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

12

1

2

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

23

4

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

35

6

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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101112131415161718192021222324252627282930313233

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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

5

3435

363738394041424344454647484950515253545556575859606162639

10

(#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.

6

6465666768697071

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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

7

727374

13

14

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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17

18

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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20

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

11

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84

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22

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

12

858687

23

24

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

1325

26

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

14

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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

18

114

35

36

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