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Table A1. Population names, sample codes, sample sizes, date of collection, tissue source, and collectors for genetic samples (used in genetic analysis)
Region (province as in Fig. 1)
PopulationSample
code N Date Tissue Collector
Northeastern Sakhalin(51)
Piltun River 1 8 1997-1999 skin/scales Sergey Safronov
Val River 2 14 August 3-4, 2011 fin clips Andrey Yurchenko, Dmitri Didenko
Dagi River 3A 31 Sept. 13-21, 2009 fin clips Anatoly Semenchenko, Dmitri Didenko, Andrey Yurchenko, Lev Zhivotovsky
Dagi Bay 3B 9 June, 2005 skin/scales Sergey Safronov
Tym River 4 11 July 31, 2011 fin clips Andrey Yurchenko, Dmitri Didenko
Nabil River5A 9 September 11, 1999 fin clips Bronov
5B 11 October, 2009 fin clips Dmitri Didenko
Langeri River 6 10 September 9-11, 2011 fin clips Dmitri Didenko, Lev Zhivotovsky
Terpenie Bay(73)
Poronay River 7 11 June - October, 2008 fin clips Dmitri Didenko
Onorka River 8 12 August, 2010 fin clips Andrey Yurchenko, Anatoly Semenchenko, Sergey Zolotukhin
Brusnichnaya River 9 11 September 19, 2009 fin clips Sergey Safronov
Elnaya River 10 21 August, 2010 fin clips Andrey Yurchenko, Anatoly Semenchenko, Sergey Zolotukhin
Nevskoe Lake 11 8 November 4, 2006 skin/scales Sergey Safronov
Southeastern Sakhalin(84)
Tunaicha Lake12A 10 2006 skin/scales Sergey Safronov
12B 6 May, 2012 fin clips Vladimir Samarsky
Vavaiskoe Lake 13A 10 2005 skin/scales Sergey Safronov
13B 18 September, 1999 fin clips Sergey Safronov1
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Urjum River 14 3 August, 2011 fin clips Sergey Makeev, Andrey Yurchenko
Uljanovka River15A 4 July, 2011 fin clips Sergey Makeev, Andrey Yurchenko
15B 7 2001 skin/scales Sergey Safronov
Moguchi River 16 6 October, 2011 fin clips Sergey Makeev
Iturup Island(74)
Lebedinoe Lake 17 7 2011 fin clips Victor Pogodin
Kuibyshevka River 18 7 Sept. 16-19, 2010 fin clips Sergey Borzov, Lev Zhivotovsky
Kunashir Island(94)
Valentina Lake 19 6 1998 skin/scales Dmitry Sokov
Hokkaido Sarafutsu River 20 9 2006 fin clips Michio Fukushima
Southwestern Sakhalin (83)
Tainoe Lake 21 9 October, 2013 fin clips Aleksey Taibulatov, Sergey Makeev, Lev Zhivotovsky
Western Sakhalin(72)
Ainskoe Lake
22A 30 September, 2010 fin clips Anatoly Semenchenko, Andrey Yurchenko, Lev Zhivotovsky
22B 20 2002 skin/scales Sergey Safronov
22C 10 1998 skin/scales Sergey Safronov
Agnevo River23A 3 June, 2009 fin clips Dmitri Didenko
23B 10 August 8, 2002 skin/scales Sergey Safronov
Viakhtu River 24A 32 June-July, 2010 fin clips Vladimir Samarsky, Anna Lapshina
Viakhtu Bay 24B 10 2002 skin/scales Sergey Safronov
Tyk Bay 25 10 July 4, 2002 skin/scales Sergey Safronov
Ulika River 26 15 June-July, 2011 fin clips Sergey Zolotukhin
Tumnin River 27A 17 June 9-15, 2011 fin clips Andrey Yurchenko, Sergey Zolotukhin
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Khabarovsky Krai
27B 9 September, 2011 fin clips Sergey Zolotukhin
Koppi River28A 13 June 18-22, 2010 fin clips Andrey Yurchenko
28B 11 July, 2011 fin clips Sergey Zolotukhin
Primorye (82) Samarga River 29 9 2004 fin clips ---
Primorye (100)
Kievka River 30 6 1997 fin clips Alisa Poljakova
Khabarovsk fish market
--- 13 2012 fin clips Sergey Zolotukhin
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Table A2. Microsatellite markers involved in the study
Microsatellite marker Source
Omy301 Jackson et al. 1998
Oki10-G Smith et al. 1998
Smm17 Crane et al. 2004
BleTet5, BleTri3 Froufe et al. 2004
Hper4-G, Hper5, Hper6-G, Hper15, Hper16-G, Hper25-G
Hatakeyama et al. (2005)
Pper1-G, Pper2-G, Pper3-G, Pper5, Pper6-G, Pper7-G, Pper8-G, Pper11-G
Kopun et al. (2008)
Note. “G” stands for loci with newly designed primers to fit the size of amplification products (Shitova et al. 2012). The products were fractionated by electrophoresis in 6% polyacrylamide gels, stained with ethidium bromide and documented under ultraviolet light. The allele sizes for each locus were determined by using both an external standard and a sequenced reference sample in each gel to insure exact scoring and facilitate cross-referencing among gels.
REFERENCESCrane PA, CJ Lewis, EJ Kretschmer, SJ Miller, WJ Spearman, AL DeCicco, MJ Lisac,
and JK Wenburg (2004) Characterization and inheritance of seven microsatellite loci from Dolly Varden, Salvelinus malma, and cross-species amplification in Arctic char, S. alpinus. Cons Gen 5:737-741.
Froufe E, K Sefc, P Alexandrino, and S Weiss (2004) Isolation and characterization of Brachymystax lenok microsatellite loci and cross‐species amplification in Hucho spp. and Parahucho perryi. Mole Ecol Notes 4:150-152.
Hatakeyama, M, T Watanabe, M Ikeda, M Nakajima, H Kawamula, and N Taniguchi (2005) Isolation and characterization of microsatellite DNA loci for endangered fish, Japanese huchen (Hucho perryi). Mol Ecol Notes 5:893-895.
Jackson TR, MM Ferguson, RG Danzmann, AG Fishback, PE. Ihssen, MO'Connell, and TJ Crease (1998) Identification of two QTL influencing upper temperature tolerance in three rainbow trout (Oncorhynchus mykiss) half-sib families. Heredity 80:143-151.
Kopun T, KA Winkler, and S Weiss (2009) Eight new polymorphic microsatellite DNA markers for Sakhalin taimen Parahucho perryi. Cons Gen 10:1089-1091.
Shitova M, A Yurchenko, E Shaykhaev, and L Zhivotovsky (2012) A panel of microsatellite loci for population studies of Sakhalin taimen Parahucho perryi (Brevoort). Rus J Gen 48:831-837.
Smith C, B Koop, and R Nelson (1998) Isolation and characterization of coho salmon (Oncorhynchus kisutch) microsatellites and their use in other salmonids. Mol Ecol 7:1614-1616.
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Table A3. Relative biomass (g/m2) of Sakhalin taimen in the watersheds of Sakhalin Island (rows sum up to 1). Population codes are given in Fig. 1.
PopulationWatershed segment
Tributary Lake Upper Middle Lower Estuary Lagoon Seashore
Piltun (1) --- --- --- 0.188 0.206 0.264 0.342 ---Val (2) --- --- --- 0.055 0.258 0.293 0.394 ---Dagi (3) --- --- --- 0.041 0.204 0.512 0.244 ---Nabil (5) --- --- --- 0.090 0.208 0.236 0.466 ---Chamgu (6) 0.240 --- --- 0.080 0.284 0.189 --- 0.207Bogataya (6) 0.223 --- --- 0.125 0.291 0.146 --- 0.216Poronay (7-10) 0.269 --- 0.440 0.292 --- --- --- ---Tunaicha (12) --- 0.558 0.054 0.081 0.165 0.141 --- ---Vavaiskoe (13) --- 0.507 0.040 0.173 0.119 0.162 --- ---Tambovka (14) 0.212 --- --- 0.111 0.372 0.091 --- 0.214Uljanovka (15) 0.139 --- --- 0.137 0.294 0.125 --- 0.305Ainskoe (22) --- 0.573 0.034 0.227 0.034 0.131 --- ---Agnevo (23) 0.203 --- --- 0.083 0.104 0.106 --- 0.504Viakhtu (24) --- --- --- 0.111 0.338 0.206 0.345 ---Tyk (25) --- --- --- 0.161 0.230 0.228 0.380 ---
Note 1. These samples were taken from locations of fish during the active feeding period (from the end of July to October) to study life-history characteristics of Sakhalin taimen and evaluate population-specific spatial distribution of Sakhalin taimen with respect to their natal river. Our goal was to generate an index that would reflect to some extent the population eco-type with respect to migratory patterns (e.g. resident, lake, and estuary). Sample catch data were collected from 1999 to 2011 (collectors: S.N. Safronov and V.D. Nikitin). To relate these data to the genetic ones, we estimated Sakhalin taimen biomass from watershed segments (habitat types) across the majority of Sakhalin Island watersheds listed in Fig.1.
These surveys were carried out in the upper, middle, and lower courses of these river systems as well as in lakes, tributaries, estuaries, lagoons, and the adjacent seashore, defining eight different habitat types. Fish were sampled with: beach seines in coastal waters, lakes, lagoons, and estuaries; drag nets up to ten meters long in rivers not wider than 35 m; and scoop-nets in small creeks up to two meters wide. To effectively sample large-size fish in stronger current, we temporarily blocked the river with upstream and downstream set nets with a mesh size 45-50 mm and dragged nets from the upstream net to the downstream net.For each sample effort, the weight of all fish captured was divided by the netted area to determine biomass density (i.e. catch per unit of effort or the weight of fish captured per square meter of netted area). Multiple samples within each watershed segment were averaged to estimate biomass in each segment. These segment biomass estimates were converted to relative biomass values by dividing them into the total sum of biomass estimates over the entire watershed and adjoining coastal area, for each of the watersheds.
Note 2. This list of Sakhalin Island populations is taken for analysis of the biomass distributions only, differ from the genetic samples (Fig.1), and is incomplete compared to those in Fig.1. Namely, the Tym River population (#4 in Fig.1) is absent as its migration behavior is greatly affected by the salmon hatcheries, although the river drains into a well developed lagoon similarly to that found in neighboring populations Val, Dagi and Nabil. The Nevskoe taimen
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(#11) were observed in the channel from the lake to offshore waters and in the adjacent seashore (the semi-anadromous behavior), but could not be officially registered. Missing data on migration behavior of the taimen in Langeri (#6) and Urjum (#14) were substituted by those for the neighboring populations denoted by the corresponding population codes; the latter can also hold for Moguchi (#16). Genetic samples 7-10 correspond to the same watershed, the Poronay River system.
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Table A4. Significance (p-values) for evaluating deviation from Hardy-Weinberg expectations. Significant deviations from HWE (p<0.05)are shown with grey shading. Superscripts + and - stand respectively for positive and negative values of the inbreeding coefficient f.
SampleLocus
Pper1g Pper2g Pper3gPper5g Hper25E Pper8g Smm17 Omy301
Piltun (1) 0.064 0.105 0.094 0.529 1 0.529 1 1Val (2) 0.087 0.142 0.606 0.375 1 0.461 1 1Dagi (3A) 0.518 0.921 0.354 0.022+ 0.689 0.383 0.704 0.624Dagi Bay (3B) 0.367 0.752 0.704 0.702 1 1 1 1Tym (4) 0.614 0.519 0.344 0.658 0.437 0.297 1 1Nabil (5A) 0.785 0.454 1 1 1 1 1 1Nabil (5B) 0.600 0.135 0.358 1 1 0.585 1 1Langeri (6) 0.543 0.406 0.962 0.429 0.218 0.575 1 0.046-
Poronay (7) 0.100 0.965 0.213 1 0.503 1 0.277 1Onorka (8) 0.260 1 0.120 1 0.595 0.179 1 0.486Brysnichnaya (9) 0.077 0.752 0.198 0.232 0.108 0.407 1 0.257Elnaya (10) 0.240 0.187 0.498 0.254 1 0.234 1 1Nevskoe (11) 0.041+ 0.132 0.026+ 0.218 1 0.047+ 1 0.386Tunaicha (12A) 0.038+ 0.0015+ 0.436 0.046+ 1 1 1 1Tunaicha (12B) 0.332 0.833 0.446 0.518 1 0.030+ 1 1Vavaiskoe (13A) 0.090 0.091 0.170 1 1 0.373 0.215 1Vavaiskoe (13B) 0.222 0.0023+ 0.968 1 0.0052+ 0.536 0.271 0.251Urjum (14) 0.600 1 0.599 1 1 1 1 1Uljanovka (15A) 1 1 1 1 1 1 1 1Uljanovka (15B) 1 0.143 0.034+ 0.110 1 0.440 1 1Moguchi (16) 0.769 0.168 0.638 0.237 1 0.633 1 1Lebedinoe (17) 1 0.327 1 1 0.160 1 1 1Kyibishevka (18) 1 0.664 0.442 1 1 1 1 1
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Valentina (19) 1 0.258 0.619 1 1 0.396 1 1Sarafutsu (20) 1 0.011+ 0.770 0.317 1 0.531 0.249 1Tainoe (21) 0.290 0.294 0.239 1 1 0.059 1 1Ainskoe (22A) 0.077 0.307 0.357 0.437 0.711 0.199 1 1Ainskoe (22B) 0.0020+ 0.897 0.598 0.150 1 0.568 0.242 1Ainskoe (22C) 0.209 0.105 0.170 0.269 1 0.126 0.572 1Agnevo (23A) 1 0.332 1 1 1 0.200 1 0.198Agnevo (23B) 0.576 0.442 0.609 0.335 0.246 0.130 0.443 1Viakhtu (24A) 0.503 0.386 0.110 0.279 0.732 0.412 0.137 1Viahtu (24B) 0.0023+ 0.663 0.718 0.029+ 1 0.0023+ 0.269 1Tyk (25) 0.648 0.655 0.367 1 1 0.643 0.157 1Ulika (26) 0.040+ 0.191 0.547 0.851 0.259 0.565 1 0.328Tumnin (27A) 0.416 0.225 0.346 0.762 0.329 0.400 0.809 0.287Tumnin (27B) 0.775 1 0.554 0.551 1 0.173 1 1Koppi (28A) 0.433 0.013+ 0.186 0.482 1 0.15 0.093 0.500Koppi (28B) 1 1 1 0.440 0.538 0.441 0.066 1Samarga (29) 1 0.620 1 1 0.340 0.341 1 0.495Kievka (30) 0.932 0.792 0.297 1 0.092 1 0.271 0.274
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Table A4 (continued).
SampleLocus
Pper11g Hper15E Hper4E Hper16E Hper6E Pper6gPper7g Bletri3 BleTet5 Hper5E Oki10g
Piltun (1) 0.301 0.138 1 0.015+ 1 0.433 1 1 1 0.440 0.095Val (2) 0.603 0.608 1 0.026+ 0.075 0.616 1 0.489 1 0.319 0.476Dagi (3A) 0.536 1 1 0.222 0.359 0.765 1 0.102 1 0.259 0.263Dagi Bay (3B) 0.297 0.713 1 0.421 1 0.386 1 1 1 0.273 0.330Tym (4) 0.240 1 1 0.0094- 0.02+ 1 0.916 1 1 0.553 0.030+
Nabil (5A) 0.555 0.443 1 0.531 0.0053+ 0.144 0.538 0.641 1 0.227 0.433Nabil (5B) 0.333 0.473 1 0.604 1 0.106 0.629 0.304 1 0.576 0.029+
Langeri (6) 0.442 0.772 0.306 0.022+ 0.479 1 1 1 1 1 1Poronay (7) 0.696 0.404 1 1 1 0.062 0.402 1 1 0.213 0.882Onorka (8) 0.034+ 0.303 0.592 1 1 0.662 0.067 1 1 1 0.242Brysnichnaya (9) 0.181 1 1 0.441 1 0.093 1 0.502 1 1 0.087Elnaya (10) 0.985 0.826 0.192 1 1 0.119 1 1 1 0.642 0.173Nevskoe (11) 0.353 0.776 1 1 1 0.578 0.199 0.078 1 1 0.096Tunaicha (12A) 0.053 0.064 1 0.199 0.0092+ 0.18 0.182 1 1 1 0.030+
Tunaicha (12B) 0.298 1 1 1 1 0.588 1 1 1 1 0.612Vavaiskoe (13A) 0.434 0.305 1 0.215 1 0.18 1 1 1 0.108 0.393Vavaiskoe (13B) 0.455 0.272 1 0.374 1 0.659 0.255 1 1 0.290 0.896Urjum (14) 1 1 1 1 1 0.198 1 1 1 1 1Uljanovka (15A) 0.772 1 1 1 1 0.085 0.086 1 1 1 0.315Uljanovka (15B) 1 1 1 1 1 0.0098+ 0.106 1 1 0.090 1Moguchi (16) 0.644 1 1 1 1 0.654 1 1 1 0.191 0.071Lebedinoe (17) 1 0.476 1 0.442 1 1 1 1 1 1 1Kyibishevka (18) 0.133 1 1 1 0.012+ 0.719 1 0.105 1 1 0.190Valentina (19) 0.203 0.101 1 1 1 0.653 0.099 1 1 0.305 0.050Sarafutsu (20) 0.767 1 1 0.073 1 0.764 1 0.216 1 0.458 0.878
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Tainoe (21) 0.343 0.703 1 1 1 0.682 1 1 1 0.725 0.035+
Ainskoe (22A) 0.031+ 0.454 1 0.230 1 0.198 0.505 0.084 0.338 0.469 0.110Ainskoe (22B) 0.622 0.654 1 0.689 1 0.974 0.307 0.159 1 0.535 0.547Ainskoe (22C) 0.557 0.7 1 1 1 0.316 1 1 1 1 0.682Agnevo (23A) 1 0.598 1 1 1 1 1 0.598 1 1 1Agnevo (23B) 0.265 0.448 1 1 1 0.887 1 1 1 0.226 0.129Viakhtu (24A) 0.120 0.0066+ 1 0.024+ 0.136 0.506 0.744 0.778 0.614 1 0.262Viahtu (24B) 0.486 0.358 0.052 0.324 1 0.562 0.197 0.052 1 1 0.113Tyk (25) 0.516 1 1 0.448 0.480 0.926 1 1 1 1 0.142Ulika (26) 0.500 0.117 1 0.418 1 0.4 0.269 1 1 1 0.0032+
Tumnin (27A) 0.762 0.511 1 0.0030+ 1 0.308 0.658 0.384 0.179 0.043+ 0.783Tumnin (27B) 0.775 0.645 1 0.636 1 0.860 0.167 0.127 1 1 1Koppi (28A) 0.033+ 0.741 1 0.505 1 0.133 0.769 0.257 0.475 0.258 0.820Koppi (28B) 0.313 0.510 1 0.176 1 0.355 0.545 0.546 0.175 1 0.752Samarga (29) 0.487 0.641 1 0.398 1 0.567 0.225 0.336 0.3 1 0.173Kievka (30) 0.271 0.271 1 1 1 0.429 1 0.031+ 0.151 1 0.047+
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Table A5. Summary statistics of microsatellite variation in genetic samples of Sakhalin taimen (473 individuals). Shown is the number of samples typed for each locus, the total number of different alleles, the expected heterozygosity (He), and the estimated FST across all samples for each locus.
Locus Sample size
# alleles He
FST estimate
ΘP
Pper1g 460 54 0.957 0.077Pper2g 464 24 0.929 0.107Pper3g 460 25 0.929 0.097Pper5g 465 11 0.610 0.145Hper25E 468 2 0.489 0.099Pper8g 471 8 0.777 0.192Smm17 469 7 0.471 0.175Omy301 473 2 0.341 0.174Pper11g 452 20 0.882 0.124Hper15E 470 8 0.651 0.156Hper4E 472 4 0.104 0.174Hper16E 467 9 0.633 0.191Hper6E 452 7 0.260 0.040Pper6g 464 16 0.834 0.118Pper7g 466 7 0.540 0.116Bletri3 466 9 0.548 0.189BleTet5 471 11 0.248 0.181Hper5E 465 3 0.471 0.145Oki10g 455 34 0.922 0.098
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Table A6. Overall statistics averaged across loci for each genetic sample. Shown are: sample name (code); D, allelic diversity (or expected heterozygosity, He); Ho, observed heterozygosity; f, the inbreeding coefficient.
Sample Allele diversity,D (He)
Observedheterozygosity, Ho
Inbreedingcoefficient, f
Piltun (1) 0.47 0.42 0.12Val (2) 0.51 0.49 0.05Dagi (3A) 0.48 0.49 -0.02Dagi Bay (3B) 0.56 0.56 -0.01Tym (4) 0.51 0.5 0.02Nabil (5A) 0.55 0.56 -0.02Nabil (5B) 0.57 0.54 0.05Langeri (6) 0.57 0.62 -0.1Poronay (7) 0.53 0.52 0.03Onorka (8) 0.44 0.48 -0.09Brysnichnaya (9) 0.49 0.43 0.13Elnaya (10) 0.54 0.55 -0.02Nevskoe (11) 0.60 0.47 0.22Tunaicha (12A) 0.50 0.42 0.17Tunaicha (12B) 0.53 0.54 0Vavaiskoe (13A) 0.55 0.56 -0.02Vavaiskoe (13B) 0.55 0.53 0.03Urjum (14) 0.48 0.51 -0.06Uljanovka (15A) 0.46 0.47 -0.03Uljanovka (15B) 0.43 0.33 0.24Moguchi (16) 0.54 0.51 0.06Lebedinoe (17) 0.31 0.37 -0.24Kyibishevka (18) 0.38 0.39 -0.02Valentina (19) 0.53 0.57 -0.09Sarafutsu (20) 0.54 0.56 -0.04Tainoe (21) 0.34 0.32 0.07Ainskoe (22A) 0.61 0.58 0.05
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Ainskoe (22B) 0.57 0.57 0Ainskoe (22C) 0.59 0.56 0.06Agnevo (23A) 0.59 0.6 -0.01Agnevo (23B) 0.58 0.58 0.01Viakhtu (24A) 0.54 0.52 0.04Viahtu (24B) 0.56 0.48 0.15Tyk (25) 0.49 0.48 0.02Ulika (26) 0.55 0.52 0.05Tumnin (27A) 0.60 0.57 0.04Tumnin (27B) 0.57 0.58 -0.03Koppi (28A) 0.60 0.58 0.04Koppi (28B) 0.60 0.63 -0.05Samarga (29) 0.58 0.6 -0.03Kievka (30) 0.46 0.39 0.17
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Table A7. Matrix of pairwise FST estimates θP between genetic samples (sample sizes and sample codes are listed in Appendix A1)
2 0.06973A 0.0508 0.03613B 0.0706 0.0433 0.0091•
4 0.2165 0.1307 0.1488 0.09715A 0.0836 0.0648 0.0555 0.0229• 0.09865B 0.0648 0.0481 0.0349 0.0059• 0.1061 0.0005•
6 0.1569 0.0799 0.0872 0.0734 0.1288 0.0777 0.05997 0.1522 0.1491 0.1491 0.1383 0.2465 0.1451 0.1274 0.10558 0.2373 0.2092 0.2043 0.2014 0.3064 0.1922 0.1873 0.1464 0.07539 0.1651 0.1517 0.1477 0.1285 0.2048 0.1424 0.1125 0.0998 0.0708 0.149910 0.1276 0.1133 0.124 0.1095 0.1762 0.1007 0.0807 0.0977 0.0767 0.1390 0.057711 0.0994 0.0685 0.1031 0.0608 0.11 0.0594 0.0312 0.0546 0.0935 0.1539 0.0865 0.040012A 0.0840 0.1196 0.1257 0.1040 0.1837 0.1091 0.0804 0.1545 0.1737 0.2727 0.1687 0.1153 0.054212B 0.1373 0.1420 0.1343 0.0936 0.1711 0.0954 0.0574 0.1134 0.1619 0.2273 0.1291 0.0907 0.014713A 0.1730 0.1429 0.1839 0.1331 0.1635 0.1366 0.1122 0.1600 0.2018 0.2793 0.2142 0.1563 0.072113B 0.1404 0.1243 0.1442 0.1067 0.17 0.1144 0.0863 0.1338 0.1642 0.2418 0.1765 0.1335 0.070014 0.1249 0.0913 0.1368 0.1097 0.215 0.0818 0.0810 0.1155 0.1595 0.2188 0.1915 0.1360 0.026215A 0.1447 0.1472 0.1310 0.1174 0.2218 0.1070 0.0973 0.1287 0.1411 0.2433 0.1274 0.1029 0.077615B 0.1434 0.1390 0.1596 0.1498 0.2169 0.1322 0.1234 0.1525 0.1564 0.2235 0.1386 0.1017 0.070716 0.1251 0.1244 0.1175 0.0802 0.1634 0.0622 0.0600 0.0944 0.1204 0.1978 0.1205 0.0755 0.005617 0.3157 0.256 0.2526 0.2284 0.2243 0.2382 0.2320 0.2424 0.3315 0.4221 0.3229 0.2697 0.234918 0.2298 0.1739 0.1874 0.1634 0.2019 0.1785 0.1776 0.2043 0.2648 0.3300 0.2632 0.2036 0.154219 0.1126 0.1015 0.1345 0.1057 0.1629 0.1023 0.0787 0.1179 0.1408 0.2262 0.1586 0.0925 0.036020 0.1278 0.0798 0.1293 0.1116 0.1562 0.1030 0.0981 0.1014 0.1366 0.2147 0.1349 0.1098 0.057221 0.2107 0.1917 0.1863 0.1715 0.3191 0.1876 0.1480 0.2422 0.2901 0.3584 0.2902 0.2016 0.165222A 0.0742 0.0582 0.0788 0.0498 0.1269 0.0539 0.0305 0.0688 0.0989 0.1606 0.1011 0.0530 0.000222B 0.0630 0.0628 0.0709 0.0581 0.1443 0.0742 0.0447 0.0836 0.0984 0.1810 0.0926 0.0464 0.0207
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27
28
22C 0.0749 0.0678 0.0748 0.0497 0.1387 0.0670 0.0372 0.0677 0.0947 0.1698 0.1034 0.0623 0.012223A 0.1116 0.0701 0.0676 0.0393 0.1067 0.0425 0.0334 0.0526 0.1337 0.2170 0.1458 0.1041 0.037723B 0.1154 0.0727 0.1083 0.0915 0.1423 0.1050 0.0737 0.0820 0.1560 0.2162 0.1623 0.1037 0.044024A 0.1257 0.1009 0.1310 0.1313 0.1763 0.1205 0.1051 0.1201 0.1781 0.2623 0.1702 0.1273 0.098224B 0.0671 0.0735 0.0889 0.0815 0.1708 0.0876 0.0615 0.0945 0.1279 0.2231 0.1153 0.0855 0.052525 0.1321 0.106 0.1485 0.1536 0.1857 0.1508 0.1312 0.1328 0.1764 0.2853 0.1795 0.1332 0.082326 0.1245 0.0976 0.1258 0.1137 0.2016 0.1241 0.082 0.1149 0.1447 0.1987 0.1335 0.0933 0.081827A 0.0866 0.0733 0.0900 0.0818 0.1462 0.0925 0.0738 0.0779 0.1354 0.2060 0.1190 0.0908 0.052727B 0.1318 0.0913 0.1406 0.1200 0.1682 0.1120 0.0909 0.1154 0.1619 0.2264 0.1353 0.0748 0.036028A 0.0971 0.1003 0.1032 0.0888 0.1678 0.1048 0.0855 0.0949 0.1306 0.1893 0.1255 0.0959 0.078328B 0.1390 0.1309 0.1483 0.1224 0.1722 0.1212 0.1144 0.1329 0.1665 0.2314 0.1550 0.1211 0.108129 0.1941 0.1838 0.1976 0.1686 0.2164 0.1830 0.1588 0.1592 0.1883 0.2602 0.1865 0.1636 0.156630 0.3164 0.3024 0.3014 0.2677 0.3248 0.2954 0.2634 0.2643 0.2772 0.3722 0.2902 0.2599 0.2550
1 2 3A 3B 4 5A 5B 6 7 8 9 10 11
Table A7 (continued)
12B 0.070913A 0.1043 0.090413B 0.0896 0.0759 0.0028•
14 0.1424 0.1081 0.1099 0.121615A 0.1151 0.0892 0.1783 0.1403 0.156515B 0.0930 0.1321 0.1664 0.1581 0.1600 0.154116 0.0892 0.0250 0.1150 0.0916 0.0441 0.0456 0.105917 0.2608 0.2668 0.2803 0.2451 0.3938 0.3077 0.3900 0.289318 0.1951 0.2044 0.2278 0.2188 0.2143 0.2346 0.2508 0.2222 0.240319 0.0737 0.1058 0.1091 0.1070 0.1082 0.1538 0.1134 0.0868 0.3076 0.227120 0.1460 0.1312 0.1473 0.1305 0.1289 0.1278 0.1387 0.1045 0.2230 0.1916 0.1167
15
90
91
92
29
30
21 0.1938 0.2207 0.2429 0.1986 0.2408 0.2491 0.2966 0.1852 0.4600 0.3935 0.2340 0.269822A 0.0608 0.0444 0.0770 0.0647 0.0392 0.0764 0.0952 0.0291 0.2048 0.1504 0.0367 0.068222B 0.0539 0.0704 0.1036 0.0795 0.0967 0.0850 0.100 0.0610 0.2250 0.1781 0.0423 0.068022C 0.0722 0.0506 0.1087 0.0757 0.0767 0.0773 0.1195 0.0511 0.2228 0.1798 0.0489 0.091223A 0.1018 0.0731 0.1189 0.0957 0.1381 0.1125 0.1347 0.0683 0.2494 0.2010 0.1187 0.082823B 0.0976 0.0820 0.1252 0.1144 0.1073 0.1318 0.1613 0.0980 0.2616 0.1976 0.0899 0.088024A 0.1183 0.1157 0.1507 0.1321 0.1729 0.1414 0.1667 0.1279 0.2309 0.2151 0.1586 0.081824B 0.0666 0.0710 0.1191 0.0972 0.1338 0.073 0.0653 0.0932 0.2474 0.1847 0.0914 0.070325 0.1185 0.1317 0.1720 0.1559 0.1781 0.1518 0.1693 0.1361 0.2820 0.2232 0.1593 0.088226 0.1033 0.1111 0.1446 0.1047 0.1446 0.1287 0.1362 0.1285 0.2888 0.2399 0.1082 0.135927A 0.0678 0.0715 0.1084 0.0947 0.1027 0.0777 0.0908 0.0812 0.2116 0.1474 0.0916 0.076327B 0.0955 0.0847 0.1118 0.0956 0.1088 0.113 0.0848 0.0747 0.2750 0.2022 0.1004 0.076328A 0.0825 0.0978 0.1458 0.1229 0.1447 0.1207 0.1148 0.1079 0.2452 0.1838 0.1003 0.103128B 0.1132 0.1230 0.1553 0.1387 0.1720 0.148 0.1514 0.1403 0.2382 0.1902 0.1400 0.114029 0.1605 0.1822 0.1940 0.1753 0.2335 0.1973 0.2092 0.1849 0.2839 0.2583 0.1814 0.166330 0.2539 0.2722 0.2899 0.2577 0.3662 0.3015 0.3034 0.2686 0.4156 0.3964 0.3015 0.2860
12A 12B 13A 13B 14 15A 15B 16 17 18 19 20
Table A7 (continued)
22A 0.120522B 0.1373 0.0039•
22C 0.1314 0.0050• -0.0002•
23A 0.2642 0.0319 0.0499 0.049623B 0.1975 0.0318 0.0485 0.0427 0.0285•
24A 0.2432 0.0808 0.0851 0.1213 0.0732 0.077424B 0.2072 0.053 0.0470 0.0613 0.0377 0.0594 0.055525 0.2939 0.0835 0.0938 0.1272 0.1249 0.0769 0.0075• 0.049726 0.2046 0.0653 0.0679 0.0675 0.119 0.0913 0.1174 0.0805 0.137227A 0.193 0.0522 0.0485 0.0629 0.0401 0.0534 0.0583 0.0332 0.0704 0.0472
16
93
94
31
32
27B 0.2264 0.0472 0.0609 0.0871 0.0892 0.0778 0.073 0.0584 0.0834 0.045 0.022528A 0.2191 0.0591 0.0551 0.0705 0.0443 0.0605 0.0816 0.0538 0.1019 0.054 0.0126 0.047928B 0.2643 0.0868 0.0922 0.108 0.0548 0.0943 0.0936 0.0852 0.1301 0.0819 0.0238 0.05129 0.3205 0.1292 0.1325 0.1435 0.0836 0.1218 0.1488 0.1252 0.1899 0.1228 0.0685 0.106130 0.4423 0.2206 0.2311 0.2472 0.1981 0.2324 0.2262 0.2261 0.284 0.2064 0.1483 0.2103
21 22A 22B 22C 23A 23B 24A 24B 25 26 27A 27B
Table A7 (continued)
28B 0.0039•
29 0.0366 0.0103•
30 0.1081 0.0936 0.062828A 28B 29
• Insignificant FST estimates, i.e. those falling within the 95% confidence intervals obtained by bootstrapping over loci. All other pairwise FST estimates are considered to be significant.
Note. Samples from the same population differ from each another insignificantly, except for a small difference between samples from the Tumnin population (#27, A&B), and great differences for Tunaicha Lake (#12, A&B) and Uljanovka River (#15, A&B). While the summer and fall samples in the same year from the Tumnin River population show not highly significant differentiation, probably caused by small sample sizes, the highly significant difference in allele frequencies between two samples from Tunaicha Lake (in 2006 and 2012) may be due to either temporal genetic change within the same generation or samples drawn from different subpopulations. The latter seems more plausible because both samples were obtained from within the same generation given the fact that taimen mature at the age of 6-8 and spawn up to the age of 20 and the later sample included mature fish only. Tunaicha is a large lake with a few tributaries, and thus it is conceivable that a few subpopulations are extant in the watershed. It is unclear how to explain the great divergence of samples from the Uljanovka River population (taken in 2001 and 2011); probably its heterogeneity was coupled with a great change in allele frequencies due to a dramatic decrease in effective size (Table A9). As was hypothesized in the main text, taimen from the Viakhtu River may consist of a few genetically distinct subpopulations as well (section 3.3).
17
95
96
97
98
99100101102103104105106107108109110111112113
33
34
Table A8. Recent migration rates between Sakhalin taimen populations estimated with the method of Wilson and Rannala (2003).Estimates greater than their threefold standard deviations are shaded grey.
Migration intoMigration from
51-LG 51-SA 73-FR1 2 3 4 5 6 7 8 9 10
51-LG
Piltun (1) 0.6780 0.0088 0.0792 0.0083 0.0082 0.0090 0.0095 0.0094 0.0086 0.0095±0.0107 ±0.0088 ±0.0273 ±0.0080 ±0.0079 ±0.0083 ±0.0091 ±0.0092 ±0.0084 ±0.0088
Val (2) 0.0069 0.6763 0.1199 0.0078 0.0083 0.0080 0.0072 0.0078 0.0071 0.0072±0.0066 ±0.0094 ±0.0205 ±0.0071 ±0.0079 ±0.0077 ±0.0073 ±0.0072 ±0.0065 ±0.0073
Dagi (3) 0.0053 0.0056 0.8423 0.0057 0.0050 0.0048 0.0061 0.0066 0.0073 0.0059±0.0050 ±0.0055 ±0.0219 ±0.0054 ±0.0046 ±0.0050 ±0.0059 ±0.0060 ±0.0059 ±0.0059
Tym (4) 0.0084 0.0090 0.0757 0.7060 0.0081 0.0075 0.0083 0.0083 0.0088 0.0085±0.0077 ±0.0095 ±0.0310 ±0.0232 ±0.0071 ±0.0067 ±0.0079 ±0.0089 ±0.0083 ±0.0085
Nabil (5) 0.0060 0.0068 0.1358 0.0062 0.6829 0.0062 0.0066 0.0064 0.0063 0.0059±0.0056 ±0.0070 ±0.0359 ±0.0064 ±0.0206 ±0.0064 ±0.0065 ±0.0063 ±0.0057 ±0.0053
51-SA Langeri (6) 0.0082 0.0083 0.0316 0.0089 0.0091 0.6792 0.0072 0.0090 0.0097 0.0125±0.0083 ±0.0081 ±0.0184 ±0.0081 ±0.0089 ±0.0134 ±0.0070 ±0.0090 ±0.0090 ±0.0118
73-FR
Poronay (7) 0.0077 0.0085 0.0130 0.0080 0.0084 0.0079 0.6781 0.0723 0.0103 0.0299±0.0074 ±0.0077 ±0.0111 ±0.0077 ±0.0079 ±0.0077 ±0.0114 ±0.0303 ±0.0105 ±0.0179
Onorka (8) 0.0072 0.0076 0.0096 0.0074 0.0081 0.0089 0.0078 0.7708 0.0083 0.0111±0.0074 ±0.0078 ±0.0086 ±0.0071 ±0.0077 ±0.0094 ±0.0080 ±0.0236 ±0.0077 ±0.0098
Brusnichnaya (9) 0.0090 0.0074 0.0080 0.0084 0.0076 0.0087 0.0075 0.0116 0.6920 0.0891±0.0085 ±0.0067 ±0.0079 ±0.0086 ±0.0073 ±0.0076 ±0.0077 ±0.0094 ±0.0322 ±0.0403
Elnaya (10) 0.0075 0.0067 0.0064 0.0063 0.0069 0.0071 0.0064 0.0070 0.0061 0.8052±0.0069 ±0.0071 ±0.0059 ±0.0077 ±0.0064 ±0.0067 ±0.0058 ±0.0077 ±0.0060 ±0.0234
73-LG Nevskoe (11) 0.0082 0.0084 0.0096 0.0089 0.0109 0.0092 0.0097 0.0091 0.0095 0.0201
19
115116117
37
38
±0.0086 ±0.0080 ±0.0085 ±0.0089 ±0.0096 ±0.0101 ±0.0093 ±0.0089 ±0.0085 ±0.0131
84-LKTunaicha (12) 0.0082 0.0079 0.0105 0.0070 0.0075 0.0071 0.0078 0.0078 0.0079 0.0074
±0.0079 ±0.0071 ±0.0084 ±0.0067 ±0.0078 ±0.0073 ±0.0073 ±0.0073 ±0.0072 ±0.0067
Vavaiskoe (13) 0.0054 0.0058 0.0113 0.0053 0.0060 0.0051 0.0054 0.0045 0.0066 0.0071±0.0055 ±0.0052 ±0.0089 ±0.0048 ±0.0057 ±0.0049 ±0.0052 ±0.0052 ±0.0054 ±0.0065
84-SA
Urum (14) 0.0095 0.0100 0.0112 0.0113 0.0103 0.0105 0.0112 0.0116 0.0098 0.0097±0.0088 ±0.0095 ±0.0110 ±0.0102 ±0.0100 ±0.0097 ±0.0105 ±0.0116 ±0.0087 ±0.0099
Uljanovka (15) 0.0105 0.0107 0.0092 0.0096 0.0110 0.0102 0.0105 0.0101 0.0097 0.0096±0.0094 ±0.0101 ±0.0083 ±0.0093 ±0.0103 ±0.0099 ±0.0095 ±0.0099 ±0.0098 ±0.0093
Moguchi (16) 0.0099 0.0075 0.0094 0.0091 0.0088 0.0100 0.0094 0.0099 0.0100 0.0092±0.0092 ±0.0069 ±0.0089 ±0.0090 ±0.0087 ±0.0096 ±0.0093 ±0.0092 ±0.0093 ±0.0086
74Lebedinoe (17) 0.0096 0.0074 0.0101 0.0100 0.0099 0.0100 0.0091 0.0098 0.0095 0.0091
±0.0083 ±0.0076 ±0.0094 ±0.0092 ±0.0094 ±0.0090 ±0.0082 ±0.0089 ±0.0090 ±0.0079
Kuibyshevka (18) 0.0089 0.0091 0.0160 0.0088 0.0098 0.0091 0.0082 0.0100 0.0104 0.0090±0.0087 ±0.0082 ±0.0177 ±0.0085 ±0.0090 ±0.0099 ±0.0078 ±0.0102 ±0.0095 ±0.0083
94 Valentina (19) 0.0087 0.0085 0.0142 0.0093 0.0093 0.0092 0.0088 0.0101 0.0087 0.0094±0.0078 ±0.0080 ±0.0128 ±0.0097 ±0.0084 ±0.0092 ±0.0083 ±0.0099 ±0.0082 ±0.0089
Hokkaido Sarafutsu (20) 0.0084 0.0083 0.0098 0.0079 0.0083 0.0080 0.0092 0.0110 0.0086 0.0134±0.0087 ±0.0089 ±0.0088 ±0.0074 ±0.0083 ±0.0077 ±0.0086 ±0.0106 ±0.0085 ±0.0124
83 Tainoe (21) 0.0093 0.0086 0.0079 0.0084 0.0084 0.0084 0.0093 0.0091 0.0093 0.0080±0.0089 ±0.0085 ±0.0081 ±0.0078 ±0.0069 ±0.0089 ±0.0085 ±0.0090 ±0.0084 ±0.0073
72-LK Ainskoe (22) 0.0037 0.0038 0.0081 0.0038 0.0037 0.0034 0.0042 0.0037 0.0029 0.0068±0.0039 ±0.0034 ±0.0072 ±0.0043 ±0.0035 ±0.0038 ±0.0036 ±0.0033 ±0.0026 ±0.0063
72-SA Agnevo (23) 0.0080 0.0082 0.0095 0.0069 0.0075 0.0081 0.0074 0.0074 0.0075 0.0078±0.0078 ±0.0075 ±0.0087 ±0.0065 ±0.0073 ±0.0078 ±0.0074 ±0.0075 ±0.0069 ±0.0076
72-LG Viakhtu (24) 0.0059 0.0058 0.0110 0.0056 0.0072 0.0060 0.0052 0.0051 0.0052 0.0068±0.0054 ±0.0063 ±0.0089 ±0.0052 ±0.0067 ±0.0049 ±0.0049 ±0.0055 ±0.0047 ±0.0061
2039
40
71
Ulika (26) 0.0070 0.0069 0.0090 0.0075 0.0071 0.0081 0.0076 0.0073 0.0067 0.0085±0.0066 ±0.0065 ±0.0082 ±0.0087 ±0.0068 ±0.0082 ±0.0067 ±0.0075 ±0.0065 ±0.0082
Tumnin (27) 0.0056 0.0065 0.0087 0.0062 0.0074 0.0057 0.0059 0.0059 0.0061 0.0075±0.0063 ±0.0057 ±0.0073 ±0.0067 ±0.0063 ±0.0057 ±0.0055 ±0.0060 ±0.0055 ±0.0072
Koppi (28) 0.0064 0.0053 0.0080 0.0064 0.0052 0.0059 0.0061 0.0071 0.0065 0.0103±0.0062 ±0.0056 ±0.0097 ±0.0059 ±0.0050 ±0.0066 ±0.0059 ±0.0069 ±0.0064 ±0.0098
82 Samarga (29) 0.0073 0.0073 0.0086 0.0070 0.0077 0.0082 0.0080 0.0082 0.0074 0.0087±0.0071 ±0.0072 ±0.0077 ±0.0073 ±0.0072 ±0.0075 ±0.0081 ±0.0079 ±0.0072 ±0.0077
100 Kievka (30) 0.0099 0.0094 0.0099 0.0103 0.0094 0.0104 0.0085 0.0089 0.0094 0.0100±0.0094 ±0.0092 ±0.0095 ±0.0105 ±0.0082 ±0.0094 ±0.0082 ±0.0082 ±0.0092 ±0.0104
21
118
41
42
Table A8 continued
Migration intoMigration from
73-LG 84-LK 84-SA 74 94 Hokkaido11 12 13 14 15 16 17 18 19 20
51-LG
Piltun (1) 0.0080 0.0168 0.0084 0.0097 0.0083 0.0089 0.0085 0.0091 0.0078 0.0085±0.0080 ±0.0116 ±0.0081 ±0.0091 ±0.0085 ±0.0086 ±0.0076 ±0.0092 ±0.0072 ±0.0084
Val (2) 0.0078 0.0080 0.0079 0.0069 0.0082 0.0075 0.0081 0.0068 0.0075 0.0078±0.0075 ±0.0075 ±0.0072 ±0.0070 ±0.0082 ±0.0076 ±0.0083 ±0.0071 ±0.0069 ±0.0073
Dagi (3) 0.0059 0.0049 0.0049 0.0061 0.0048 0.0057 0.0058 0.0051 0.0063 0.0058±0.0057 ±0.0051 ±0.0047 ±0.0061 ±0.0050 ±0.0052 ±0.0058 ±0.0049 ±0.0065 ±0.0052
Tym (4) 0.0079 0.0078 0.0071 0.0075 0.0082 0.0081 0.0083 0.0079 0.0077 0.0078±0.0081 ±0.0069 ±0.0076 ±0.0075 ±0.0087 ±0.0081 ±0.0079 ±0.0078 ±0.0075 ±0.0076
Nabil (5) 0.0065 0.0071 0.0061 0.0065 0.0062 0.0057 0.0062 0.0066 0.0068 0.0060±0.0069 ±0.0068 ±0.0065 ±0.0057 ±0.0058 ±0.0058 ±0.0064 ±0.0072 ±0.0068 ±0.0056
51-SA Langeri (6) 0.0085 0.0084 0.0074 0.0080 0.0083 0.0089 0.0092 0.0092 0.0086 0.0084±0.0080 ±0.0084 ±0.0077 ±0.0078 ±0.0078 ±0.0085 ±0.0091 ±0.0088 ±0.0086 ±0.0076
73-FR
Poronay (7) 0.0079 0.0081 0.0083 0.0074 0.0082 0.0085 0.0083 0.0094 0.0074 0.0078±0.0086 ±0.0084 ±0.0084 ±0.0076 ±0.0082 ±0.0081 ±0.0088 ±0.0087 ±0.0071 ±0.0077
Onorka (8) 0.0072 0.0081 0.0090 0.0076 0.0085 0.0085 0.0081 0.0079 0.0077 0.0083±0.0070 ±0.0075 ±0.0083 ±0.0070 ±0.0076 ±0.0086 ±0.0081 ±0.0078 ±0.0072 ±0.0095
Brusnichnaya (9) 0.0080 0.0077 0.0069 0.0077 0.0073 0.0083 0.0079 0.0096 0.0074 0.0078±0.0074 ±0.0085 ±0.0068 ±0.0069 ±0.0076 ±0.0081 ±0.0075 ±0.0089 ±0.0068 ±0.0078
Elnaya (10) 0.0061 0.0074 0.0055 0.0066 0.0063 0.0072 0.0067 0.0060 0.0071 0.0065±0.0055 ±0.0071 ±0.0057 ±0.0060 ±0.0061 ±0.0070 ±0.0062 ±0.0059 ±0.0066 ±0.0068
73-LG Nevskoe (11) 0.6778 0.0107 0.0089 0.0091 0.0091 0.0091 0.0079 0.0085 0.0081 0.0097
22
119120121
43
44
±0.0109 ±0.0097 ±0.0086 ±0.0086 ±0.0087 ±0.0089 ±0.0079 ±0.0078 ±0.0076 ±0.0087
84-LKTunaicha (12) 0.0082 0.7073 0.0156 0.0065 0.0076 0.0066 0.0070 0.0082 0.0079 0.0072
±0.0080 ±0.0330 ±0.0110 ±0.0065 ±0.0069 ±0.0067 ±0.0070 ±0.0075 ±0.0078 ±0.0076
Vavaiskoe (13) 0.0061 0.0053 0.8190 0.0046 0.0068 0.0062 0.0062 0.0066 0.0055 0.0064±0.0061 ±0.0051 ±0.0230 ±0.0047 ±0.0067 ±0.0066 ±0.0053 ±0.0057 ±0.0046 ±0.0060
84-SA
Urum (14) 0.0099 0.0105 0.0108 0.6793 0.0099 0.0096 0.0100 0.0101 0.0113 0.0090±0.0092 ±0.0096 ±0.0101 ±0.0117 ±0.0094 ±0.0090 ±0.0097 ±0.0098 ±0.0109 ±0.0089
Uljanovka (15) 0.0098 0.0095 0.0105 0.0107 0.6791 0.0098 0.0098 0.0102 0.0098 0.0104±0.0091 ±0.0090 ±0.0094 ±0.0106 ±0.0118 ±0.0096 ±0.0094 ±0.0096 ±0.0092 ±0.0106
Moguchi (16) 0.0089 0.0091 0.0099 0.0090 0.0089 0.6779 0.0089 0.0094 0.0088 0.0087±0.0088 ±0.0090 ±0.0096 ±0.0088 ±0.0083 ±0.0107 ±0.0081 ±0.0090 ±0.0083 ±0.0093
74Lebedinoe (17) 0.0097 0.0093 0.0089 0.0098 0.0097 0.0086 0.7355 0.0090 0.0108 0.0089
±0.0084 ±0.0079 ±0.0080 ±0.0098 ±0.0090 ±0.0081 ±0.0237 ±0.0085 ±0.0098 ±0.0088
Kuibyshevka (18) 0.0095 0.0094 0.0083 0.0087 0.0095 0.0097 0.0102 0.6902 0.0089 0.0096±0.0092 ±0.0092 ±0.0083 ±0.0082 ±0.0089 ±0.0091 ±0.0118 ±0.0254 ±0.0090 ±0.0088
94 Valentina (19) 0.0084 0.0092 0.0090 0.0090 0.0094 0.0097 0.0095 0.0094 0.6800 0.0099±0.0083 ±0.0089 ±0.0089 ±0.0088 ±0.0091 ±0.0091 ±0.0088 ±0.0094 ±0.0138 ±0.0091
Hokkaido Sarafutsu (20) 0.0090 0.0086 0.0101 0.0082 0.0091 0.0083 0.0082 0.0080 0.0080 0.6843±0.0084 ±0.0088 ±0.0091 ±0.0078 ±0.0086 ±0.0084 ±0.0080 ±0.0081 ±0.0083 ±0.0170
83 Tainoe (21) 0.0088 0.0092 0.0079 0.0094 0.0090 0.0104 0.0091 0.0081 0.0087 0.0099±0.0081 ±0.0089 ±0.0077 ±0.0092 ±0.0072 ±0.0113 ±0.0086 ±0.0076 ±0.0096 ±0.0096
72-LK Ainskoe (22) 0.0041 0.0040 0.0053 0.0035 0.0033 0.0040 0.0037 0.0040 0.0036 0.0034±0.0037 ±0.0036 ±0.0055 ±0.0032 ±0.0030 ±0.0038 ±0.0033 ±0.0039 ±0.0028 ±0.0031
72-SA Agnevo (23) 0.0074 0.0077 0.0076 0.0076 0.0081 0.0085 0.0075 0.0076 0.0076 0.0078±0.0070 ±0.0072 ±0.0075 ±0.0079 ±0.0081 ±0.0083 ±0.0073 ±0.0077 ±0.0076 ±0.0074
72-LG Viakhtu (24) 0.0047 0.0055 0.0060 0.0055 0.0052 0.0059 0.0044 0.0059 0.0054 0.0049±0.0044 ±0.0053 ±0.0059 ±0.0054 ±0.0052 ±0.0057 ±0.0044 ±0.0054 ±0.0046 ±0.0047
2345
46
71
Ulika (26) 0.0070 0.0076 0.0079 0.0078 0.0069 0.0074 0.0076 0.0066 0.0076 0.0068±0.0070 ±0.0076 ±0.0074 ±0.0074 ±0.0063 ±0.0068 ±0.0083 ±0.0069 ±0.0083 ±0.0070
Tumnin (27) 0.0056 0.0068 0.0069 0.0062 0.0060 0.0070 0.0067 0.0058 0.0058 0.0057±0.0059 ±0.0069 ±0.0062 ±0.0056 ±0.0058 ±0.0069 ±0.0067 ±0.0048 ±0.0058 ±0.0060
Koppi (28) 0.0061 0.0066 0.0053 0.0060 0.0060 0.0065 0.0064 0.0053 0.0055 0.0053±0.0053 ±0.0069 ±0.0054 ±0.0059 ±0.0062 ±0.0054 ±0.0065 ±0.0049 ±0.0060 ±0.0051
82 Samarga (29) 0.0085 0.0081 0.0084 0.0076 0.0078 0.0085 0.0072 0.0078 0.0072 0.0079±0.0078 ±0.0075 ±0.0081 ±0.0074 ±0.0078 ±0.0083 ±0.0069 ±0.0071 ±0.0074 ±0.0083
100 Kievka (30) 0.0087 0.0089 0.0093 0.0106 0.0096 0.0096 0.0098 0.0092 0.0097 0.0092±0.0079 ±0.0088 ±0.0083 ±0.0107 ±0.0083 ±0.0099 ±0.0100 ±0.0087 ±0.0099 ±0.0089
24
122
47
48
Table A8 continued
Migration intoMigration from
83 72-LK 72-SA 72-LG 71 82 10021 22 23 24 26 27 28 29 30
51-LG
Piltun (1) 0.0077 0.0099 0.0090 0.0083 0.0083 0.0081 0.0085 0.0087 0.0090±0.0077 ±0.0095 ±0.0085 ±0.0081 ±0.0080 ±0.0074 ±0.0086 ±0.0076 ±0.0081
Val (2) 0.0071 0.0077 0.0078 0.0074 0.0077 0.0070 0.0075 0.0073 0.0075±0.0062 ±0.0074 ±0.0073 ±0.0071 ±0.0074 ±0.0065 ±0.0068 ±0.0074 ±0.0072
Dagi (3) 0.0053 0.0070 0.0046 0.0052 0.0054 0.0061 0.0052 0.0056 0.0058±0.0046 ±0.0063 ±0.0048 ±0.0055 ±0.0055 ±0.0056 ±0.0047 ±0.0053 ±0.0053
Tym (4) 0.0080 0.0097 0.0069 0.0090 0.0070 0.0073 0.0080 0.0083 0.0089±0.0081 ±0.0085 ±0.0070 ±0.0080 ±0.0073 ±0.0071 ±0.0076 ±0.0076 ±0.0080
Nabil (5) 0.0059 0.0176 0.0059 0.0063 0.0059 0.0070 0.0069 0.0060 0.0056±0.0056 ±0.0110 ±0.0057 ±0.0067 ±0.0061 ±0.0068 ±0.0064 ±0.0055 ±0.0056
51-SA Langeri (6) 0.0085 0.0604 0.0092 0.0089 0.0099 0.0091 0.0085 0.0088 0.0078±0.0081 ±0.0329 ±0.0084 ±0.0094 ±0.0095 ±0.0085 ±0.0089 ±0.0082 ±0.0084
73-FR
Poronay (7) 0.0083 0.0091 0.0083 0.0084 0.0083 0.0080 0.0077 0.0087 0.0078±0.0078 ±0.0090 ±0.0079 ±0.0076 ±0.0080 ±0.0077 ±0.0076 ±0.0080 ±0.0075
Onorka (8) 0.0085 0.0080 0.0092 0.0091 0.0075 0.0074 0.0068 0.0083 0.0075±0.0078 ±0.0080 ±0.0100 ±0.0090 ±0.0077 ±0.0068 ±0.0067 ±0.0079 ±0.0071
Brusnichnaya (9) 0.0082 0.0078 0.0079 0.0077 0.0086 0.0079 0.0079 0.0086 0.0076±0.0078 ±0.0074 ±0.0077 ±0.0077 ±0.0076 ±0.0075 ±0.0082 ±0.0083 ±0.0072
Elnaya (10) 0.0075 0.0119 0.0070 0.0074 0.0073 0.0077 0.0062 0.0071 0.0072±0.0074 ±0.0109 ±0.0085 ±0.0075 ±0.0069 ±0.0076 ±0.0061 ±0.0068 ±0.0061
73-LG Nevskoe (11) 0.0088 0.0671 0.0086 0.0085 0.0100 0.0092 0.0080 0.0090 0.0084
25
123124125
49
50
±0.0082 ±0.0282 ±0.0085 ±0.0078 ±0.0098 ±0.0092 ±0.0084 ±0.0080 ±0.0084
84-LKTunaicha (12) 0.0073 0.0800 0.0077 0.0079 0.0076 0.0069 0.0077 0.0070 0.0069
±0.0070 ±0.0326 ±0.0077 ±0.0080 ±0.0073 ±0.0070 ±0.0079 ±0.0078 ±0.0074
Vavaiskoe (13) 0.0064 0.0172 0.0062 0.0066 0.0049 0.0063 0.0064 0.0052 0.0058±0.0067 ±0.0123 ±0.0060 ±0.0071 ±0.0057 ±0.0064 ±0.0058 ±0.0046 ±0.0050
84-SA
Urum (14) 0.0106 0.0440 0.0108 0.0095 0.0099 0.0100 0.0105 0.0098 0.0095±0.0105 ±0.0199 ±0.0102 ±0.0086 ±0.0094 ±0.0097 ±0.0095 ±0.0100 ±0.0086
Uljanovka (15) 0.0094 0.0518 0.0096 0.0100 0.0098 0.0097 0.0089 0.0101 0.0099±0.0091 ±0.0253 ±0.0093 ±0.0090 ±0.0090 ±0.0096 ±0.0086 ±0.0090 ±0.0099
Moguchi (16) 0.0087 0.0741 0.0091 0.0088 0.0086 0.0093 0.0095 0.0104 0.0088±0.0084 ±0.0281 ±0.0083 ±0.0087 ±0.0082 ±0.0086 ±0.0090 ±0.0100 ±0.0081
74Lebedinoe (17) 0.0102 0.0134 0.0087 0.0086 0.0090 0.0098 0.0086 0.0086 0.0083
±0.0094 ±0.0132 ±0.0086 ±0.0084 ±0.0077 ±0.0090 ±0.0085 ±0.0086 ±0.0084
Kuibyshevka (18) 0.0097 0.0518 0.0095 0.0090 0.0088 0.0099 0.0096 0.0091 0.0093±0.0094 ±0.0317 ±0.0087 ±0.0089 ±0.0079 ±0.0091 ±0.0096 ±0.0085 ±0.0088
94 Valentina (19) 0.0100 0.0640 0.0096 0.0093 0.0095 0.0095 0.0096 0.0092 0.0098±0.0095 ±0.0281 ±0.0092 ±0.0088 ±0.0081 ±0.0089 ±0.0087 ±0.0088 ±0.0100
Hokkaido Sarafutsu (20) 0.0078 0.0700 0.0081 0.0113 0.0087 0.0141 0.0083 0.0083 0.0085±0.0074 ±0.0394 ±0.0084 ±0.0100 ±0.0086 ±0.0124 ±0.0088 ±0.0078 ±0.0077
83 Tainoe (21) 0.7530 0.0082 0.0082 0.0093 0.0100 0.0093 0.0081 0.0082 0.0086±0.0234 ±0.0089 ±0.0085 ±0.0089 ±0.0097 ±0.0085 ±0.0080 ±0.0078 ±0.0078
72-LK Ainskoe (22) 0.0041 0.8752 0.0040 0.0075 0.0031 0.0088 0.0054 0.0042 0.0048±0.0043 ±0.0186 ±0.0036 ±0.0071 ±0.0032 ±0.0059 ±0.0047 ±0.0038 ±0.0040
72-SA Agnevo (23) 0.0070 0.1088 0.6758 0.0115 0.0082 0.0110 0.0076 0.0068 0.0076±0.0071 ±0.0275 ±0.0089 ±0.0119 ±0.0077 ±0.0093 ±0.0072 ±0.0065 ±0.0073
72-LG Viakhtu (24) 0.0053 0.0174 0.0046 0.8279 0.0050 0.0056 0.0068 0.0056 0.0045±0.0056 ±0.0154 ±0.0046 ±0.0224 ±0.0050 ±0.0053 ±0.0071 ±0.0049 ±0.0044
2651
52
71
Ulika (26) 0.0086 0.0087 0.0073 0.0072 0.7215 0.0712 0.0134 0.0065 0.0069±0.0088 ±0.0090 ±0.0081 ±0.0069 ±0.0390 ±0.0533 ±0.0128 ±0.0062 ±0.0077
Tumnin (27) 0.0053 0.0355 0.0051 0.0093 0.0057 0.7890 0.0095 0.0058 0.0067±0.0055 ±0.0212 ±0.0058 ±0.0080 ±0.0048 ±0.0260 ±0.0077 ±0.0062 ±0.0066
Koppi (28) 0.0073 0.0139 0.0064 0.0078 0.0057 0.0864 0.7343 0.0063 0.0059±0.0072 ±0.0105 ±0.0058 ±0.0077 ±0.0059 ±0.0571 ±0.0492 ±0.0061 ±0.0066
82 Samarga (29) 0.0085 0.0087 0.0082 0.0078 0.0076 0.0084 0.1051 0.6802 0.0082±0.0074 ±0.0081 ±0.0081 ±0.0077 ±0.0074 ±0.0082 ±0.0304 ±0.0166 ±0.0085
100 Kievka (30) 0.0098 0.0092 0.0097 0.0097 0.0099 0.0181 0.0490 0.0104 0.6835±0.0095 ±0.0089 ±0.0094 ±0.0091 ±0.0092 ±0.0121 ±0.0244 ±0.0102 ±0.0170
27
126
53
54
Table A9. Point estimates and 95%-confidence intervals (CI) for effective population size based on linkage disequilibrium (Wapples and Do 2010), heterozygote excess (Pudovkin et al. 2010), and molecular coancestry (Nomura 2008) methods (software “NeEstimator2” by Do et al. 2013).
Sample
ESTIMATING METHOD
LINKAGE DISEQUILIBRIUM HETEROZYGOTE
EXCESS MOLECULAR COANCESTRY
Estimate Parametric CI Estimate Parametric CI Estimate Jackknife CI
Piltun (1) inf 50,7 inf inf inf inf inf inf infVal (2) 33,5 16,5 197,2 inf 13,7 inf 7,5 3,3 13,4Dagi (3A) 212,9 70,4 inf 127 10,1 inf 21,7 0,5 80,1Dagi (3B) inf 70,4 inf 182,4 8,9 inf inf inf infTym (4) 10,4 5,4 23 inf 7,6 inf 6,4 3,3 10,4Nabil (5A) inf 57,2 inf inf 8,3 inf inf inf infNabil (5B) 1101 29,1 inf inf 14,8 inf 13 2,2 33,2Langeri (6) 30,2 12,7 inf 10,2 5,2 inf 11 4,6 20,2Poronay (7) 49,9 15,9 inf inf 9,3 inf 21,1 5,8 46,3Onorka (8) 2,6 2 4,7 6,5 3,6 52,5 7,6 3,7 13Brusnichnaya (9) 14,7 6,5 70,6 inf inf inf 12,5 0 62,7Elnaya (10) 11 8,1 15,2 38,1 8,5 inf 9,6 5,3 15,3Nevskoe (11) inf 32,4 inf inf inf inf 8,2 3,9 14,2Tunaicha (12A) inf 31,5 inf inf inf inf inf inf infTunaicha (12B) inf inf inf inf 8,7 inf inf inf infVavaiskoe (13A) 22,3 11 107,3 inf 8,6 inf 89 0,1 446,7Vavaiskoe (13B) 45,5 24,5 166,2 inf 16,7 inf 11,8 2,8 27Urjum (14) inf inf inf 16 4,5 inf 47,1 0 236,7Uljanovka (15A) inf 2,4 inf 13,1 3,5 inf 31,9 0 160,3
28
127128129
55
56
Uljanovka (15B) inf 10 inf inf inf inf 13,7 0,3 50,7Moguchi (16) inf 8,9 inf inf 11,9 inf 5,8 2,8 9,9Lebedinoe (17) 3,3 1,4 inf 3,8 2,4 9,9 inf inf infKuibyshevka (18) 19,9 2,6 inf 31,2 3,9 inf 12,5 2,1 32,1Valentina (19) 17,6 3,3 inf 12,5 4,1 inf 7,4 3,6 12,4Sarafutsu (20) 42,5 13,8 inf inf 7,6 inf 8,9 4,6 14,5Tainoe (21) 4,4 2,2 13,2 inf 16,2 inf 2,1 1 3,5Ainskoe (22A) 126,5 65,9 755,5 inf inf inf inf inf infAinskoe (22B) inf 108,6 inf inf 16,9 inf inf inf infAinskoe (22C) inf 41,1 inf inf 57,4 inf 15,8 1,9 44Agnevo (23A) inf inf inf 205 4,4 inf 36,2 0 181,7Agnevo (23B) inf 60,8 inf inf 12,8 inf inf inf infViakhtu (24A) 21,6 16,5 29,4 inf 172,1 inf 8,2 4 13,9Viakhtu (24B) inf 35,6 inf inf inf inf 9,1 0,7 28,2Tyk (25) 43,2 15,2 inf inf 10,5 inf 7,7 2,3 16,3Ulika (26) 19 11 42,3 inf inf inf 5 3,4 7Tumnin (27A) 119,3 46,6 inf inf 13,8 inf 8,1 3,4 14,8Tumnin (27B) inf 56,5 inf 130,8 9,8 inf 17,6 4,3 40,3Koppi (28A) 219 27,5 inf 10 4,8 inf 12,9 5 24,5Koppi (28B) inf 73,9 inf inf 45,6 inf inf inf infSamarga (29) inf 32,9 inf 55,7 7,8 inf 9 2,7 19,1Kievka (30) 1,6 1,1 2,4 inf 28,6 inf 2 1,3 2,8
‘inf’ stands for an infinite value.
Note. The linkage disequilibrium estimates of effective population size may be biased downward up to 30% because the samples are represented by individuals of different ages (Waples RS, Antao T, and Luikart G (2014) Effects of overlapping generations on linkage disequilibrium estimates of effective population size. Genetics, 197, 769–780).
29
130
131132133
57
58