 6) is symptomatic.
Another demonstration of exchanges is the Turnov hatchery strains (in
Czech Republic) originating from Italy and Austria. Furthermore, a ge­
netic similitude was observed among French and Italian stocks (Fig. 5
and partly Fig. 6). This closeness has been already suggested by Caputo
et al. (2004) who detected in Italian domestic strains several mtDNA
haplotypes identical to Danish haplotypes described by Hansen and
Loeschcke (1996). We concluded that this observation was in accor­
dance with the Danish (or Scandinavian) origin of domestic Atlantic
8
Aquaculture 544 (2021) 737043
trout as previously proposed by Tortonese (1970) and Giuffra et al.
(1996).
On the other hand, there are also signs of differentiation, even among
the larger group of samples with presumed common Atlantic origin.
Pairwise FST estimates are highly significant in all cases (Table 4), which
indicates genetic drift coupled with no recent exchanges of genetic
materials among the hatcheries. Local stocks may have been “enriched”
by local wild fish or by exchanges between hatcheries. For example, in
Poland, most hatcheries breed their own stock, without or with only
occasional inclusion of wild fish. However, it has been observed that
some river managers stock their own waters with imported fish, and
after a few seasons they may capture adult specimens for broodstock
renovation. In Poland this process occurs on a small scale (Bernaś and
Wąs-Barcz 2020) and a clear genetic separation between Polish northern
and southern strains has been detected (Figs. 5 and 6). The situation in
Poland illustrates how some mixing of imported domestic strains with
local wild populations may proceed, and how hatchery stocks from
different geographic areas may still be genetically similar. Another
example is given by Kohout et al. (2012) showing that the Východná and
Slovryb hatcheries (here St. 13 and 14), settled in the Danube basin,
were composed of only 1/4 to 1/3 of Danubian lineage, admixed with
the Atlantic one. The exchange of breeding material between Czech,
Slovak and Polish breeding centers has and had a long tradition, strongly
related to the history of this region. Geographically, this area is drained
by the upper catchment areas of the Elbe, Vistula and Danube rivers.
Therefore, the presence of mixed lines in this area is largely the result of
human activity (Kohout et al. 2012; Bernaś and Wąs-Barcz 2020).
The second main result concerns levels of polymorphism within
strains. High genetic variability at the intra-population level and low
differentiation at the inter-population level are quite common within
domestic trout stocks (Bohling et al. 2016). While it is frequently
claimed that with time, due to management leading to consanguinity (i.
e. low effective population sizes at hatcheries), captive populations
should lose genetic diversity (Li et al. 2004), the present hatchery strains
show generally high levels of genetic variability. The level of poly­
morphism is similar to that of French hatcheries investigated earlier,
considered to be highly polymorphic in comparison with wild pop­
ulations and displaying high values at all measured parameters (0.67
\Hnb\0.78 and 5.7\A\8.3, Berrebi et al. 2000; Bohling et al. 2016). In
the present survey, 85% of the strains showed high (0.61 < Hnb < 0.70)
to very high (0.71 < Hnb < 0.81) heterozygosity (Table 3). This high
level of genetic diversity is potentially driven by past admixture (gene
flow) mediated by imports of fish from other hatcheries (Chevassus et al.
1992). As discussed above, fish exchanges between trout farms is a
frequent practice in Europe (van Houdt et al. 2005). Therefore, this
practice has most likely created a high genetic variation in the main
domestic strain as a whole, and at the same time reduced regional and
local differentiation among local hatchery derivatives of this common
strain.
Low estimates of effective size (<30) were observed in eight strains,
indicating that the level of inbreeding is probably high. The associated
parentage analysis also confirms this interpretation, since a clear family
structure could be observed in more than half the strains (Table 5).
The third main result showed that, despite an apparent common
nature of domestic trout all around Europe, what may be called “local
strains” (i.e. domesticated from local wild fish) are not rare. In Sweden,
the three samples included (St. 1 to 3) are all from hatchery strains
known to be recently derived from local natural populations (Palm et al.
2003, 2012). In France, the St. 18 (Doubs River flowing to the Medi­
terranean Rhône River), St. 21 (from Gravezon small river flowing to
Mediterranean Orb River, near Montpellier, strain created with only 15
genitors 15 years ago) and St. 20 (Dronne Atlantic River flowing to the
Dordogne-Garonne) are also local strains. In Spain, the O Veral strain
(St. 25) is clearly of local origin, according to the present results, so of
Atlantic lineage. All of these strains were found to have high numbers of
private alleles.
P. Berrebi et al.
Fig. 6. Bootstrapped neighbor joining (NJ) construction revealing two uneven independent subgroups. The first one, composed of several imbricated subgroups,
concentrates 24 samples belonging to the Atlantic lineage. The second includes only two Mediterranean stocks (St. 18, St. 21, in purple) clearly separated with high
bootstrap support from Atlantic samples. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)
Considering the results of this study, several collective recommen­
dations for local authorities managing breeding programs could be
made. In closed breeding stocks, it is essential to keep number of
effective breeders (Nb) high. This is the most important because it
prevents the effects of inbreeding and genetic drift (Tave 1999; Bentsen
and Olesen 2002). In the case of open farms, engaged in local breeding
programs, renewing the stock, they should be based on local fish, pref­
erably from the same river. This will keep the genetic distance between
breeding and wild fish at a low level. Above all, fishing users should stick
to the principle of not mixing the population. In addition, some breeding
farms also conduct a directional selection of the desired traits, e.g.
phenotypic or related to rapid growth (e.g. Sanchez et al. 2001; Mam­
brini et al. 2004). However, we must be aware of the consequences of
releasing such fish, especially given the possibility of non-directional
selection with unknown effects on the population (O'Sullivan et al.
2019).
This study highlights the need for caution before stocking. As
observed herein (Table 3) and by Valiquette et al. (2014) in their study
of lake trout, stocking may induce locally increased levels of genetic
polymorphism that is simultaneously associated with loss of inter-
population diversity and of local adaptation. The main criticism of
stocking with domestic trout is the loss of fitness in the recipient pop­
ulation (Feulner et al. 2013; Miller et al. 2004; Wollebaek et al. 2012;
Hansen et al. 2009). Artificial selection increasing survival in fish cul­
ture but not in the wild, has often been cited as the most likely expla­
nation for lower fitness. An alternative hypothesis, however, concerns
DNA methylation (epigenetic modifications). Coho salmon
9
Aquaculture 544 (2021) 737043
(Oncorhynchus kisutch) has been shown to have this type of difference
between the wild form and a genetically identical domestic line. The
differently methylated regions affect biological functions linked to the
capacity of the young stages to migrate towards the ocean (Le Luyer
et al. 2017). Epigenetic modifications induced by the captive environ­
ment are therefore a potential explanation for reductions in fitness of
stocked populations.
Another potential impact of domestic trout releases into the natural
environment relates to deleterious mutations. In a study on conse­
quences of stocking based on nearly 5000 SNPs, supplemented lake trout
populations were found to have fewer deleterious alleles than unstocked
ones, despite an overall increase in neutral genetic diversity in the
former group (Ferchaud et al. 2018). An earlier study had also revealed a
decrease in genetic integrity of the same stocked lake trout populations
as they regrouped in assignment analyzes according to their common
stocking source (Valiquette et al. 2014). These studies suggest that
elevated gene flow due to stocking may assist with the purging of
deleterious mutations in small local populations, where genetic drift
may otherwise overrule natural selection. At the same time, however, it
is important to consider the source of the stocked fish in order to pre­
serve local adaptations and genetic integrity of recipient populations.
From a biogeographic and conservation point of view, stocking
without obvious necessity can lead to a reduction in the overall genetic
diversity of brown trout on the European scale. Even when a local strain
is created with broodstock from nearby rivers, it is advisable to release
domestic trout only in the area inhabited by genetically similar pop­
ulations. Note that such locally derived stocks may still become quickly
P. Berrebi et al. Aquaculture 544 (2021) 737043

Table 5
Results from the sibship assignment method adopted by COLONY (Wang 2004) at one typing error rate (0.001). Non default COLONY job settings as follows: typing
error rate 0.001, mating system I: male and female polygamy, mating system II: with inbreeding, length of run: medium, analysis method: full-likelihood, rest of setting
as default. Fullsib and halfsib dyad are displayed both as absolute value and relative frequency (between brackets).
N◦ Map Hatchery name Fullsib families Unrelated dyads Fullsib dyads Halfsib dyads Ne (CI95 L - U)

St. 01 Dalälven (VBF river strain) 0 303 (93.5%) 0 21 (6.5%) 29 (17–61)

St. 02 Dalälven (HBF river strain) 0 246 (96.1%) 0 10 (3.9%) 48 (24–143)
St. 03 Gullspang (Lake Vänern strain) 2 1033 (94.9%) 1 (0.1%) 55 (5.1%) 37 (23–62)
St. 04 Bartush 1 495 (93.6%) 1 (0.2%) 33 (6.2%) 29 (17–55)
St. 05 Rutki 0 1501 (93.8%) 0 99 (6.2%) 32 (19–55)
St. 06 Dabie 1 764 (90.8%) 1 (0.1%) 76 (9.0%) 21 (11–39)
St. 07 Aquamar 1 862 (95.7%) 1 (0.1%) 38 (4.2%) 44 (27–83)
St. 08 Czarci Jar 0 584 (93.4%) 0 41 (6.6%) 29 (16–52)
St. 09 Folutsz 1 502 (94.9%) 1 (0.2%) 26 (4.9%) 36 (22–65)
St. 10 Turnov (Austrian strain) 1 694 (95.2%) 1 (0.1%) 34 (4.7%) 39 (22–70)
St. 11 Turnov (Italian strain) 3 496 (68.0%) 112 (15.4%) 121 (16.6%) 4 (2− 12)
St. 12 Borová Lada 0 750 (95.7%) 0 34 (4.3%) 44 (26–76)
St. 13 Východná 3 749 (95.5%) 5 (0.6%) 30 (3.8%) 38 (24–68)
St. 14 Slovryb 0 556 (96.5%) 0 20 (3.5%) 55 (33–107)
St. 15 Lillafüred 5 857 (95.2%) 7 (0.8%) 36 (4.0%) 35 (21–84)
St. 16 Cantiano 3 1734 (93.8%) 32 (1.7%) 83 (4.5%) 25 (15–44)
St. 17 Visso 0 1549 (96.8%) 0 51 (3.2%) 38 (21–79)
St. 18 Roquebillière 3 790 (93.9%) 3 (0.3%) 48 (5.7%) 30 (18–54)
St. 19 Isère 1 847 (94.1%) 1 (0.1%) 52 (5.8%) 61 (39–95)
St. 20 Brantôme (Dronne strain) 1 3021 (96.3%) 3 (0.1%) 112 (3.6%) 52 (34–79)
St. 21 Babeau (Gravezon strain) 3 1352 (84.5%) 53 (3.3%) 195 (12.2%) 10 (5–24)
St. 22 Soueich 0 819 (97.4%) 0 22 (2.6%) 74 (44–147)
St. 23 Cauterets 0 986 (96.3%) 0 38 (3.7%) 52 (33–89)
St. 24 Baga 3 579 (92.6%) 12 (1.9%) 34 (5.4%) 21 (11–42)
St. 25 O Veral-Lugo 0 702 (96.3%) 0 27 (3.7%) 50 (30–94)
St. 26 Lanesboro 0 930 (96.8%) 0 31 (3.2%) 45 (26–86)

differentiated from wild recipient populations through drift and
domestication. In general, stocking should thus be avoided if there are
not good reasons, e.g. to assist recovery of local stocks after their main
problems have been remedied. Stocking into areas with naturally
reproducing populations is generally questionable (Fernández-Cebrián
et al. 2014), due to the biological risks associated with such stocking
aimed at supporting “put and take” fisheries (with bycatches of wild
trout, genetic introgression, etc.). In Britain, where self-reproducing
salmonids population persist, only stocking with triploid female in­
dividuals is permitted, on the other hand, supportive breeding with local
strains is allowed, but rarely done (Andrew Ferguson personal
communication). Still, in the Mediterranean countries (mainly Italy or
France), stocking with local strains is often interpreted as a simple
replacement of the commercial brown Atlantic trout by the so-called
“Mediterranean trout” without worrying about the numerous diffi­
culties affecting the management of wild biodiversity (Laikre et al.
2020). There is a risk of simply substituting wild populations by
domesticated ones, without any advantage in conservation and biodi­
versity of freshwater fish.
The results obtained in this work should be developed in further
studies using new technologies and allowing for a deeper analysis of the
observed processes. Particularly promising and interesting would be the
analysis of selection signals occurring in breeding stocks and by
checking their generality. Recent studies in genomics using medium and
high-dense SNP microarray methods have shown the ability to detect
such phenomena (e.g. Gutierrez et al. 2016; Linløkken et al. 2017) and
indicate that other selection processes may take place in breeding stocks
and in wild populations (Bernaś et al. 2020). In addition to SNP
microarrays, RAD-Seq technology should be applied as a tool for rapid
and efficient generation of QTL-targeted and genome-wide marker data
(Houston et al. 2012). The high efficiency of methods based on RAD
sequencing in population differentiation may reveal further patterns of
genetic differentiation, in addition to those identified herein, between
brown trout breeding populations from different parts of the species'
range (cf. Bradbury et al. 2015; Lemopoulos et al. 2019).
In conclusion, the most important finding is that we observed a
common hatchery strain (slightly diversified due to local practices)
derived from “cosmopolitan” fish of presumed Atlantic lineage origin
(ComATL) in most investigated European countries (possibly except
Sweden, although analysis of additional samples from Northern Euro­
pean hatcheries appears necessary), and in North America where the
species has been introduced from Europe. This huge nebula of geneti­
cally similar strains, used for restocking at the continental level,
necessarily reduces the natural diversity of the species. However, we
have also observed several hatcheries breeding local strains from
restricted areas with seemingly local characteristics, capable of limiting
this loss of overall diversity if locally used for stocking.
Declaration of Competing Interest
The following authors declare no conflict of interest.
Acknowledgements
The authors are grateful to numerous colleagues who have provided
hatchery fin clips for analyses: Jan Kohout, Liběchov, Czech Republic;
Vincenzo Caputo Barucchi, Ancona, Italy; Eric Ravel, Octon, France;
Francis Dauba, Castanet-Tolosan, France; José-Luis García-Marín, Ger­
ona, Spain; Carmen Bouza, Lugo, Spain; Douglas Dieterman, Lake City,
Minnesota, USA. Sampling in Hungary was supported by the Ministry of
Innovation and Technology within the framework of the Thematic
Excellence Programme 2020, Institutional Excellence Subprogramme
(TKP2020-IKA-12). In Poland work was supported by project 2016/21/
D/NZ9/00405 of the Ministry of Science and Higher Education and
statutory topic S030/005 in the IFI Olsztyn. The authors also thank José-
Luis García-Marín (Universitat de Girona) for reviewing an earlier
version of the text.
Appendix A. Supplementary data
Supplementary data to this article can be found online at https://doi.
org/10.1016/j.aquaculture.2021.737043.

10
P. Berrebi et al. Aquaculture 544 (2021) 737043

References Dieterman, D.J., Hoxmeier, R.J.H., Staples, D.F., 2012. Factors influencing growth of
individual brown trout in three streams of the upper Midwestern United States. Ecol.
Freshw. Fish 21, 483–493.
Almódovar, A., Nicola, G.G., Elvira, B., Garcia-Marin, J.-L., 2006. Introgression
Doadrio, I., Perea, S., Yahyaoui, A., 2015. Two new species of Atlantic trout
variability among Iberian brown trout evolutionary significant units: the influence of
(Actinopterygii, Salmonidae) from Morocco. Graellsia 71, e031.
local management and environmental features. Freshw. Biol. 51, 1175–1187.
Earl, D.A., von Holdt, B.M., 2012. STRUCTURE HARVESTER: a website and program for
Angers, B., Bernatchez, L., Angers, A., Desgroseillers, L., 1995. Specific microsatellite loci
visualizing STRUCTURE output and implementing the Evanno method. Conserv.
for brook charr reveal strong population subdivision on a microgeographic scale.
Genet. Resour. 4, 359–361.
J. Fish Biol. 47, 177–185.
Elliott, J.M., 1989. Wild brown trout Salmo trutta: an important national and
Antunes, A., Apostolidis, A., Berrebi, P., Duguid, A., Ferguson, A., García-Marín, J.-L.,
international resource. Freshw. Biol. 21, 1–5.
Guyomard, R., Hansen, M.M., Hindar, K., Koljonen, M.L., Laikre, L., Largiadèr, C.,
Estoup, A., Largiader, C.R., Perrot, E., Chourrout, D., 1996. Rapid one-tube DNA
Martínez, P., Nielsen, E.E., Palm, S., Ruzzante, D., Ryman, N., Triantaphyllidis, C.,
extraction for reliable PCR detection of fish polymorphic markers and transgenes.
1999. Conservation genetic management of brown trout (Salmo trutta) in Europe.
Mol. Mar. Biol. Biotechnol. 5, 295–298.
Concerted Action on Identification, Management and Exploitation of Genetic
Evanno, G., Regnaut, S., Goudet, J., 2005. Detecting the number of clusters of individuals
Resources in the Brown Trout (Salmo trutta) (“TROUTCONCERT”; EU FAIR CT97-
using the software STRUCTURE: a simulation study. Mol. Ecol. 14, 2611–2620.
3882). Laikre, L. ed. 91 pp.
Ferchaud, A.-L., Perrier, C., April, J., Hernandez, C., Dionne, M., Bernatchez, L., 2016.
Aparicio, E., Garcia-Berthou, E., Araguas, R.M., Martinez, P., Garcia-Marin, J.-L., 2005.
Making sense of the relationships between Ne, Nb and Nc towards defining
Body pigmentation pattern to assess introgression by hatchery stocks in native Salmo
conservation thresholds in Atlantic salmon (Salmo salar). Heredity 117, 268–278.
trutta Mediterranean streams. J. Fish Biol. 67, 931–949.
Ferchaud, A.-L., Laporte, M., Perrier, C., Bernatchez, L., 2018. Impact of supplementation
Apostolidis, A., Karakousis, Y., Triantaphyllidis, C., 1996. Genetic divergence and
on deleterious mutation distribution in an exploited salmonid. Evol. Appl. 11,
phylogenetic relationships among Salmo trutta L. (brown trout) populations from
1053–1065.
Greece and other European countries. Heredity 76, 551–560.
Fernández-Cebrián, R., Araguas, R.M., García-Marín, J.-L., 2014. Genetic risks of
Bardakci, F., Degerli, N., Ozdemir, O., Basibuyuk, H.H., 2006. Phylogeography of the
supplementing trout populations with native stocks: a simulation case study from
Turkish brown trout Salmo trutta L.: mitochondrial DNA PCR-RFLP variation. J. Fish
current Pyrenean populations. Can. J. Fish. Aquat. Sci. 71, 1243–1255.
Biol. 68, 36–55.
Feulner, P.G.D., Gratten, J., Kijas, J.W., Visscher, P.M., Pemberton, J.M., Slate, J., 2013.
Barton, N.H., Slatkin, M., 1986. A quasi-equilibrium theory of the distribution of rare
Introgression and the fate of domesticated genes in a wild mammal population. Mol.
alleles in a subdivided population. Heredity. 56, 409–415.
Ecol. 22, 4210–4221.
Belkhir, K., Borsa, P., Goudet, J., Bonhomme, F., 2004. GENETIX 4.05: logiciel sous
Foulley, J.L., Ollivier, L., 2006. Estimating allelic richness and its diversity. Livest. Sci.
Windows pour la génétique des populations. Laboratoire Génome et Population,
101, 150–158.
CNRS-UPR, Université de Montpellier II, Montpellier, France.
French, W.E., Vondracek, B., Ferrington Jr., J.C., Finlay, J.C., Dieterman, D.J., 2016.
Bentsen, H.B., Olesen, I., 2002. Designing aquaculture mass selection programs to avoid
Winter diet of brown trout Salmo trutta in groundwater-dominated streams: influence
high inbreeding rates. Aquaculture 204, 349–359.
of environmental factors on spatial and temporal variation. J. Fish Biol. 89,
Benzécri, J.P., 1973. L'analyse des données. Dunod, Paris.
2449–2464.
Bernaś, R., Wąs-Barcz, A., 2020. Genetic structure of important resident brown trout
Fruciano, C., Pappalardo, A.M., Tigano, C., Ferrito, V., 2014. Phylogeographical
breeding lines in Poland. J. Appl. Genet. 61, 239–247.
relationships of Sicilian brown trout and the effects of genetic introgression on
Bernaś, R., Poćwierz-Kotus, A., Árnyasi, M., Kent, M.P., Lien, S., Wenne, R., 2020.
morphospace occupation. Biol. J. Linn. Soc. 112, 387–398.
Genetic differentiation in hatchery and stocked populations of sea trout in the
Giuffra, E., Forneris, G., Guyomard, R., 1996. Diversita genetica e filogenesi dei
southern Baltic: selection evidence at SNP loci. Genes 11, 184.
salmonidi del bacino del Po. In: Proceedings of the Fourth AIIAD National Meeting,
Bernatchez, L., Guyomard, R., Bonhomme, F., 1992. DNA sequence variation of the
Riva del Garda. TEMI, Trento, pp. 21–32.
mitochondrial control region among geographically and morphologically remote
Gjedrem, T., 2000. Genetic improvement of cold-water fish species. Aquac. Res. 31,
European brown trout Salmo trutta populations. Mol. Ecol. 1, 161–173.
25–33.
Berrebi, P., Poteaux, C., Fissier, M., Cattaneo-Berrebi, G., 2000. Stocking impact and
Gutierrez, A.P., Yáñez, J.M., Davidson, W.S., 2016. Evidence of recent signatures of
allozyme diversity in brown trout from Mediterranean southern France. J. Fish Biol.
selection during domestication in an Atlantic salmon population. Mar. Genomics 26,
56, 949–960.
41–50.
Berrebi, P., Jesenšek, D., Crivelli, A.J., 2017. Natural and domestic introgressions in the
Hansen, M.M., Loeschcke, V., 1994. Effect of releasing hatchery-reared brown trout to
marble trout population of Soca River (Slovenia). Hydrobiologia 785, 277–291.
wild trout populations. Conserv. Genet. 68, 273–289.
Berrebi, P., Caputo Barrucchi, V., Splendiani, A., Muracciole, S., Sabatini, S., Palmas, F.,
Hansen, M.M., Loeschcke, V., 1996. Genetic differentiation among Danish brown trout
Tougard, C., Arculeo, M., Marić, S., 2019. Brown trout (Salmo trutta L.) high genetic
populations, as detected by RFLP analysis of PCR amplified mitochondrial DNA
diversity around Tyrrhenian Sea as revealed by nuclear and mitochondrial markers.
segments. J. Fish Biol. 48, 422–436.
Hydrobiologia 826, 209–231.
Hansen, M.M., Ruzzante, D.E., Nielsen, E.E., Mensberg, K.-L.D., 2000. Microsatellite and
Berrebi, P., Marić, S., Snoj, A., Hasegawa, K., 2020. Brown trout in Japan - introduction
mitochondrial DNA polymorphism reveals life-history dependent interbreeding
history, distribution and genetic structure. Knowl. Manag. Aquat. Ec. 421, 1–16.
between hatchery and wild brown trout (Salmo trutta L.). Mol. Ecol. 9, 583–594.
Bohling, J., Haffray, P., Berrebi, P., 2016. Genetic diversity and population structure of
Hansen, M.M., Fraser, D.J., Meier, K., Mensberg, K.-L.D., 2009. Sixty years of
domestic brown trout (Salmo trutta) in France. Aquaculture 462, 1–9.
anthropogenic pressure: a spatio-temporal genetic analysis of brown trout
Bradbury, I.R., Hamilton, L.C., Dempson, B., Robertson, M.J., Bourret, V., Bernatchez, L.,
populations subject to stocking and population declines. Mol. Ecol. 18, 2549–2562.
Verspoor, E., 2015. Transatlantic secondary contact in Atlantic salmon, comparing
Holm, L.E., Bendixen, C., 2000. Oncorhynchus mykiss Clone TAA72-13, Sequence Tagged
microsatellites, a single nucleotide polymorphism array and restriction-site
Site [available on internet at http://www.ncbi.nlm.nih.gov/genbank/]. Accession
associated DNA sequencing for the resolution of complex spatial structure. Mol. Ecol.
number AF239038.
24, 5130–5144.
Houston, R.D., Davey, J.W., Bishop, S.C., Lowe, N.R., Mota-Velasco, J.C., Hamilton, A.,
Caputo, V., Giovannotti, M., Nisi Cerioni, P., Caniglia, M.L., Splendiani, A., 2004. Genetic
Guy, D.R., Tinch, A.E., Thomson, M.L., Blaxter, M.L., Gharbi, K., Bron, J.E.,
diversity of brown trout in central Italy. J. Fish Biol. 65, 403–418.
Taggart, J.B., 2012. Characterisation of QTL-linked and genome-wide restriction
Charles, K., Guyomard, R., Hoyheim, B., Ombredane, D., Baglinière, J.-L., 2005. Lack of
site-associated DNA (RAD) markers in farmed Atlantic salmon. BMC Genomics 13,
genetic differentiation between anadromous and resident sympatric brown trout
244.
(Salmo trutta) in a Normandy population. Aquat. Living Resour. 18, 65–69.
Hoxmeier, R.J.H., Dieterman, D.J., 2013. Seasonal movement, growth and survival of
Chevassus, B., Krieg, F., Guyomard, R., Blanc, J., Quillet, E., 1992. The genetics of the
brook trout in sympatry with brown trout in Midwestern US streams. Ecol. Freshw.
brown trout: twenty years of French research. Icel. Agric. Sci. 6, 109–124.
Fish 22, 530–542.
Chevassus, B., Quillet, E., Krieg, F., Hollebecq, M.-G., Mambrini, M., Fauré, A., Labbé, L.,
ICES, 2019. Baltic salmon and trout assessment working group (WGBAST). ICES Sci. Rep.
Hiseux, J.-P., Vandeputte, M., 2004. Enhanced individual selection for selecting fast
1 (23) https://doi.org/10.17895/ices.pub.4979, 312 pp.
growing fish: the “PROSPER” method, with application on brown trout (Salmo trutta
Jones, O.R., Wang, J.I., 2010. COLONY: a program for parentage and sibship inference
fario). Genet. Sel. Evol. 36, 643–661.
from multilocus genotype data. Mol. Ecol. Resour. 10, 551–555.
Cortey, M., Pla, C., Garcia-Marin, J.-L., 2004. Historical biogeography of Mediterannean
Kalinowski, S.T., 2005. HP-rare: a computer program for performing rarefaction on
Trout. The role of allopatry and dispersal events. Mol. Phylogenet. Evol. 33,
measures of allelic diversity. Mol. Ecol. Notes 5, 187–189.
831–844.
Klütsch, C.F.C., Maduna, S.N., Polikarpova, N., Forfang, K., Aspholm, P.E., Nyman, T.,
Czerniawski, R., Pilecka-Rapacz, M., Domagała, J., 2010. Growth and survival of brown
Eiken, H.G., Amundsen, P.A., Hagen, S.B., 2019. Genetic changes caused by
trout fry (Salmo trutta M. fario L.) in the wild, reared in the hatchery on different
restocking and hydroelectric dams in demographically bottlenecked brown trout in a
feed. Electron. J. Pol. Agricult. Univ. (EJPAU) 13 (2). #04 (Available Online: http
transnational subarctic riverine system. Ecol. Evol. 9 (10), 6068–6081.
://www.ejpau.media.pl/volume13/issue2/art-04.html.
Kohout, J., Jaskova, I., Papousek, I., Sediva, A., Slechta, V., 2012. Effects of stocking on
Delling, B., 2010. Diversity of western and southern Balkan trouts, with the description
the genetic structure of brown trout, Salmo trutta, in Central Europe inferred from
of a new species from the Louros River, Greece (Teleostei: Salmonidae). Ichthyol.
mitochondrial and nuclear DNA markers. Fish. Manag. Ecol. 19, 252–263.
Explor. Fres. 21, 331–344.
Kottelat, M., Freyhof, J., 2007. Handbook of European Freshwater Fishes. Publications
Delling, B., Doadrio, I., 2005. Systematics of the trouts endemic to Moroccan lakes, with
Kottelat, Cornol, Switzerland.
description of a new species (Teleostei: Salmonidae). Ichthyol. Explor. Fres. 16,
Laikre, L., Hoban, S., Bruford, M.W., Segelbacher, G., Allendorf, F.W., Gajardo, G.,
49–64.
González Rodríguez, A., Hedrick, P.W., Heuertz, M., Hohenlohe, P.A., Jaffé, R.,
Delling, B., Crivelli, A., Rubin, J.-F., Berrebi, P., 2000. Morphological variation in hybrids
Johannesson, K., Liggins, L., MacDonald, A.J., OrozcoterWengel, P., Reusch, T.B.H.,
between Salmo marmoratus and alien Salmo species in the Volarja stream, Soca River
Rodríguez-Correa, H., Russo, I.-R.M., Ryman, N., Vernesi, C., 2020. Post-2020 goals
basin, Slovenia. J. Fish Biol. 57, 1199–1212.
overlook genetic diversity. Science 367, 1083–1085.

11
P. Berrebi et al.
Largiadèr, C.R., Scholl, A., 1995. Effects of stocking on the genetic diversity of brown
trout populations of the Adriatic and Danubian drainages in Switzerland. J. Fish Biol.
47, 209–225.
Le Luyer, J., Laporte, M., Beacham, T., Kaukinen, K., Whithler, R., Leong, J.S.,
Rondeau, E.B., Koop, B., Bernatchez, L., 2017. Parallel epigenetic modifications
induced by hatchery rearing in a Pacific Salmon. P. Natl. Acad. Sci. Biol. 114,
12964–12969.
Leitwein, M., Gagnaire, P.-A., Desmarais, D., Berrebi, P., Guinand, B., 2018. Genomic
consequences of a recent three-way admixture in supplemented wild brown trout
populations revealed by ancestry tracts. Mol. Ecol. 27, 3466–3483.
Lemopoulos, A., Prokkola, J.M., Uusi-Heikkilä, S., Vasemägi, A., Huusko, A.,
Hyvärinen, P., Koljonen, M.-L., Koskiniemi, J., Vainikka, A., 2019. Comparing
RADseq and microsatellites for estimating genetic diversity and relatedness
–implications for brown trout conservation. Ecol. Evol. 9 (4), 2106–2120.
Lerceteau-Köhler, E., Schliewen, U., Kopun, T., Weiss, S., 2013. Genetic variation in
brown trout Salmo trutta across the Danube, Rhine, and Elbe headwaters: a failure of
the phylogeographic paradigm? BMC Evol. Biol. 13, 176.
Li, Q., Park, C., Endo, T., Kijima, A., 2004. Loss of genetic variation at microsatellite loci
in hatchery strains of the Pacific abalone (Haliotis discus hannai). Aquaculture 235,
207–222.
Linløkken, A.N., Haugen, T.O., Kent, M.P., Lien, S., 2017. Genetic differences between
wild and hatchery-bred brown trout (Salmo trutta L.) in single nucleotide
polymorphisms linked to selective traits. Ecol. Evol. 7, 4963–4972.
Mambrini, M., Medale, F., Sanchez, M.P., Recalde, B., Chevassus, B., Labbe, L.,
Quillet, E., Boujard, T., 2004. Selection for growth in brown trout increases feed
intake capacity without affecting maintenance and growth requirements. J. Anim.
Sci. 82, 2865–2875.
Marić, S., Sušnik Bajec, S., Schöffmann, J., Kostov, V., Snoj, A., 2017. Phylogeography of
stream-dwelling trout in the Republic of Macedonia and a molecular genetic basis for
revision of the taxonomy proposed by S. Karaman. Hydrobiologia 785, 249–260.
Miller, L.M., Close, T., Kapuscinski, R., 2004. Lower fitness of hatchery and hybrid
rainbow trout compared to naturalized populations in Lake Superior tributaries. Mol.
Ecol. 13, 3379–3388.
Naish, K.A., Taylor, J.E., Levin, P.S., Quinn, T.P., Winton, J.R., Huppert, D., Hilborn, R.,
2008. An evaluation of the effects of conservation and fishery enhancement
hatcheries on wild populations of salmon. Adv. Mar. Biol. 53, 61–194.
Nei, M., 1972. Genetic distance between populations. Am. Nat. 106, 283–292.
Nei, M., 1978. Estimation of average heterozygosity and genetic distance from a small
number of individuals. Genetics 89, 583–590.
O'Reilly, P.T., Hamilton, L.C., McConnell, S.K., Wright, J.M., 1996. Rapid analysis of
genetic variation in Atlantic salmon (Salmo salar) by PCR multiplexing of
dinucleotids and tetranucleotids microsatellites. Can. J. Fish. Aquat. Sci. 53,
2292–2298.
O’Sullivan, R.J., Aykanat, T., Johnston, S.E., Kane, A., Poole, R., Rogan, G., Prodöhl, P.
A., Primmer, C.R., McGinnity, P., Reed, T.E., 2019. Evolutionary stasis of a heritable
morphological trait in a wild fish population despite apparent directional selection.
Ecol. Evol. 9, 7096–7111.
Palm, S., Dannewitz, J., Järvi, T., Petersson, E., Prestegaard, T., Ryman, N., 2003. Lack of
molecular genetic divergence between sea-ranched and wild sea trout (Salmo trutta).
Mol. Ecol. 12, 2057–2071.
Palm, S., Dannewitz, J., Järvi, T., Koljonen, M.-L., Prestegaard, T., Olsén, K.H., 2008. No
indications of Atlantic salmon (Salmo salar) shoaling with kin in the Baltic Sea. Can.
J. Fish. Aquat. Sci. 65, 1738–1748.
Palm, S., Dannewitz, J., Johansson, D., Laursen, F., Norrgård, J., Prestegaard, T.,
Sandström, A., 2012. Populationsgenetisk kartläggning av Vänerlax. Aqua reports
2012, 4. Institutionen för akvatiska resurser, Sveriges lantbruksuniversitet,
Drottningholm Lysekil Öregrund, 64 pp. (In Swedish with English Abstract).
Poteaux, C., Guyomard, R., Berrebi, P., 2000. Single and joint gene segregation in
intraspecific hybrids of brown trout (Salmo trutta L.) lineages. Aquaculture 186,
1–12.
Presa, P., Guyomard, R., 1996. Conservation of microsatellites in three species of
salmonids. J. Fish Biol. 49, 1326–1329.
Presa, P., Krieg, F., Estoup, A., Guyomard, R., 1994. Diversité et gestion génétique de la
truite commune: apport de l’étude du polymorphisme des locus protéiques et
microsatellites. Genet. Sel. Evol. 26 (Suppl. 1), 183–202.
Pritchard, J.K., Stephens, M., Donnelly, P., 2000. Inference of population structure using
multilocus genotype data. Genetics 155, 945–959.
Rexroad, C.E., Coleman, R.L., Hershberger, W.K., Killefer, J., 2002. Rapid
communication: thirty-eight polymorphic microsatellite markers for mapping in
rainbow trout. J. Anim. Sci. 80, 541–542.
12
Aquaculture 544 (2021) 737043
Sanchez, M., Chevassus, B., Labbé, L., Quillet, E., Mambrini, M., 2001. Selection for
growth of brown trout (Salmo trutta) affects feed intake but not feed efficiency.
Aquat. Living Resour. 14, 41–48.
Sanz, N., 2018. Phylogeographic history of brown trout: a review. In: Lobon-Cervia, J.,
Sanz, N. (Eds.), Brown Trout: Biology, Ecology and Management. John Wiley & Sons
Ltd., pp. 17–63
Scribner, K.T., Gust, J.R., Fields, R.L., 1996. Isolation and characterization of novel
salmon microsatellite loci: cross-species amplification and population genetic
applications. Can. J. Fish. Aquat. Sci. 53, 833–841.
She, J.X., Autem, M., Kotoulas, G., Pasteur, N., Bonhomme, F., 1987. Multivariate
analysis of genetic exchanges between Solea aegyptiaca and Solea senegalensis
(Teleosts, Soleidae). Biol. J. Linn. Soc. 32, 357–371.
Skaala, Ø., Høyheim, B., Glover, K., Dahle, G., 2004. Microsatellite analysis in
domesticated and wild Atlantic salmon (Salmo salar L.): allelic diversity and
identification of individuals. Aquaculture 240, 131–143.
Slatkin, M., 1985. Rare alleles as indicators of gene flow. Evolution. 39, 53–65.
Slettan, A., Olsaker, I., Lie, Ø., 1995. Atlantic salmon, Salmo salar, microsatellites at the
SSOSL25, SSOSL85, SSOSL311, SSOSL417 loci. Anim. Genet. 26, 277–285.
Slettan, A., Olsaker, I., Lie, Ø., 1996. Polymorphic Atlantic salmon, Salmo salar L.,
microsatellites at the SSOSL438, SSOSL439 and SSOSL444 loci. Anim. Genet. 27,
57–64.
Suarez, J., Bautista, J.M., Almodovar, A., Machordom, A., 2001. Evolution of the
mitochondrial control region in Palaearctic brown trout (Salmo trutta) populations:
the biogeographical role of the Iberian Peninsula. Heredity 87, 198–206.
Takezaki, N., Nei, M., Tamura, K., 2010. POPTREE2: software for constructing
population trees from allele frequency data and computing other population
statistics with windows interface. Mol. Biol. Evol. 27, 747–752.
Tave, D., 1999. Inbreeding and brood stock management. In: FAO Fisheries Technical
Paper 392. FAO, Rome, 122 pp.
Tortonese, E., 1970. Osteichthyes, parte I. Fauna d’Italia, Vol. X. Calderini, Bologna.
Tougard, C., Justy, F., Guinand, B., Douzery, E.J.P., Berrebi, P., 2018. Salmo macrostigma
(Teleostei, Salmonidae): nothing more than a brown trout (S. trutta) lineage? J. Fish
Biol. 93, 302–310.
Turan, D., Kottelat, M., Engin, S., 2009. Two new species of trouts, resident and
migratory, sympatric in streams of northern Anatolia (Salmoniformes: Salmonidae).
Ichthyol. Explor. Fres. 20, 333–364.
Turan, D., Kottelat, M., Engin, S., 2010. Two new species of trouts, resident and
migratory, sympatric in streams of northern Anatolia (Salmoniformes: Salmonidae).
Ichthyol. Explor. Fres. 20, 289–384.
Turan, D., Kottelat, M., Bektas, Y., 2011. Salmo tigridis, a new species of trout from the
Tigris River, Turkey (Teleostei: Salmonidae). Zootaxa 2993, 23–33.
Turan, D., Kottelat, M., Engin, S., 2012. The trouts of the Mediterranean drainages of
southern Anatolia, Turkey, with description of three new species (Teleostei:
Salmonidae). Ichthyol. Explor. Fres. 23, 219–236.
Turan, D., Doğan, E., Kaya, C., Kanyılmaz, M., 2014a. Salmo kottelati, a new species of
trout from Alakır stream, draining to the Mediterranean in southern Anatolia,
Turkey (Teleostei, Salmonidae). ZooKeys 462, 135–151.
Turan, D., Kottelat, M., Engin, S., 2014b. Two new species of trouts from the Euphrates
drainage, Turkey (Teleostei: Salmonidae). Ichthyol. Explor. Fres. 24, 275–287.
Vähä, J.P., Erkinaro, J., Niemelä, E., Primmer, C.R., 2007. Life-history and habitat
features influence the within-river genetic structure of Atlantic salmon. Mol. Ecol.
16, 2638–2654.
Valiquette, E., Perrier, C., Thibault, I., Bernatchez, L., 2014. Loss of genetic integrity in
wild lake trout populations following stocking: insights from an exhaustive study of
72 lakes from Québec, Canada. Evol. Appl. 7, 625–644.
van Houdt, J.K.J., Pinceel, J., Flamand, M.-C., Briquet, M., Dupont, E., Volckaert, F.A.M.,
Bare, P.V., 2005. Migration barriers protect indigenous brown trout (Salmo trutta)
populations from introgression with stocked hatchery fish. Conserv. Genet. 6,
175–191.
Wang, J., 2009. A new method for estimating effective population sizes from a single
sample of multilocus genotypes. Mol. Ecol. 18, 2148–2164.
Waples, R.S., Luikart, G., Faulkner, J.R., Tallmon, D.A., 2013. Simple life history traits
explain key effective population size ratios across diverse taxa. Proc. R. Soc. B 280,
20131339.
Wąs, A., Bernaś, R., 2016. Long-term and seasonal genetic differentiation in wild and
enhanced stocks of sea trout (Salmo trutta m. trutta L.) from the Vistula River, in the
southern Baltic - management implications. Fish. Res. 175, 57–65.
Weir, B., Cockerham, C., 1984. Estimating F-statistics for the analysis of population
structure. Evolution 38, 1358–1370.
Wollebaek, J., Knut, H.R., Brabrand, A., Heggenes, J., 2012. Interbreeding of genetically
distinct native brown trout (Salmo trutta) populations designates offspring fitness.
Aquaculture 356, 158–168.