Figure S1: Genetic structure within individual drainages. Unless otherwise indicated,
STRUCTURE analyses were based on neutral microsatellite loci using the default settings
outlined in the manuscript. All location names correspond to Fig. 1 and Table S1. The
best supported number of groups (K) was inferred from plots of the likelihood
distribution or, if no clear mode was detected, based on ΔK proposed by Evanno et al.
(2005).
LU
BI
BO
LO
MA
Fig. S1a) STRUCTURE plot for K=3 based on five samples from the Ticino (Po drainage).
TI
ZA
BR
LA
CA
LP
SO
PI
Fig. S1b) STRUCTURE plot for K=3 based on eight samples from the Poschiavino (Po
drainage). Note that this analysis was based on a model which utilized information about
sampling locations.
SA
SC
HE
KI RU AN
RO
SB
LB
FR
SE
BL
GO
SA
SC
HE
KI RU AN
RO
SB
LB
FR
SE
BL
GO
Fig. S1c) STRUCTURE plots for K=2 (top) and K=6 (bottom) based on 13 samples from
the Rhine drainage. Substructure could only be resolved when information about the
sampling locations was included. Under this model, ΔK (Evanno method) peaked at K=2,
and the log likelihood values increased slightly up to K=6.
BU
PR
AL
MI
Fig. S1d) STRUCTURE plot for K=2 based on four samples from the Allaine (Rhone
drainage).
Table S1: Sampling locations in three major European drainages. Within the Po drainage,
the two geographically separated Poschiavino and Ticino river systems are indicated. Site
ID corresponds to Figure 1 of the manuscript. Altitude in m above sea level. N= sample
size.
Drainage
Po - Poschiavino
Po - Poschiavino
Po - Poschiavino
Po - Poschiavino
Po - Poschiavino
Po - Poschiavino
Po - Poschiavino
Po - Poschiavino
Po - Ticino
Po - Ticino
Po - Ticino
Po - Ticino
Po - Ticino
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhone - Allaine
Rhone - Allaine
Rhone - Allaine
Rhone - Allaine
Site
Tirano
Zalende
Brusio
Lago di Poschiavo
Canton
Le Prese
San Carlo
Pisciadel
Magliasina
Biasca
Bodio
Loderio
Lukmanier
Ruppoldingen
Kiesen
Schwarzenburg
Heimenegg
Sangernboden
Rotbach
Andermatt
Goldach
Blumenegg
Sertigbach
Frauenfeld
Luetisburg
Schwanzbrugg
Buix
Porrentruy
Alle
Miécourt
ID
TI
ZA
BR
LA
CA
LP
SO
PI
MA
BI
BO
LO
LU
RU
KI
SC
HE
SA
RO
AN
GO
BL
SE
FR
LB
SB
BU
PR
AL
MI
Altitude
430
562
600
962
966
975
1077
1336
277
295
317
356
1802
398
560
653
856
915
415
1428
439
474
1776
399
555
759
381
422
452
486
N
30
29
25
31
31
25
30
30
34
29
27
19
30
11
26
26
31
30
30
27
30
30
39
30
27
30
26
30
30
30
Longitude
10.1532
10.1374
10.1329
10.0826
10.0832
10.0730
10.0622
10.0673
8.8904
8.9583
8.9139
8.9748
8.8095
7.8814
7.5721
7.3202
7.7085
7.3290
8.3555
8.5844
9.4587
9.4401
9.8426
8.8923
9.0853
9.1856
7.0347
7.0778
7.1300
7.1819
Latitude
46.2167
46.2363
46.2412
46.2912
46.2966
46.3026
46.3463
46.3782
45.9756
46.3507
46.3746
46.3823
46.5463
47.3124
46.8074
46.8262
46.8070
46.7161
47.1158
46.6394
47.4723
47.4610
46.7357
47.5570
47.3933
47.2996
47.4755
47.4213
47.4267
47.4280
Table S2: Microsatellite markers used in this study. The repeat motive is given for the
sequence available on Genbank. Assignment to linkage groups is based on Gharbi et al.
(2006) unless indicated otherwise. Putative function refers to known or unknown genes in
physical proximity to the marker. MP=PCR multiplex; μM = primer concentration in the
primer mix; UTT = upper temperature tolerance; A=number of alleles; null=average null
allele frequency (estimated in FreeNA). The sequence 5’-GTTTCTT-3’ was added to the
5' end of all reverse primers to encourage the addition of an A overhang by Taq
polymerase and reduce the frequency of 1bp stutter peaks (PIG-tail; Brownstein et al.
1996). Most neutral markers were selected from the list available at the Trout Concerted
Action website (http://www.qub.ac.uk/bb-old/prodohl/TroutConcert/TroutConcert.htm)
where references to the original publications are provided. For all other loci, the source
column contains the references to the original description of the markers and the relevant
QTL mapping studies.
Type
Anonymous
Anonymous
Locus name
SsoSL438
Ssa100NVH
Repeat motive
(GT)26
(AC)38
Forward primer (5'-3')
GACAACACACAACCAAGGCAC
CTGTCATTCCCTTGGCAC
Reverse primer (5'-3')
TTATGCTAGGTCTTTATGCATTGT
GATGCTGCTAGGAGAGAG
Dye
cy5.5
cy5
MP
1
1
µM
4
0.5
Linkage group
BT-13
BT-31
A
10
15
Null
0.053
0.006
Anonymous
Anonymous
Anonymous
Anonymous
Anonymous
Str15INRA
Str60INRA
Strutta58
Str73INRA
(TC)13
(GT)13
(GT)36
(TG)3...(TG)13
TGCAGGCAGACGGATCAGGC
CGGTGTGCTTGTCAGGTTTC
AACAATGACTTTCTCTGAC
CCTGGAGATCCTCCAGCAGGA
AATCCTCTACGTAAGGGATTTGC
GTCAAGTCAGCAAGCCTCAC
AAGGACTTGAAGGACGAC
CTATTCTGCTTGTAACTAGACCTA
cy5
cy7
cy5.5
cy7
1
1
2
2
2
0.4
2
1.5
BT-12
BT-10
BT-26
BT-27
8
8
49
11
0.020
0.019
0.034
0.014
Str85INRA
(CT)22
GGAAGGAAGGGAGAAAGGT
TCTCCCAGTGCCCATCAG§§
cy7
2
1
BT-02
15
0.024
Diagnostic
Diagnostic
Candidate
Str543INRA
JMS1_M1
JMS2_M1
Ssa60NVH
(CT)13
(TG)nTT(TG)5
very complex
(TG)n
TCCAAGCAAAAGGTCAGCTC§§
GGATGGGAATTCCTTTGTGG
CTGGTGGCAGGATTTGA
TTGTGGAGTATTTAGCAATC
TGGGCATCTGGTCAGTTTCT§§
GGAATACACAAATAAAGACAAATAC
CTGTCTTTCGTTCTTTCTCGG
ATTGGCAGACATGCACTC
cy5
cy7
cy5
cy5.5
2
1
2
1
0.5
0.5
1
2
BT-17
NA
BT-07
BT-01
25
4
20
45
0.019
0.024
0.020
Candidate
Ssa-UBA
(CA)21A(CA)2
GGAGAGCTGCCCAGATGACTT
CAATTACCACAAGCCCGCTC
cy5
1
2
BT-29*
27
0.319
Candidate
Ssa-TAP2b
(TC)2...(CT)2
GCGGGACACCGTCAGGGCAGT
GTCCTGATGTTGGCTCCCAGG
cy5.5
1
4§
BT-20**
13
0.011
Candidate
Ssa-TAP2a
(TG)3..(TG)2
GCGGGACACCGTCAGGGCAGT
CCTGATATTGTCTGCCAGATC
cy5.5
3
3
BT-29*
4
0.020
Candidate
Omy325
(GT)22
CTCCAGCACTAAGCATACATC
CGGAGTCCGTATCCTTCCC
cy5
3
3
BT-28
49
0.085
Candidate
Ssa14
(TC)10N15(TC)3N2(AC)12(TC)3N5(CA)4
CCTTTTGACAGATTTAGGATTTC
CAAACCAAACATACCTAAAGCC
cy5
3
3
NA
3
0.150
Candidate
Ssa85DU
(CA)14
AGGTGGGTCCTCCAAGCTAC
ACCCGCTCCTCACTTAATC
cy5.5
3
2
BT-04
11
0.027
Candidate
Ots515NWFSC (CA)8GA(CA)12
ACAGTGATGGAGCTTGATTC
ACGATTTCTATTTGTCTCCG
cy5.5
3
2
BT-14***
3
0.017
Candidate
SsoSL417
cy7
3
2
BT-35
24
0.013
Anonymous
(TG)25
TTGTTCAGTGTATATGTGTCCCAT GATCTTCACTGCCACCTTATGACC
Type
Anonymous
Anonymous
Locus name
SsoSL438
Ssa100NVH
Putative function
none
none
Anonymous
Anonymous
Anonymous
Anonymous
Anonymous
Str15INRA
Str60INRA
Strutta58
Str73INRA
none
none
none
none
Source
trout concerted action
unpublished; see Giger et al. 2006,
supplementary material
trout concerted action
trout concerted action
trout concerted action
trout concerted action
Str85INRA
none
trout concerted action
Anonymous
Diagnostic
Diagnostic
Candidate
Str543INRA
JMS1_M1
JMS2_M1
Ssa60NVH
trout concerted action
Estoup et al. (2000)
Estoup et al. (2000)
Gharbi et al. (2006, 2009)
Candidate
Ssa-UBA
none
none
none
antigen presentation (linked to MHC II, locus
DAA, in Atlantic salmon)
antigen presentation (3' untranslated tail of
MHC IA in Atlantic salmon)
Candidate
Ssa-TAP2b
antigen presentation (intron 5 of transporter
associated with antigen processing, region
MHC IB, of Atlantic salmon)
Grimholt et al. (2002)
Candidate
Ssa-TAP2a
antigen presentation (intron 5 of transporter
associated with antigen processing, region
MHC IA, of Atlantic salmon)
Grimholt et al. (2002)
Candidate
Omy325
O'Connell et al. (1997), Jackson et al. (1998),
McClelland & Naish (2010)
Candidate
Ssa14
Candidate
Ssa85DU
QTL for UTT and body size in rainbow trout,
QTL for growth rate and body size in coho
salmon
QTL for UTT in rainbow trout and Arctic
charr
QTL for UTT and spawning date in rainbow
trout and Arctic charr
Candidate
Ots515NWFSC
Naish & Park (2002), O'Malley et al (2003)
Candidate
SsoSL417
QTL for spawning date and body weight in
rainbow trout
QTL for spawning data in rainbow trout†
Grimholt et al. (2002)
McConnell et al. (1995), Jackson et al.
(1998), Somorjai et al. (2003)
O'Reilly et al. (1996), Jackson et al. (1998),
Sakamoto et al. (1999), Somorjai et al. (2003)
Slettan et al. (1995), Sakamoto et al. (1999),
Leder et al. (2006)
Footnotes
§
§§
*
**
***
The mix contained 75% labelled forward primer and 25% unlabelled forward primer.
Newly designed primers
AS-15 of Atlantic salmon (Lukacs et al. 2007) which is homologous to BT-29 (Gharbi et al. 2006)
AS-3 of Atlantic salmon (Lukacs et al. 2007) which is homologous to BT-20 (Gharbi et al. 2006)
RT-11 of rainbow trout (Danzmann et al. 2005) which is homologous to BT-14 (Gharbi et al. 2006)
SsoSL417 is closely linked to the clock gene in Atlantic salmon linkage group AS-2 (http://www.asalbase.org/sal-bin/index). Marker OmyFGT12TUF
of Sakamoto et al. (1999) and Leder et al. (2006) could not be amplified in trout.
†
References
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
13.
Brownstein, M.J., et al. (1996) Modulation of non-templated nucleotide addition by Taq DNA polymerase: primer modifications that facilitate
genotyping. BioTechniques 20, 1004-1010
Danzmann, R.G., et al.. (2005) A comparative analysis of the rainbow trout genome with 2 other species of fish (Arctic charr and Atlantic salmon)
within the tetraploid derivative Salmonidae family (subfamily: Salmoninae). Genome 48, 1037-1051
Estoup, A., et al. (2000) Juxtaposed microsatellite systems as diagnostic markers for admixture: an empirical evaluation with brown trout (Salmo trutta)
as model organism. Molecular Ecology 9, 1873-1886
Giger, T., et al. (2006) Life history shapes gene expression in salmonids. Current Biology 16, R281-R282
Gharbi, K., et al. (2006) A linkage map for brown trout (Salmo trutta): Chromosome homeologies and comparative genome organization with other
salmonid fish. Genetics 172, 2405-2419
Gharbi, K., et al. (2009) Genetic dissection of MHC-associated susceptibility to Lepeophtheirus salmonis in Atlantic salmon. BMC Genetics 10, 20
Grimholt, U., et al. (2002) The major histocompatibility class I locus in Atlantic salmon (Salmo salar L.): polymorphism, linkage analysis and protein
modelling. Immunogenetics 54, 570-581
Jackson, T.R., et al. (1998) Identification of two QTL influencing upper temperature tolerance in three rainbow trout (Oncorhynchus mykiss) half-sib
families. Heredity 80, 143-151
Leder, E.H., et al. (2006) The candidate gene, Clock, localizes to a strong spawning time quantitative trait locus region in rainbow trout. Journal of
Heredity 97, 74-80l
Lukacs, M.F., et al. (2007) Genomic organization of duplicated major histocompatibility complex class I region in Atlantic salmon (Salmo salar). BMC
Genomics 8, 251
McClelland, E.K. & Naish, K.A. (2010) Quantitative trait locus analysis of hatch timing, weight, length and growth rate in coho salmon,
Onchorhynchus kisutch. Heredity 105, 562-573
McConnell, S.K., et al. (1995) Polymorphic microsatellite loci from Atlantic salmon (Salmo salar): Genetic differentiation of North American and
European populations. Canadian Journal of Fisheries and Aquatic Sciences 52, 1863-1872
Naish, K.A. & Park, L.K. (2002) Linkage relationships for 35 new microsatellite loci in chinook salmon Oncorhynchus tshawytscha. Animal Genetics
30, 312-327
14. O’Connell, M., et al. (1997) Differentiation of rainbow trout (Oncorhynchus mykiss) populations in Lake Ontario and the evaluation of the stepwise
mutation and the infinite allele mutation models using microsatellite variability. Canadian Journal of Fisheries and Aquatic Sciences 54, 1391-1399
15. O'Malley, K.G., et al. (2003) Quantitative trait loci for spawning date and body weight in rainbow trout: Testing for conserved effects across ancestrally
duplicated chromosomes. Journal of Heredity 94, 273-284
16. O’Reilly, P.T., et al. (1996) Rapid analysis of genetic variation in Atlantic salmon (Salmo salar) by PCR multiplexing of dinucleotide and tetranucleotide microsatellites. Canadian Journal of Fisheries and Aquatic Sciences 53, 2292-2298.
17. Sakamoto, T., et al. (1999) Linkage analysis of quantitative trait loci associated with spawning time in rainbow trout (Oncorhynchus mykiss).
Aquaculture 173, 33-43
18. Slettan, A., et al. (1995) Atlantic salmon, Salmo salar, microsatellites at the SSOSL25, SSOSL85, SSOSL311, SSOSL417 loci. Animal Genetics 26,
281-282.
19. Somorjai, I.M.L., et al. (2003) Distribution of temperature tolerance quantitative trait loci in Arctic charr (Salvelinus alpinus) and inferred homologies
in rainbow trout (Oncorhynchus mykiss). Genetics 165, 1443-1456
Table S3: Pairwise FST values calculated based on ten neutral loci. Values not significantly different from zero (P>0.05) are italicised, and
within-drainage comparisons are highlighted in yellow.
TI
Po - Poschiavino
Po - Poschiavino
Po - Poschiavino
Po - Poschiavino
Po - Poschiavino
Po - Poschiavino
Po - Poschiavino
Po - Poschiavino
Po - Ticino
Po - Ticino
Po - Ticino
Po - Ticino
Po - Ticino
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Allaine
Allaine
Allaine
Allaine
Tirano
Zalende
Brusio
Lago di Poschiavo
Canton
Le Prese
San Carlo
Pisciadel
Magliasina
Biasca
Bodio
Loderio
Lukmanier
Ruppoldingen
Kiesen
Schwarzenburg
Heimenegg
Sangernboden
Rotbach
Andermatt
Goldach
Blumenegg
Sertigbach
Frauenfeld
Luetisburg
Schwanzbrugg
Buix
Porrentruy
Alle
Miécourt
TI
ZA
BR
LA
CA
LP
SO
PI
MA
BI
BO
LO
LU
RU
KI
SC
HE
SA
RO
AN
GO
BL
SE
FR
LB
SB
BU
PR
AL
MI
ZA
0.009
0.006 0.004
0.006 -0.002
0.005 0.001
0.017 0.015
0.027 0.015
0.005 0.004
0.045 0.057
0.034 0.030
0.060 0.063
0.044 0.043
0.047 0.053
0.050 0.060
0.032 0.043
0.031 0.044
0.031 0.038
0.032 0.052
0.027 0.036
0.051 0.055
0.042 0.044
0.037 0.042
0.066 0.060
0.028 0.038
0.051 0.050
0.054 0.055
0.074 0.090
0.097 0.107
0.032 0.042
0.059 0.071
BR
LA
CA
POSCHIAVINO
0.001
0.003 -0.002
0.004 0.003 0.004
0.012 0.007 0.008
0.000 -0.002 -0.003
0.056 0.061 0.054
0.051 0.042 0.033
0.075 0.063 0.050
0.056 0.049 0.039
0.062 0.053 0.041
0.067 0.072 0.046
0.052 0.051 0.044
0.049 0.053 0.040
0.041 0.047 0.037
0.055 0.062 0.049
0.047 0.050 0.037
0.064 0.068 0.064
0.052 0.055 0.039
0.047 0.057 0.037
0.062 0.060 0.043
0.039 0.047 0.037
0.055 0.054 0.042
0.055 0.064 0.042
0.092 0.094 0.099
0.107 0.111 0.115
0.051 0.056 0.045
0.081 0.082 0.073
LP
0.009
0.011
0.067
0.055
0.072
0.063
0.064
0.076
0.067
0.053
0.045
0.061
0.055
0.073
0.054
0.061
0.065
0.053
0.060
0.064
0.098
0.111
0.061
0.076
SO
0.014
0.056
0.034
0.056
0.048
0.040
0.069
0.046
0.040
0.038
0.056
0.039
0.054
0.034
0.039
0.027
0.041
0.032
0.043
0.111
0.124
0.058
0.082
PI
MA
0.063
0.040
0.066
0.057
0.051
0.064
0.052
0.045
0.041
0.054
0.044
0.064
0.050
0.051
0.064
0.041
0.058
0.064
0.099
0.120
0.052
0.090
0.037
0.060
0.042
0.051
0.039
0.019
0.022
0.022
0.033
0.023
0.046
0.015
0.030
0.059
0.014
0.028
0.038
0.086
0.106
0.036
0.056
BI
BO
LO
LU
TICINO
0.008
0.002
0.020
0.058
0.023
0.017
0.027
0.031
0.023
0.036
0.015
0.032
0.057
0.026
0.029
0.045
0.104
0.118
0.047
0.073
0.008
0.030
0.075
0.044
0.035
0.044
0.060
0.050
0.070
0.042
0.066
0.077
0.054
0.049
0.058
0.125
0.135
0.068
0.090
0.031
0.064
0.031
0.029
0.041
0.044
0.041
0.057
0.032
0.044
0.073
0.044
0.039
0.045
0.111
0.119
0.060
0.073
0.042
0.034
0.028
0.024
0.044
0.036
0.038
0.029
0.038
0.056
0.039
0.026
0.034
0.133
0.147
0.065
0.085
RU
Po - Poschiavino
Po - Poschiavino
Po - Poschiavino
Po - Poschiavino
Po - Poschiavino
Po - Poschiavino
Po - Poschiavino
Po - Poschiavino
Po - Ticino
Po - Ticino
Po - Ticino
Po - Ticino
Po - Ticino
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Allaine
Allaine
Allaine
Allaine
Tirano
Zalende
Brusio
Lago di Poschiavo
Canton
Le Prese
San Carlo
Pisciadel
Magliasina
Biasca
Bodio
Loderio
Lukmanier
Ruppoldingen
Kiesen
Schwarzenburg
Heimenegg
Sangernboden
Rotbach
Andermatt
Goldach
Blumenegg
Sertigbach
Frauenfeld
Luetisburg
Schwanzbrugg
Buix
Porrentruy
Alle
Miécourt
TI
ZA
BR
LA
CA
LP
SO
PI
MA
BI
BO
LO
LU
RU
KI
SC
HE
SA
RO
AN
GO
BL
SE
FR
LB
SB
BU
PR
AL
MI
0.042
0.049
0.029
0.047
0.026
0.059
0.034
0.028
0.065
0.027
0.041
0.031
0.128
0.153
0.053
0.068
KI
0.004
0.010
0.014
0.008
0.022
0.008
0.023
0.046
0.004
0.024
0.024
0.082
0.102
0.023
0.047
SC
0.007
0.001
0.012
0.016
0.007
0.024
0.056
0.013
0.032
0.036
0.087
0.109
0.027
0.056
HE
0.013
0.003
0.016
0.004
0.022
0.051
0.005
0.024
0.026
0.081
0.102
0.030
0.041
SA
0.013
0.017
0.021
0.022
0.059
0.010
0.044
0.046
0.080
0.098
0.028
0.043
RO
AN
GO
BL
SE
FR
LB
SB
BU
PR
AL
MI
RHINE
0.029
0.009
0.009
0.046
0.000
0.021
0.020
0.094
0.116
0.032
0.052
0.020
0.032
0.069
0.026
0.044
0.056
0.102
0.123
0.050
0.067
0.009
0.039
0.008
0.013
0.014
0.098
0.116
0.036
0.052
0.028
0.012
0.013
0.007
0.112
0.129
0.037
0.054
0.044
0.023
0.031
0.128
0.140
0.060
0.077
0.018
0.020
0.087
0.106
0.028
0.049
0.008
0.122
0.134
0.047
0.064
0.138
0.152
0.058
0.071
0.003
0.029
0.043
ALLAINE
0.047
0.053
0.021
Table S4: Difference between the observed Hardy-Weinberg heterozygosity (He) and the expectation at mutation-drift equilibrium (Heq) under a
stepwise mutation model.
Neutral loci (non-outliers)
Drainage
Poschiavino
Poschiavino
Poschiavino
Poschiavino
Poschiavino
Poschiavino
Poschiavino
Poschiavino
Ticino
Ticino
Ticino
Ticino
Ticino
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Allaine
Allaine
Allaine
Allaine
Site
TI
ZA
BR
LA
CA
LP
SO
PI
MA
BI
BO
LO
LU
RU
KI
SC
HE
SA
RO
AN
GO
BL
SE
FR
LB
SB
BU
PR
AL
MI
Ssa100
-0.025
0.004
-0.018
-0.009
0.004
-0.025
-0.06
0.011
-0.021
-0.029
-0.071
-0.039
0.006
0.068
-0.033
0.027
0.01
-0.037
0.004
-0.057
0.02
0.018
-0.134
0.051
-0.017
-0.015
0.042
-0.044
-0.018
-0.042
Str15
0.04
-0.02
-0.046
0.012
0.055
0.052
0.021
0.063
0.011
0.042
0.061
0.049
-0.088
0.056
0.108
0.016
0.109
0.056
0.052
0.128
0.072
0.042
-0.048
0.016
0.077
-0.075
0.052
0.023
0.102
0.092
SL438
0.081
0.098
0.099
0.102
0.063
0.077
0.089
0.116
0.017
-0.017
0.031
0.018
0.059
0.039
0.035
0.066
0.095
0.002
0.07
0.071
0.047
-0.021
0.019
0.04
0.104
0.055
-0.082
0.02
-0.028
0.029
Str73
0
-0.006
0.061
0.037
0.02
-0.013
0.013
0.001
-0.029
-0.089
-0.134
0.047
-0.09
0.145
-0.104
0.009
0.038
0.054
0.038
-0.186
0.038
0.036
-0.076
-0.054
-0.237
-0.034
0.085
0.088
0.06
-0.01
Str85
-0.027
-0.017
-0.066
-0.143
-0.105
-0.085
-0.088
-0.072
-0.082
-0.043
-0.277
-0.211
-0.098
0.006
-0.068
-0.103
-0.098
0.032
-0.055
0.036
-0.054
-0.031
0.014
-0.029
-0.135
-0.157
-0.076
-0.042
0.012
0.027
Str543
-0.013
-0.054
-0.047
-0.049
-0.036
-0.09
-0.11
-0.061
-0.082
-0.056
-0.019
-0.013
-0.157
-0.01
-0.039
-0.026
-0.171
-0.078
-0.03
-0.151
-0.118
-0.025
-0.164
-0.058
-0.134
-0.105
0.011
-0.01
0.018
-0.046
Strutta58
0.001
-0.024
-0.062
-0.018
-0.063
-0.035
-0.019
-0.002
-0.091
-0.049
-0.013
-0.015
-0.003
0.014
-0.015
0.008
-0.006
-0.022
-0.017
-0.017
-0.042
-0.054
-0.042
-0.026
-0.025
-0.012
-0.007
0.009
-0.021
0.019
SsoSL417
0.02
-0.013
-0.015
0.016
0.011
-0.002
-0.053
0.026
-0.011
-0.077
-0.047
-0.109
-0.082
0.02
0
-0.015
0.024
0.036
0.005
0.025
0.012
0.044
-0.039
-0.004
0.029
-0.01
-0.066
-0.046
-0.008
0.001
Omy325
0.004
-0.042
0.004
-0.008
0.007
-0.001
-0.013
-0.021
-0.019
-0.012
-0.003
0.021
-0.019
0.005
0.005
0.007
0.004
-0.008
-0.002
-0.058
0.012
-0.007
0.009
-0.003
-0.022
0.01
0
-0.025
0.004
-0.006
Ssa85
0.051
-0.013
-0.063
-0.137
0.028
-0.025
-0.107
-0.057
-0.016
-0.099
-0.09
-0.027
-0.155
0.077
-0.027
-0.04
-0.098
-0.046
-0.06
-0.165
-0.065
-0.023
-0.09
0.053
-0.083
-0.088
0.014
0.013
0.047
0.015
Ots515
-0.093
0.068
0.06
0.03
0.14
0.06
0.178
0.001
-0.277
-0.141
-0.189
-0.224
0.059
-0.002
-0.017
-0.052
0.031
-0.262
-0.16
-0.178
0.071
0.171
0.274
-0.14
-0.029
0.223
0
-0.379
-0.062
-0.133
MHC class I linked
Drainage
Poschiavino
Poschiavino
Poschiavino
Poschiavino
Poschiavino
Poschiavino
Poschiavino
Poschiavino
Ticino
Ticino
Ticino
Ticino
Ticino
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Rhine
Allaine
Allaine
Allaine
Allaine
Site
TI
ZA
BR
LA
CA
LP
SO
PI
MA
BI
BO
LO
LU
RU
KI
SC
HE
SA
RO
AN
GO
BL
SE
FR
LB
SB
BU
PR
AL
MI
UBA
0.029
-0.014
-0.008
0.009
0.016
-0.017
-0.026
-0.015
-0.009
-0.135
-0.073
0.039
-0.058
0.061
-0.016
0.063
-0.064
0.008
-0.079
-0.005
0.014
0.005
-0.047
-0.019
-0.007
-0.063
0.011
0.009
0.009
0.018
TAP2a
0.075
0.052
0.083
0.065
0.079
0.099
0.202
0.039
0.093
0.103
0.1
0.086
0.1
0.07
0.053
0.093
0.12
0.106
0.11
0.136
0.096
0.1
0.097
0.106
0.128
0.041
0.025
-0.029
0.1
0.098
TAP2b
-0.014
-0.047
-0.008
0.02
0.027
0.025
0.032
0.014
-0.053
0.017
0.009
-0.022
0.003
-0.035
-0.043
-0.02
-0.05
-0.08
-0.068
0.024
-0.025
-0.037
-0.04
-0.141
-0.028
-0.102
-0.046
0
0.045
0.017
MHC class
II linked
Ssa60
-0.004
0.003
NA
-0.007
-0.018
NA
NA
0.001
-0.015
NA
NA
-0.018
NA
-0.048
NA
0.004
0.009
-0.025
-0.003
NA
-0.023
-0.017
-0.011
-0.008
NA
NA
NA
NA
NA
NA
Outlier loci
Ssa14
0.226
0.058
-0.028
-0.027
0.14
0.109
0.012
0.188
0
-0.22
0
0
0
0
-0.184
0
-0.078
-0.19
-0.182
0
-0.178
0
-0.012
0
0
-0.017
0.122
-0.062
0.253
0.199
Str60
0.003
0.142
0.249
0.003
0.212
0.235
0.262
0.072
-0.106
0.145
0.253
-0.093
-0.082
-0.21
-0.048
0.058
-0.111
0.053
-0.058
0.025
-0.077
0.022
0.247
0.255
0.23
0.021
-0.176
-0.23
-0.094
-0.089
JMS1M1
-0.187
-0.202
-0.066
-0.186
-0.125
-0.092
-0.23
-0.236
-0.215
-0.44
-0.395
-0.08
0
0
-0.218
-0.209
-0.223
-0.185
-0.231
0
0
-0.351
0
-0.195
-0.214
0
0.233
0.068
-0.024
0.094
JMS2M1
-0.044
-0.039
-0.022
-0.031
-0.011
-0.074
-0.02
-0.083
-0.177
-0.211
-0.31
-0.148
-0.2
0.082
-0.1
-0.053
-0.1
-0.154
-0.028
-0.217
-0.211
-0.152
-0.136
-0.288
-0.221
-0.097
-0.095
-0.028
-0.153
-0.177
Table S4 continued: P-values from a one sample t-test of the null hypothesis that the true mean across populations is equal to zero and the lower
and upper limits of the 95% confidence interval for the mean.
Neutral loci (non-outliers)
P-value
95% confidence intervall
lower limit
upper limit
Ssa100
Str15
SL438
Str73
Str85
Str543
Strutta58
SsoSL417
Omy325
Ssa85
Ots515
0.059
0.000
0.000
0.526
0.000
0.000
0.000
0.127
0.060
0.001
0.263
-0.029
0.001
0.018
0.057
0.029
0.064
-0.041
0.021
-0.094
-0.041
-0.084
-0.044
-0.031
-0.012
-0.025
0.003
-0.012
0.000
-0.066
-0.019
-0.090
0.026
MHC class
II linked
TAP2b
Ssa60
MHC class I linked
P-value
95% confidence
lower limit
upper limit
UBA
TAP2a
0.129
0.000
0.012
-0.028
0.004
0.073
0.102
-0.037
-0.005
Outlier loci
Ssa14
Str60
JMS1M1
JMS2M1
0.006
0.849
0.195
0.000
0.000
-0.019
-0.004
-0.041
0.050
-0.020
0.094
-0.186
-0.075
-0.150
-0.083
Table S5: Frequency of Atlantic-like (AT), marble trout-like (MA) and Mediterranean-like (ME) alleles (see footnote) at the two diagnostic microsatellite markers
JMS1M1 and JMS2M1 for all populations. Further, we provide all allele frequencies
for marker Ssa14 where an association between alleles 142 and 144 with non-Atlantic
lineages is suspected (see text for details). Cells containing values ≥0.05 are shaded in
grey. The site identifiers correspond to Fig. 1 of the manuscript.
Drainage
Poschiavino
Ticino
Rhine
Allaine
Site
TI
ZA
BR
LA
CA
LP
SO
PI
MA
BI
BO
LO
LU
RU
KI
SC
HE
SA
RO
AN
GO
BL
SE
FR
LB
SB
BU
PR
AL
MI
JMS1M1
AT
MA
0.83 0.15
0.85 0.12
0.90 0.10
0.84 0.10
0.81 0.19
0.77 0.13
0.87 0.08
0.80 0.15
1
0
0.95 0.03
0.93 0.04
0.90 0.11
1
0
1
0
1
0
1
0
0.98 0.02
1
0
1
0
1
0
1
0
0.98
0
1
0
1
0
1
0
1
0
0.42
0
0.47
0
0.75
0
0.78
0
ME
0.02
0.03
0
0.07
0
0.10
0.05
0.05
0
0.02
0.04
0
0
0
0
0
0
0
0
0
0
0.02
0
0
0
0
0.58
0.53
0.25
0.22
AT
0.62
0.64
0.58
0.63
0.60
0.69
0.63
0.53
0.99
0.85
0.96
0.90
0.95
0.91
0.87
0.98
0.77
0.90
0.98
0.98
0.98
0.93
0.89
0.98
0.96
0.95
0.50
0.37
0.71
0.58
JMS2M1
MA
ME
0.23
0.13
0.26
0.09
0.26
0.10
0.23
0.13
0.15
0.16
0.17
0.11
0.20
0.07
0.18
0.22
0
0.02
0.12
0
0
0
0.08
0
0.02
0.03
0
0
0
0
0
0
0
0.03
0
0.02
0
0
0
0
0
0
0
0
0.01
0.08
0
0
0
0
0
0
‡
0 0.25 (0.46)
0 0.35 (0.53)
0 0.12 (0.26)
0 0.17 (0.23)
140
0.62
0.64
0.70
0.71
0.53
0.56
0.65
0.45
1
0.98
1
1
1
1
0.96
1
0.90
0.97
0.97
1
0.97
1
0.87
1
1
0.87
0.25
0.10
0.50
0.67
Ssa14
142
0.38
0.17
0.26
0.19
0.29
0.28
0.32
0.30
0
0.02
0
0
0
0
0.04
0
0.10
0.03
0.03
0
0.03
0
0.13
0
0
0.13
0.75
0.90
0.50
0.33
144
0
0.19
0.04
0.10
0.18
0.16
0.03
0.25
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
‡
The classification of alleles as AT-, MA- or ME-like is based on Estoup et al. 2000 Mol. Ecol. At
locus JMS2M1, we observed additional alleles not reported by Estoup et al., all at a low average
frequency across populations (≤ 3.2%). These alleles were not considered in Table S5.
Within the Allaine, however, one of these “novel” alleles was observed at population frequencies of 721%. The allele most likely represents ME-like variation as it is one repeat unit shorter than typical
ME-like alleles but 5 repeat units longer than typical AT-alleles. In parentheses, we indicate the
frequency of ME-like variation if this allele is included. Note that these estimates are very close to
those obtained for JMS1M1.